generated/google/apis/genomics_v1/service.rb in google-api-client-0.11.2 vs generated/google/apis/genomics_v1/service.rb in google-api-client-0.11.3

- old
+ new

@@ -45,1775 +45,1828 @@ def initialize super('https://genomics.googleapis.com/', '') @batch_path = 'batch' end - # Searches for references which match the given criteria. + # Searches for reference sets which match the given criteria. # For the definitions of references and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) # Implements - # [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0. - # 5.1/src/main/resources/avro/referencemethods.avdl#L146). - # @param [Google::Apis::GenomicsV1::SearchReferencesRequest] search_references_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/ + # v0.5.1/src/main/resources/avro/referencemethods.avdl#L71) + # @param [Google::Apis::GenomicsV1::SearchReferenceSetsRequest] search_reference_sets_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchReferencesResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::SearchReferencesResponse] + # @return [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/references/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchReferencesRequest::Representation - command.request_object = search_references_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchReferencesResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchReferencesResponse - command.query['fields'] = fields unless fields.nil? + def search_reference_sets(search_reference_sets_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/referencesets/search', options) + command.request_representation = Google::Apis::GenomicsV1::SearchReferenceSetsRequest::Representation + command.request_object = search_reference_sets_request_object + command.response_representation = Google::Apis::GenomicsV1::SearchReferenceSetsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::SearchReferenceSetsResponse command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets a reference. + # Gets a reference set. # For the definitions of references and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) # Implements - # [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/ - # src/main/resources/avro/referencemethods.avdl#L158). - # @param [String] reference_id - # The ID of the reference. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5. + # 1/src/main/resources/avro/referencemethods.avdl#L83). + # @param [String] reference_set_id + # The ID of the reference set. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Reference] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::ReferenceSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Reference] + # @return [Google::Apis::GenomicsV1::ReferenceSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_reference(reference_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/references/{referenceId}', options) - command.response_representation = Google::Apis::GenomicsV1::Reference::Representation - command.response_class = Google::Apis::GenomicsV1::Reference - command.params['referenceId'] = reference_id unless reference_id.nil? - command.query['fields'] = fields unless fields.nil? + def get_reference_set(reference_set_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/referencesets/{referenceSetId}', options) + command.response_representation = Google::Apis::GenomicsV1::ReferenceSet::Representation + command.response_class = Google::Apis::GenomicsV1::ReferenceSet + command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Lists the bases in a reference, optionally restricted to a range. - # For the definitions of references and other genomics resources, see + # Updates a call set. + # For the definitions of call sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0. - # 5.1/src/main/resources/avro/referencemethods.avdl#L221). - # @param [String] reference_id - # The ID of the reference. - # @param [String] page_token - # 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. - # @param [Fixnum] page_size - # The maximum number of bases to return in a single page. If unspecified, - # defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base - # pairs). - # @param [Fixnum] start_position - # The start position (0-based) of this query. Defaults to 0. - # @param [Fixnum] end_position - # The end position (0-based, exclusive) of this query. Defaults to the length - # of this reference. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # This method supports patch semantics. + # @param [String] call_set_id + # The ID of the call set to be updated. + # @param [Google::Apis::GenomicsV1::CallSet] call_set_object + # @param [String] update_mask + # An optional mask specifying which fields to update. At this time, the only + # mutable field is name. The only + # acceptable value is "name". If unspecified, all mutable fields will be + # updated. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ListBasesResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::ListBasesResponse] + # @return [Google::Apis::GenomicsV1::CallSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def list_reference_bases(reference_id, page_token: nil, page_size: nil, start_position: nil, end_position: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/references/{referenceId}/bases', options) - command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation - command.response_class = Google::Apis::GenomicsV1::ListBasesResponse - command.params['referenceId'] = reference_id unless reference_id.nil? - command.query['pageToken'] = page_token unless page_token.nil? - command.query['pageSize'] = page_size unless page_size.nil? - command.query['start'] = start_position unless start_position.nil? - command.query['end'] = end_position unless end_position.nil? - command.query['fields'] = fields unless fields.nil? + def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:patch, 'v1/callsets/{callSetId}', options) + command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation + command.request_object = call_set_object + command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation + command.response_class = Google::Apis::GenomicsV1::CallSet + command.params['callSetId'] = call_set_id unless call_set_id.nil? + command.query['updateMask'] = update_mask unless update_mask.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Lists datasets within a project. - # For the definitions of datasets and other genomics resources, see + # Gets a call set by ID. + # For the definitions of call sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] page_token - # 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. - # @param [Fixnum] page_size - # The maximum number of results to return in a single page. If unspecified, - # defaults to 50. The maximum value is 1024. - # @param [String] project_id - # Required. The Google Cloud project ID to list datasets for. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] call_set_id + # The ID of the call set. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ListDatasetsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::ListDatasetsResponse] + # @return [Google::Apis::GenomicsV1::CallSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def list_datasets(page_token: nil, page_size: nil, project_id: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/datasets', options) - command.response_representation = Google::Apis::GenomicsV1::ListDatasetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::ListDatasetsResponse - command.query['pageToken'] = page_token unless page_token.nil? - command.query['pageSize'] = page_size unless page_size.nil? - command.query['projectId'] = project_id unless project_id.nil? - command.query['fields'] = fields unless fields.nil? + def get_call_set(call_set_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/callsets/{callSetId}', options) + command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation + command.response_class = Google::Apis::GenomicsV1::CallSet + command.params['callSetId'] = call_set_id unless call_set_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Creates a new dataset. - # For the definitions of datasets and other genomics resources, see + # Creates a new call set. + # For the definitions of call sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [Google::Apis::GenomicsV1::Dataset] dataset_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [Google::Apis::GenomicsV1::CallSet] call_set_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Dataset] + # @return [Google::Apis::GenomicsV1::CallSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/datasets', options) - command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.request_object = dataset_object - command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.response_class = Google::Apis::GenomicsV1::Dataset - command.query['fields'] = fields unless fields.nil? + def create_call_set(call_set_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/callsets', options) + command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation + command.request_object = call_set_object + command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation + command.response_class = Google::Apis::GenomicsV1::CallSet command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Sets the access control policy on the specified dataset. Replaces any - # existing policy. - # For the definitions of datasets and other genomics resources, see + # Deletes a call set. + # For the definitions of call sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a - # Policy</a> for more information. - # @param [String] resource - # REQUIRED: The resource for which policy is being specified. Format is - # `datasets/<dataset ID>`. - # @param [Google::Apis::GenomicsV1::SetIamPolicyRequest] set_iam_policy_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] call_set_id + # The ID of the call set to be deleted. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Policy] + # @return [Google::Apis::GenomicsV1::Empty] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/{+resource}:setIamPolicy', options) - command.request_representation = Google::Apis::GenomicsV1::SetIamPolicyRequest::Representation - command.request_object = set_iam_policy_request_object - command.response_representation = Google::Apis::GenomicsV1::Policy::Representation - command.response_class = Google::Apis::GenomicsV1::Policy - command.params['resource'] = resource unless resource.nil? - command.query['fields'] = fields unless fields.nil? + def delete_call_set(call_set_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:delete, 'v1/callsets/{callSetId}', options) + command.response_representation = Google::Apis::GenomicsV1::Empty::Representation + command.response_class = Google::Apis::GenomicsV1::Empty + command.params['callSetId'] = call_set_id unless call_set_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets the access control policy for the dataset. This is empty if the - # policy or resource does not exist. - # See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a - # Policy</a> for more information. - # For the definitions of datasets and other genomics resources, see + # Gets a list of call sets matching the criteria. + # For the definitions of call sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] resource - # REQUIRED: The resource for which policy is being specified. Format is - # `datasets/<dataset ID>`. - # @param [Google::Apis::GenomicsV1::GetIamPolicyRequest] get_iam_policy_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Implements + # [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5. + # 1/src/main/resources/avro/variantmethods.avdl#L178). + # @param [Google::Apis::GenomicsV1::SearchCallSetsRequest] search_call_sets_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::SearchCallSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Policy] + # @return [Google::Apis::GenomicsV1::SearchCallSetsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/{+resource}:getIamPolicy', options) - command.request_representation = Google::Apis::GenomicsV1::GetIamPolicyRequest::Representation - command.request_object = get_iam_policy_request_object - command.response_representation = Google::Apis::GenomicsV1::Policy::Representation - command.response_class = Google::Apis::GenomicsV1::Policy - command.params['resource'] = resource unless resource.nil? - command.query['fields'] = fields unless fields.nil? + def search_call_sets(search_call_sets_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/callsets/search', options) + command.request_representation = Google::Apis::GenomicsV1::SearchCallSetsRequest::Representation + command.request_object = search_call_sets_request_object + command.response_representation = Google::Apis::GenomicsV1::SearchCallSetsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::SearchCallSetsResponse command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Undeletes a dataset by restoring a dataset which was deleted via this API. - # For the definitions of datasets and other genomics resources, see + # Gets a list of reads for one or more read group sets. + # For the definitions of read group sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # This operation is only possible for a week after the deletion occurred. - # @param [String] dataset_id - # The ID of the dataset to be undeleted. - # @param [Google::Apis::GenomicsV1::UndeleteDatasetRequest] undelete_dataset_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Reads search operates over a genomic coordinate space of reference sequence + # & position defined over the reference sequences to which the requested + # read group sets are aligned. + # If a target positional range is specified, search returns all reads whose + # alignment to the reference genome overlap the range. A query which + # specifies only read group set IDs yields all reads in those read group + # sets, including unmapped reads. + # All reads returned (including reads on subsequent pages) are ordered by + # genomic coordinate (by reference sequence, then position). Reads with + # equivalent genomic coordinates are returned in an unspecified order. This + # order is consistent, such that two queries for the same content (regardless + # of page size) yield reads in the same order across their respective streams + # of paginated responses. + # Implements + # [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/ + # src/main/resources/avro/readmethods.avdl#L85). + # @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::SearchReadsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Dataset] + # @return [Google::Apis::GenomicsV1::SearchReadsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/datasets/{datasetId}:undelete', options) - command.request_representation = Google::Apis::GenomicsV1::UndeleteDatasetRequest::Representation - command.request_object = undelete_dataset_request_object - command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.response_class = Google::Apis::GenomicsV1::Dataset - command.params['datasetId'] = dataset_id unless dataset_id.nil? - command.query['fields'] = fields unless fields.nil? + def search_reads(search_reads_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/reads/search', options) + command.request_representation = Google::Apis::GenomicsV1::SearchReadsRequest::Representation + command.request_object = search_reads_request_object + command.response_representation = Google::Apis::GenomicsV1::SearchReadsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::SearchReadsResponse command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets a dataset by ID. - # For the definitions of datasets and other genomics resources, see + # Exports a read group set to a BAM file in Google Cloud Storage. + # For the definitions of read group sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] dataset_id - # The ID of the dataset. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Note that currently there may be some differences between exported BAM + # files and the original BAM file at the time of import. See + # ImportReadGroupSets + # for caveats. + # @param [String] read_group_set_id + # Required. The ID of the read group set to export. The caller must have + # READ access to this read group set. + # @param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Dataset] + # @return [Google::Apis::GenomicsV1::Operation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/datasets/{datasetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.response_class = Google::Apis::GenomicsV1::Dataset - command.params['datasetId'] = dataset_id unless dataset_id.nil? - command.query['fields'] = fields unless fields.nil? + def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/readgroupsets/{readGroupSetId}:export', options) + command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation + command.request_object = export_read_group_set_request_object + command.response_representation = Google::Apis::GenomicsV1::Operation::Representation + command.response_class = Google::Apis::GenomicsV1::Operation + command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Updates a dataset. - # For the definitions of datasets and other genomics resources, see + # Searches for read group sets matching the criteria. + # For the definitions of read group sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # This method supports patch semantics. - # @param [String] dataset_id - # The ID of the dataset to be updated. - # @param [Google::Apis::GenomicsV1::Dataset] dataset_object - # @param [String] update_mask - # An optional mask specifying which fields to update. At this time, the only - # mutable field is name. The only - # acceptable value is "name". If unspecified, all mutable fields will be - # updated. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Implements + # [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/ + # v0.5.1/src/main/resources/avro/readmethods.avdl#L135). + # @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Dataset] + # @return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:patch, 'v1/datasets/{datasetId}', options) - command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.request_object = dataset_object - command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation - command.response_class = Google::Apis::GenomicsV1::Dataset - command.params['datasetId'] = dataset_id unless dataset_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? + def search_read_group_sets(search_read_group_sets_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/readgroupsets/search', options) + command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation + command.request_object = search_read_group_sets_request_object + command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Returns permissions that a caller has on the specified resource. - # See <a href="/iam/docs/managing-policies#testing_permissions">Testing - # Permissions</a> for more information. - # For the definitions of datasets and other genomics resources, see + # Gets a read group set by ID. + # For the definitions of read group sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] resource - # REQUIRED: The resource for which policy is being specified. Format is - # `datasets/<dataset ID>`. - # @param [Google::Apis::GenomicsV1::TestIamPermissionsRequest] test_iam_permissions_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] read_group_set_id + # The ID of the read group set. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::TestIamPermissionsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::TestIamPermissionsResponse] + # @return [Google::Apis::GenomicsV1::ReadGroupSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/{+resource}:testIamPermissions', options) - command.request_representation = Google::Apis::GenomicsV1::TestIamPermissionsRequest::Representation - command.request_object = test_iam_permissions_request_object - command.response_representation = Google::Apis::GenomicsV1::TestIamPermissionsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::TestIamPermissionsResponse - command.params['resource'] = resource unless resource.nil? - command.query['fields'] = fields unless fields.nil? + def get_read_group_set(read_group_set_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}', options) + command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation + command.response_class = Google::Apis::GenomicsV1::ReadGroupSet + command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Deletes a dataset and all of its contents (all read group sets, - # reference sets, variant sets, call sets, annotation sets, etc.) - # This is reversible (up to one week after the deletion) via - # the - # datasets.undelete - # operation. - # For the definitions of datasets and other genomics resources, see + # Updates a read group set. + # For the definitions of read group sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] dataset_id - # The ID of the dataset to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # This method supports patch semantics. + # @param [String] read_group_set_id + # The ID of the read group set to be updated. The caller must have WRITE + # permissions to the dataset associated with this read group set. + # @param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object + # @param [String] update_mask + # An optional mask specifying which fields to update. Supported fields: + # * name. + # * referenceSetId. + # Leaving `updateMask` unset is equivalent to specifying all mutable + # fields. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Empty] + # @return [Google::Apis::GenomicsV1::ReadGroupSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/datasets/{datasetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['datasetId'] = dataset_id unless dataset_id.nil? - command.query['fields'] = fields unless fields.nil? + def patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:patch, 'v1/readgroupsets/{readGroupSetId}', options) + command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation + command.request_object = read_group_set_object + command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation + command.response_class = Google::Apis::GenomicsV1::ReadGroupSet + command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? + command.query['updateMask'] = update_mask unless update_mask.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Updates an annotation. Caller must have - # WRITE permission for the associated dataset. - # @param [String] annotation_id - # The ID of the annotation to be updated. - # @param [Google::Apis::GenomicsV1::Annotation] annotation_object - # @param [String] update_mask - # An optional mask specifying which fields to update. Mutable fields are - # name, - # variant, - # transcript, and - # info. If unspecified, all mutable - # fields will be updated. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Deletes a read group set. + # For the definitions of read group sets and other genomics resources, see + # [Fundamentals of Google + # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) + # @param [String] read_group_set_id + # The ID of the read group set to be deleted. The caller must have WRITE + # permissions to the dataset associated with this read group set. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Annotation] + # @return [Google::Apis::GenomicsV1::Empty] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def update_annotation(annotation_id, annotation_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:put, 'v1/annotations/{annotationId}', options) - command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation - command.request_object = annotation_object - command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation - command.response_class = Google::Apis::GenomicsV1::Annotation - command.params['annotationId'] = annotation_id unless annotation_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? + def delete_read_group_set(read_group_set_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:delete, 'v1/readgroupsets/{readGroupSetId}', options) + command.response_representation = Google::Apis::GenomicsV1::Empty::Representation + command.response_class = Google::Apis::GenomicsV1::Empty + command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Deletes an annotation. Caller must have WRITE permission for - # the associated annotation set. - # @param [String] annotation_id - # The ID of the annotation to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Creates read group sets by asynchronously importing the provided + # information. + # For the definitions of read group sets and other genomics resources, see + # [Fundamentals of Google + # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) + # The caller must have WRITE permissions to the dataset. + # ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import + # - Tags will be converted to strings - tag types are not preserved + # - Comments (`@CO`) in the input file header will not be preserved + # - Original header order of references (`@SQ`) will not be preserved + # - Any reverse stranded unmapped reads will be reverse complemented, and + # their qualities (also the "BQ" and "OQ" tags, if any) will be reversed + # - Unmapped reads will be stripped of positional information (reference name + # and position) + # @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Empty] + # @return [Google::Apis::GenomicsV1::Operation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/annotations/{annotationId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['annotationId'] = annotation_id unless annotation_id.nil? - command.query['fields'] = fields unless fields.nil? + def import_read_group_sets(import_read_group_sets_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/readgroupsets:import', options) + command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation + command.request_object = import_read_group_sets_request_object + command.response_representation = Google::Apis::GenomicsV1::Operation::Representation + command.response_class = Google::Apis::GenomicsV1::Operation command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Creates a new annotation. Caller must have WRITE permission - # for the associated annotation set. - # The following fields are required: - # * annotationSetId - # * referenceName or - # referenceId - # ### Transcripts - # For annotations of type TRANSCRIPT, the following fields of - # transcript must be provided: - # * exons.start - # * exons.end - # All other fields may be optionally specified, unless documented as being - # server-generated (for example, the `id` field). The annotated - # range must be no longer than 100Mbp (mega base pairs). See the - # Annotation resource - # for additional restrictions on each field. - # @param [Google::Apis::GenomicsV1::Annotation] annotation_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Lists fixed width coverage buckets for a read group set, each of which + # correspond to a range of a reference sequence. Each bucket summarizes + # coverage information across its corresponding genomic range. + # For the definitions of read group sets and other genomics resources, see + # [Fundamentals of Google + # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) + # Coverage is defined as the number of reads which are aligned to a given + # base in the reference sequence. Coverage buckets are available at several + # precomputed bucket widths, enabling retrieval of various coverage 'zoom + # levels'. The caller must have READ permissions for the target read group + # set. + # @param [String] read_group_set_id + # Required. The ID of the read group set over which coverage is requested. + # @param [Fixnum] page_size + # The maximum number of results to return in a single page. If unspecified, + # defaults to 1024. The maximum value is 2048. + # @param [Fixnum] start + # The start position of the range on the reference, 0-based inclusive. If + # specified, `referenceName` must also be specified. Defaults to 0. + # @param [Fixnum] target_bucket_width + # The desired width of each reported coverage bucket in base pairs. This + # will be rounded down to the nearest precomputed bucket width; the value + # of which is returned as `bucketWidth` in the response. Defaults + # to infinity (each bucket spans an entire reference sequence) or the length + # of the target range, if specified. The smallest precomputed + # `bucketWidth` is currently 2048 base pairs; this is subject to + # change. + # @param [String] reference_name + # The name of the reference to query, within the reference set associated + # with this query. Optional. + # @param [Fixnum] end_ + # The end position of the range on the reference, 0-based exclusive. If + # specified, `referenceName` must also be specified. If unset or 0, defaults + # to the length of the reference. + # @param [String] page_token + # 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. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Annotation] + # @return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_annotation(annotation_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/annotations', options) - command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation - command.request_object = annotation_object - command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation - command.response_class = Google::Apis::GenomicsV1::Annotation - command.query['fields'] = fields unless fields.nil? + def list_coverage_buckets(read_group_set_id, page_size: nil, start: nil, target_bucket_width: nil, reference_name: nil, end_: nil, page_token: nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', options) + command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse + command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? + command.query['pageSize'] = page_size unless page_size.nil? + command.query['start'] = start unless start.nil? + command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil? + command.query['referenceName'] = reference_name unless reference_name.nil? + command.query['end'] = end_ unless end_.nil? + command.query['pageToken'] = page_token unless page_token.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Creates one or more new annotations atomically. All annotations must - # belong to the same annotation set. Caller must have WRITE - # permission for this annotation set. For optimal performance, batch - # positionally adjacent annotations together. - # If the request has a systemic issue, such as an attempt to write to - # an inaccessible annotation set, the entire RPC will fail accordingly. For - # lesser data issues, when possible an error will be isolated to the - # corresponding batch entry in the response; the remaining well formed - # annotations will be created normally. - # For details on the requirements for each individual annotation resource, - # see - # CreateAnnotation. - # @param [Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest] batch_create_annotations_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Updates an annotation set. The update must respect all mutability + # restrictions and other invariants described on the annotation set resource. + # Caller must have WRITE permission for the associated dataset. + # @param [String] annotation_set_id + # The ID of the annotation set to be updated. + # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object + # @param [String] update_mask + # An optional mask specifying which fields to update. Mutable fields are + # name, + # source_uri, and + # info. If unspecified, all + # mutable fields will be updated. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse] + # @return [Google::Apis::GenomicsV1::AnnotationSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/annotations:batchCreate', options) - command.request_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest::Representation - command.request_object = batch_create_annotations_request_object - command.response_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse - command.query['fields'] = fields unless fields.nil? + def update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:put, 'v1/annotationsets/{annotationSetId}', options) + command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation + command.request_object = annotation_set_object + command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation + command.response_class = Google::Apis::GenomicsV1::AnnotationSet + command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? + command.query['updateMask'] = update_mask unless update_mask.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Searches for annotations that match the given criteria. Results are - # ordered by genomic coordinate (by reference sequence, then position). - # Annotations with equivalent genomic coordinates are returned in an - # unspecified order. This order is consistent, such that two queries for the - # same content (regardless of page size) yield annotations in the same order - # across their respective streams of paginated responses. Caller must have - # READ permission for the queried annotation sets. - # @param [Google::Apis::GenomicsV1::SearchAnnotationsRequest] search_annotations_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Creates a new annotation set. Caller must have WRITE permission for the + # associated dataset. + # The following fields are required: + # * datasetId + # * referenceSetId + # All other fields may be optionally specified, unless documented as being + # server-generated (for example, the `id` field). + # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::SearchAnnotationsResponse] + # @return [Google::Apis::GenomicsV1::AnnotationSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/annotations/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationsRequest::Representation - command.request_object = search_annotations_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchAnnotationsResponse - command.query['fields'] = fields unless fields.nil? + def create_annotation_set(annotation_set_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/annotationsets', options) + command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation + command.request_object = annotation_set_object + command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation + command.response_class = Google::Apis::GenomicsV1::AnnotationSet command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets an annotation. Caller must have READ permission + # Deletes an annotation set. Caller must have WRITE permission # for the associated annotation set. - # @param [String] annotation_id - # The ID of the annotation to be retrieved. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] annotation_set_id + # The ID of the annotation set to be deleted. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Annotation] + # @return [Google::Apis::GenomicsV1::Empty] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/annotations/{annotationId}', options) - command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation - command.response_class = Google::Apis::GenomicsV1::Annotation - command.params['annotationId'] = annotation_id unless annotation_id.nil? - command.query['fields'] = fields unless fields.nil? + def delete_annotationset(annotation_set_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:delete, 'v1/annotationsets/{annotationSetId}', options) + command.response_representation = Google::Apis::GenomicsV1::Empty::Representation + command.response_class = Google::Apis::GenomicsV1::Empty + command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Deletes a variant set including all variants, call sets, and calls within. - # This is not reversible. - # For the definitions of variant sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_set_id - # The ID of the variant set to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Searches for annotation sets that match the given criteria. Annotation sets + # are returned in an unspecified order. This order is consistent, such that + # two queries for the same content (regardless of page size) yield annotation + # sets in the same order across their respective streams of paginated + # responses. Caller must have READ permission for the queried datasets. + # @param [Google::Apis::GenomicsV1::SearchAnnotationSetsRequest] search_annotation_sets_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Empty] + # @return [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/variantsets/{variantSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? - command.query['fields'] = fields unless fields.nil? + def search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/annotationsets/search', options) + command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsRequest::Representation + command.request_object = search_annotation_sets_request_object + command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Creates a new variant set. - # For the definitions of variant sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # The provided variant set must have a valid `datasetId` set - all other - # fields are optional. Note that the `id` field will be ignored, as this is - # assigned by the server. - # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Gets an annotation set. Caller must have READ permission for + # the associated dataset. + # @param [String] annotation_set_id + # The ID of the annotation set to be retrieved. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::VariantSet] + # @return [Google::Apis::GenomicsV1::AnnotationSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variantsets', options) - command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation - command.request_object = variant_set_object - command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation - command.response_class = Google::Apis::GenomicsV1::VariantSet - command.query['fields'] = fields unless fields.nil? + def get_annotation_set(annotation_set_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/annotationsets/{annotationSetId}', options) + command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation + command.response_class = Google::Apis::GenomicsV1::AnnotationSet + command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Exports variant set data to an external destination. - # For the definitions of variant sets and other genomics resources, see + # Merges the given variants with existing variants. + # For the definitions of variants and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_set_id - # Required. The ID of the variant set that contains variant data which - # should be exported. The caller must have READ access to this variant set. - # @param [Google::Apis::GenomicsV1::ExportVariantSetRequest] export_variant_set_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Each variant will be + # merged with an existing variant that matches its reference sequence, + # start, end, reference bases, and alternative bases. If no such variant + # exists, a new one will be created. + # When variants are merged, the call information from the new variant + # is added to the existing variant. Variant info fields are merged as + # specified in the + # infoMergeConfig + # field of the MergeVariantsRequest. + # Please exercise caution when using this method! It is easy to introduce + # mistakes in existing variants and difficult to back out of them. For + # example, + # suppose you were trying to merge a new variant with an existing one and + # both + # variants contain calls that belong to callsets with the same callset ID. + # // Existing variant - irrelevant fields trimmed for clarity + # ` + # "variantSetId": "10473108253681171589", + # "referenceName": "1", + # "start": "10582", + # "referenceBases": "G", + # "alternateBases": [ + # "A" + # ], + # "calls": [ + # ` + # "callSetId": "10473108253681171589-0", + # "callSetName": "CALLSET0", + # "genotype": [ + # 0, + # 1 + # ], + # ` + # ] + # ` + # // New variant with conflicting call information + # ` + # "variantSetId": "10473108253681171589", + # "referenceName": "1", + # "start": "10582", + # "referenceBases": "G", + # "alternateBases": [ + # "A" + # ], + # "calls": [ + # ` + # "callSetId": "10473108253681171589-0", + # "callSetName": "CALLSET0", + # "genotype": [ + # 1, + # 1 + # ], + # ` + # ] + # ` + # The resulting merged variant would overwrite the existing calls with those + # from the new variant: + # ` + # "variantSetId": "10473108253681171589", + # "referenceName": "1", + # "start": "10582", + # "referenceBases": "G", + # "alternateBases": [ + # "A" + # ], + # "calls": [ + # ` + # "callSetId": "10473108253681171589-0", + # "callSetName": "CALLSET0", + # "genotype": [ + # 1, + # 1 + # ], + # ` + # ] + # ` + # This may be the desired outcome, but it is up to the user to determine if + # if that is indeed the case. + # @param [Google::Apis::GenomicsV1::MergeVariantsRequest] merge_variants_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Operation] + # @return [Google::Apis::GenomicsV1::Empty] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variantsets/{variantSetId}:export', options) - command.request_representation = Google::Apis::GenomicsV1::ExportVariantSetRequest::Representation - command.request_object = export_variant_set_request_object - command.response_representation = Google::Apis::GenomicsV1::Operation::Representation - command.response_class = Google::Apis::GenomicsV1::Operation - command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? - command.query['fields'] = fields unless fields.nil? + def merge_variants(merge_variants_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/variants:merge', options) + command.request_representation = Google::Apis::GenomicsV1::MergeVariantsRequest::Representation + command.request_object = merge_variants_request_object + command.response_representation = Google::Apis::GenomicsV1::Empty::Representation + command.response_class = Google::Apis::GenomicsV1::Empty command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Returns a list of all variant sets matching search criteria. + # Creates variant data by asynchronously importing the provided information. # For the definitions of variant sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0. - # 5.1/src/main/resources/avro/variantmethods.avdl#L49). - # @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # The variants for import will be merged with any existing variant that + # matches its reference sequence, start, end, reference bases, and + # alternative bases. If no such variant exists, a new one will be created. + # When variants are merged, the call information from the new variant + # is added to the existing variant, and Variant info fields are merged + # as specified in + # infoMergeConfig. + # As a special case, for single-sample VCF files, QUAL and FILTER fields will + # be moved to the call level; these are sometimes interpreted in a + # call-specific context. + # Imported VCF headers are appended to the metadata already in a variant set. + # @param [Google::Apis::GenomicsV1::ImportVariantsRequest] import_variants_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantSetsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::SearchVariantSetsResponse] + # @return [Google::Apis::GenomicsV1::Operation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variantsets/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchVariantSetsRequest::Representation - command.request_object = search_variant_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchVariantSetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchVariantSetsResponse - command.query['fields'] = fields unless fields.nil? + def import_variants(import_variants_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/variants:import', options) + command.request_representation = Google::Apis::GenomicsV1::ImportVariantsRequest::Representation + command.request_object = import_variants_request_object + command.response_representation = Google::Apis::GenomicsV1::Operation::Representation + command.response_class = Google::Apis::GenomicsV1::Operation command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets a variant set by ID. - # For the definitions of variant sets and other genomics resources, see + # Deletes a variant. + # For the definitions of variants and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_set_id - # Required. The ID of the variant set. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] variant_id + # The ID of the variant to be deleted. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::VariantSet] + # @return [Google::Apis::GenomicsV1::Empty] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/variantsets/{variantSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation - command.response_class = Google::Apis::GenomicsV1::VariantSet - command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? - command.query['fields'] = fields unless fields.nil? + def delete_variant(variant_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:delete, 'v1/variants/{variantId}', options) + command.response_representation = Google::Apis::GenomicsV1::Empty::Representation + command.response_class = Google::Apis::GenomicsV1::Empty + command.params['variantId'] = variant_id unless variant_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Updates a variant set using patch semantics. - # For the definitions of variant sets and other genomics resources, see + # Creates a new variant. + # For the definitions of variants and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_set_id - # The ID of the variant to be updated (must already exist). - # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object - # @param [String] update_mask - # An optional mask specifying which fields to update. Supported fields: - # * metadata. - # * name. - # * description. - # Leaving `updateMask` unset is equivalent to specifying all mutable - # fields. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [Google::Apis::GenomicsV1::Variant] variant_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::VariantSet] + # @return [Google::Apis::GenomicsV1::Variant] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:patch, 'v1/variantsets/{variantSetId}', options) - command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation - command.request_object = variant_set_object - command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation - command.response_class = Google::Apis::GenomicsV1::VariantSet - command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? + def create_variant(variant_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/variants', options) + command.request_representation = Google::Apis::GenomicsV1::Variant::Representation + command.request_object = variant_object + command.response_representation = Google::Apis::GenomicsV1::Variant::Representation + command.response_class = Google::Apis::GenomicsV1::Variant command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Lists operations that match the specified filter in the request. - # @param [String] name - # The name of the operation collection. - # @param [String] filter - # A string for filtering Operations. - # The following filter fields are supported&#58; - # * projectId&#58; Required. Corresponds to - # OperationMetadata.projectId. - # * createTime&#58; The time this job was created, in seconds from the - # [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=` - # operators. - # * status&#58; Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only - # one status may be specified. - # * labels.key where key is a label key. - # Examples&#58; - # * `projectId = my-project AND createTime >= 1432140000` - # * `projectId = my-project AND createTime >= 1432140000 AND createTime <= - # 1432150000 AND status = RUNNING` - # * `projectId = my-project AND labels.color = *` - # * `projectId = my-project AND labels.color = red` - # @param [String] page_token - # The standard list page token. - # @param [Fixnum] page_size - # The maximum number of results to return. If unspecified, defaults to - # 256. The maximum value is 2048. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Gets a list of variants matching the criteria. + # For the definitions of variants and other genomics resources, see + # [Fundamentals of Google + # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) + # Implements + # [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5. + # 1/src/main/resources/avro/variantmethods.avdl#L126). + # @param [Google::Apis::GenomicsV1::SearchVariantsRequest] search_variants_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ListOperationsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::ListOperationsResponse] + # @return [Google::Apis::GenomicsV1::SearchVariantsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def list_operations(name, filter: nil, page_token: nil, page_size: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/{+name}', options) - command.response_representation = Google::Apis::GenomicsV1::ListOperationsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::ListOperationsResponse - command.params['name'] = name unless name.nil? - command.query['filter'] = filter unless filter.nil? - command.query['pageToken'] = page_token unless page_token.nil? - command.query['pageSize'] = page_size unless page_size.nil? - command.query['fields'] = fields unless fields.nil? + def search_variants(search_variants_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/variants/search', options) + command.request_representation = Google::Apis::GenomicsV1::SearchVariantsRequest::Representation + command.request_object = search_variants_request_object + command.response_representation = Google::Apis::GenomicsV1::SearchVariantsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::SearchVariantsResponse command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets the latest state of a long-running operation. Clients can use this - # method to poll the operation result at intervals as recommended by the API - # service. - # @param [String] name - # The name of the operation resource. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Gets a variant by ID. + # For the definitions of variants and other genomics resources, see + # [Fundamentals of Google + # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) + # @param [String] variant_id + # The ID of the variant. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Operation] + # @return [Google::Apis::GenomicsV1::Variant] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_operation(name, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/{+name}', options) - command.response_representation = Google::Apis::GenomicsV1::Operation::Representation - command.response_class = Google::Apis::GenomicsV1::Operation - command.params['name'] = name unless name.nil? - command.query['fields'] = fields unless fields.nil? + def get_variant(variant_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/variants/{variantId}', options) + command.response_representation = Google::Apis::GenomicsV1::Variant::Representation + command.response_class = Google::Apis::GenomicsV1::Variant + command.params['variantId'] = variant_id unless variant_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Starts asynchronous cancellation on a long-running operation. The server makes - # a best effort to cancel the operation, but success is not guaranteed. Clients - # may use Operations.GetOperation or Operations.ListOperations to check whether - # the cancellation succeeded or the operation completed despite cancellation. - # @param [String] name - # The name of the operation resource to be cancelled. - # @param [Google::Apis::GenomicsV1::CancelOperationRequest] cancel_operation_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Updates a variant. + # For the definitions of variants and other genomics resources, see + # [Fundamentals of Google + # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) + # This method supports patch semantics. Returns the modified variant without + # its calls. + # @param [String] variant_id + # The ID of the variant to be updated. + # @param [Google::Apis::GenomicsV1::Variant] variant_object + # @param [String] update_mask + # An optional mask specifying which fields to update. At this time, mutable + # fields are names and + # info. Acceptable values are "names" and + # "info". If unspecified, all mutable fields will be updated. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Empty] + # @return [Google::Apis::GenomicsV1::Variant] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/{+name}:cancel', options) - command.request_representation = Google::Apis::GenomicsV1::CancelOperationRequest::Representation - command.request_object = cancel_operation_request_object - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['name'] = name unless name.nil? - command.query['fields'] = fields unless fields.nil? + def patch_variant(variant_id, variant_object = nil, update_mask: nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:patch, 'v1/variants/{variantId}', options) + command.request_representation = Google::Apis::GenomicsV1::Variant::Representation + command.request_object = variant_object + command.response_representation = Google::Apis::GenomicsV1::Variant::Representation + command.response_class = Google::Apis::GenomicsV1::Variant + command.params['variantId'] = variant_id unless variant_id.nil? + command.query['updateMask'] = update_mask unless update_mask.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Searches for reference sets which match the given criteria. + # Searches for references which match the given criteria. # For the definitions of references and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) # Implements - # [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/ - # v0.5.1/src/main/resources/avro/referencemethods.avdl#L71) - # @param [Google::Apis::GenomicsV1::SearchReferenceSetsRequest] search_reference_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0. + # 5.1/src/main/resources/avro/referencemethods.avdl#L146). + # @param [Google::Apis::GenomicsV1::SearchReferencesRequest] search_references_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::SearchReferencesResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] + # @return [Google::Apis::GenomicsV1::SearchReferencesResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/referencesets/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchReferenceSetsRequest::Representation - command.request_object = search_reference_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchReferenceSetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchReferenceSetsResponse - command.query['fields'] = fields unless fields.nil? + def search_references(search_references_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/references/search', options) + command.request_representation = Google::Apis::GenomicsV1::SearchReferencesRequest::Representation + command.request_object = search_references_request_object + command.response_representation = Google::Apis::GenomicsV1::SearchReferencesResponse::Representation + command.response_class = Google::Apis::GenomicsV1::SearchReferencesResponse command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets a reference set. + # Gets a reference. # For the definitions of references and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) # Implements - # [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5. - # 1/src/main/resources/avro/referencemethods.avdl#L83). - # @param [String] reference_set_id - # The ID of the reference set. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/ + # src/main/resources/avro/referencemethods.avdl#L158). + # @param [String] reference_id + # The ID of the reference. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ReferenceSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Reference] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::ReferenceSet] + # @return [Google::Apis::GenomicsV1::Reference] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/referencesets/{referenceSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::ReferenceSet::Representation - command.response_class = Google::Apis::GenomicsV1::ReferenceSet - command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil? - command.query['fields'] = fields unless fields.nil? + def get_reference(reference_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/references/{referenceId}', options) + command.response_representation = Google::Apis::GenomicsV1::Reference::Representation + command.response_class = Google::Apis::GenomicsV1::Reference + command.params['referenceId'] = reference_id unless reference_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets a list of call sets matching the criteria. - # For the definitions of call sets and other genomics resources, see + # Lists the bases in a reference, optionally restricted to a range. + # For the definitions of references and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) # Implements - # [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5. - # 1/src/main/resources/avro/variantmethods.avdl#L178). - # @param [Google::Apis::GenomicsV1::SearchCallSetsRequest] search_call_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0. + # 5.1/src/main/resources/avro/referencemethods.avdl#L221). + # @param [String] reference_id + # The ID of the reference. + # @param [Fixnum] end_position + # The end position (0-based, exclusive) of this query. Defaults to the length + # of this reference. + # @param [String] page_token + # 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. + # @param [Fixnum] page_size + # The maximum number of bases to return in a single page. If unspecified, + # defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base + # pairs). + # @param [Fixnum] start_position + # The start position (0-based) of this query. Defaults to 0. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchCallSetsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::ListBasesResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::SearchCallSetsResponse] + # @return [Google::Apis::GenomicsV1::ListBasesResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/callsets/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchCallSetsRequest::Representation - command.request_object = search_call_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchCallSetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchCallSetsResponse - command.query['fields'] = fields unless fields.nil? + def list_reference_bases(reference_id, end_position: nil, page_token: nil, page_size: nil, start_position: nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/references/{referenceId}/bases', options) + command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation + command.response_class = Google::Apis::GenomicsV1::ListBasesResponse + command.params['referenceId'] = reference_id unless reference_id.nil? + command.query['end'] = end_position unless end_position.nil? + command.query['pageToken'] = page_token unless page_token.nil? + command.query['pageSize'] = page_size unless page_size.nil? + command.query['start'] = start_position unless start_position.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Updates a call set. - # For the definitions of call sets and other genomics resources, see + # Lists datasets within a project. + # For the definitions of datasets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # This method supports patch semantics. - # @param [String] call_set_id - # The ID of the call set to be updated. - # @param [Google::Apis::GenomicsV1::CallSet] call_set_object - # @param [String] update_mask - # An optional mask specifying which fields to update. At this time, the only - # mutable field is name. The only - # acceptable value is "name". If unspecified, all mutable fields will be - # updated. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] page_token + # 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. + # @param [Fixnum] page_size + # The maximum number of results to return in a single page. If unspecified, + # defaults to 50. The maximum value is 1024. + # @param [String] project_id + # Required. The Google Cloud project ID to list datasets for. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::ListDatasetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::CallSet] + # @return [Google::Apis::GenomicsV1::ListDatasetsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:patch, 'v1/callsets/{callSetId}', options) - command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation - command.request_object = call_set_object - command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation - command.response_class = Google::Apis::GenomicsV1::CallSet - command.params['callSetId'] = call_set_id unless call_set_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? + def list_datasets(page_token: nil, page_size: nil, project_id: nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/datasets', options) + command.response_representation = Google::Apis::GenomicsV1::ListDatasetsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::ListDatasetsResponse + command.query['pageToken'] = page_token unless page_token.nil? + command.query['pageSize'] = page_size unless page_size.nil? + command.query['projectId'] = project_id unless project_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets a call set by ID. - # For the definitions of call sets and other genomics resources, see + # Sets the access control policy on the specified dataset. Replaces any + # existing policy. + # For the definitions of datasets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] call_set_id - # The ID of the call set. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a + # Policy</a> for more information. + # @param [String] resource + # REQUIRED: The resource for which policy is being specified. Format is + # `datasets/<dataset ID>`. + # @param [Google::Apis::GenomicsV1::SetIamPolicyRequest] set_iam_policy_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::CallSet] + # @return [Google::Apis::GenomicsV1::Policy] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/callsets/{callSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation - command.response_class = Google::Apis::GenomicsV1::CallSet - command.params['callSetId'] = call_set_id unless call_set_id.nil? - command.query['fields'] = fields unless fields.nil? + def set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/{+resource}:setIamPolicy', options) + command.request_representation = Google::Apis::GenomicsV1::SetIamPolicyRequest::Representation + command.request_object = set_iam_policy_request_object + command.response_representation = Google::Apis::GenomicsV1::Policy::Representation + command.response_class = Google::Apis::GenomicsV1::Policy + command.params['resource'] = resource unless resource.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Creates a new call set. - # For the definitions of call sets and other genomics resources, see + # Creates a new dataset. + # For the definitions of datasets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [Google::Apis::GenomicsV1::CallSet] call_set_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [Google::Apis::GenomicsV1::Dataset] dataset_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::CallSet] + # @return [Google::Apis::GenomicsV1::Dataset] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/callsets', options) - command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation - command.request_object = call_set_object - command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation - command.response_class = Google::Apis::GenomicsV1::CallSet - command.query['fields'] = fields unless fields.nil? + def create_dataset(dataset_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/datasets', options) + command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation + command.request_object = dataset_object + command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation + command.response_class = Google::Apis::GenomicsV1::Dataset command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Deletes a call set. - # For the definitions of call sets and other genomics resources, see + # Gets the access control policy for the dataset. This is empty if the + # policy or resource does not exist. + # See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a + # Policy</a> for more information. + # For the definitions of datasets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] call_set_id - # The ID of the call set to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] resource + # REQUIRED: The resource for which policy is being specified. Format is + # `datasets/<dataset ID>`. + # @param [Google::Apis::GenomicsV1::GetIamPolicyRequest] get_iam_policy_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Empty] + # @return [Google::Apis::GenomicsV1::Policy] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/callsets/{callSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['callSetId'] = call_set_id unless call_set_id.nil? - command.query['fields'] = fields unless fields.nil? + def get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/{+resource}:getIamPolicy', options) + command.request_representation = Google::Apis::GenomicsV1::GetIamPolicyRequest::Representation + command.request_object = get_iam_policy_request_object + command.response_representation = Google::Apis::GenomicsV1::Policy::Representation + command.response_class = Google::Apis::GenomicsV1::Policy + command.params['resource'] = resource unless resource.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets a list of reads for one or more read group sets. - # For the definitions of read group sets and other genomics resources, see + # Updates a dataset. + # For the definitions of datasets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Reads search operates over a genomic coordinate space of reference sequence - # & position defined over the reference sequences to which the requested - # read group sets are aligned. - # If a target positional range is specified, search returns all reads whose - # alignment to the reference genome overlap the range. A query which - # specifies only read group set IDs yields all reads in those read group - # sets, including unmapped reads. - # All reads returned (including reads on subsequent pages) are ordered by - # genomic coordinate (by reference sequence, then position). Reads with - # equivalent genomic coordinates are returned in an unspecified order. This - # order is consistent, such that two queries for the same content (regardless - # of page size) yield reads in the same order across their respective streams - # of paginated responses. - # Implements - # [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/ - # src/main/resources/avro/readmethods.avdl#L85). - # @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # This method supports patch semantics. + # @param [String] dataset_id + # The ID of the dataset to be updated. + # @param [Google::Apis::GenomicsV1::Dataset] dataset_object + # @param [String] update_mask + # An optional mask specifying which fields to update. At this time, the only + # mutable field is name. The only + # acceptable value is "name". If unspecified, all mutable fields will be + # updated. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchReadsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::SearchReadsResponse] + # @return [Google::Apis::GenomicsV1::Dataset] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/reads/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchReadsRequest::Representation - command.request_object = search_reads_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchReadsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchReadsResponse - command.query['fields'] = fields unless fields.nil? + def patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:patch, 'v1/datasets/{datasetId}', options) + command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation + command.request_object = dataset_object + command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation + command.response_class = Google::Apis::GenomicsV1::Dataset + command.params['datasetId'] = dataset_id unless dataset_id.nil? + command.query['updateMask'] = update_mask unless update_mask.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Creates read group sets by asynchronously importing the provided - # information. - # For the definitions of read group sets and other genomics resources, see + # Gets a dataset by ID. + # For the definitions of datasets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # The caller must have WRITE permissions to the dataset. - # ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import - # - Tags will be converted to strings - tag types are not preserved - # - Comments (`@CO`) in the input file header will not be preserved - # - Original header order of references (`@SQ`) will not be preserved - # - Any reverse stranded unmapped reads will be reverse complemented, and - # their qualities (also the "BQ" and "OQ" tags, if any) will be reversed - # - Unmapped reads will be stripped of positional information (reference name - # and position) - # @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] dataset_id + # The ID of the dataset. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Operation] + # @return [Google::Apis::GenomicsV1::Dataset] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/readgroupsets:import', options) - command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation - command.request_object = import_read_group_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::Operation::Representation - command.response_class = Google::Apis::GenomicsV1::Operation - command.query['fields'] = fields unless fields.nil? + def get_dataset(dataset_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/datasets/{datasetId}', options) + command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation + command.response_class = Google::Apis::GenomicsV1::Dataset + command.params['datasetId'] = dataset_id unless dataset_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Deletes a read group set. - # For the definitions of read group sets and other genomics resources, see + # Undeletes a dataset by restoring a dataset which was deleted via this API. + # For the definitions of datasets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] read_group_set_id - # The ID of the read group set to be deleted. The caller must have WRITE - # permissions to the dataset associated with this read group set. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # This operation is only possible for a week after the deletion occurred. + # @param [String] dataset_id + # The ID of the dataset to be undeleted. + # @param [Google::Apis::GenomicsV1::UndeleteDatasetRequest] undelete_dataset_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Empty] + # @return [Google::Apis::GenomicsV1::Dataset] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/readgroupsets/{readGroupSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? - command.query['fields'] = fields unless fields.nil? + def undelete_dataset(dataset_id, undelete_dataset_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/datasets/{datasetId}:undelete', options) + command.request_representation = Google::Apis::GenomicsV1::UndeleteDatasetRequest::Representation + command.request_object = undelete_dataset_request_object + command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation + command.response_class = Google::Apis::GenomicsV1::Dataset + command.params['datasetId'] = dataset_id unless dataset_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Exports a read group set to a BAM file in Google Cloud Storage. - # For the definitions of read group sets and other genomics resources, see + # Returns permissions that a caller has on the specified resource. + # See <a href="/iam/docs/managing-policies#testing_permissions">Testing + # Permissions</a> for more information. + # For the definitions of datasets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Note that currently there may be some differences between exported BAM - # files and the original BAM file at the time of import. See - # ImportReadGroupSets - # for caveats. - # @param [String] read_group_set_id - # Required. The ID of the read group set to export. The caller must have - # READ access to this read group set. - # @param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] resource + # REQUIRED: The resource for which policy is being specified. Format is + # `datasets/<dataset ID>`. + # @param [Google::Apis::GenomicsV1::TestIamPermissionsRequest] test_iam_permissions_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::TestIamPermissionsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Operation] + # @return [Google::Apis::GenomicsV1::TestIamPermissionsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/readgroupsets/{readGroupSetId}:export', options) - command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation - command.request_object = export_read_group_set_request_object - command.response_representation = Google::Apis::GenomicsV1::Operation::Representation - command.response_class = Google::Apis::GenomicsV1::Operation - command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? - command.query['fields'] = fields unless fields.nil? + def test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/{+resource}:testIamPermissions', options) + command.request_representation = Google::Apis::GenomicsV1::TestIamPermissionsRequest::Representation + command.request_object = test_iam_permissions_request_object + command.response_representation = Google::Apis::GenomicsV1::TestIamPermissionsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::TestIamPermissionsResponse + command.params['resource'] = resource unless resource.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Searches for read group sets matching the criteria. - # For the definitions of read group sets and other genomics resources, see + # Deletes a dataset and all of its contents (all read group sets, + # reference sets, variant sets, call sets, annotation sets, etc.) + # This is reversible (up to one week after the deletion) via + # the + # datasets.undelete + # operation. + # For the definitions of datasets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/ - # v0.5.1/src/main/resources/avro/readmethods.avdl#L135). - # @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] dataset_id + # The ID of the dataset to be deleted. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] + # @return [Google::Apis::GenomicsV1::Empty] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/readgroupsets/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation - command.request_object = search_read_group_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse - command.query['fields'] = fields unless fields.nil? + def delete_dataset(dataset_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:delete, 'v1/datasets/{datasetId}', options) + command.response_representation = Google::Apis::GenomicsV1::Empty::Representation + command.response_class = Google::Apis::GenomicsV1::Empty + command.params['datasetId'] = dataset_id unless dataset_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets a read group set by ID. - # For the definitions of read group sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] read_group_set_id - # The ID of the read group set. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Gets an annotation. Caller must have READ permission + # for the associated annotation set. + # @param [String] annotation_id + # The ID of the annotation to be retrieved. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::ReadGroupSet] + # @return [Google::Apis::GenomicsV1::Annotation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation - command.response_class = Google::Apis::GenomicsV1::ReadGroupSet - command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? - command.query['fields'] = fields unless fields.nil? + def get_annotation(annotation_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/annotations/{annotationId}', options) + command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation + command.response_class = Google::Apis::GenomicsV1::Annotation + command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Updates a read group set. - # For the definitions of read group sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # This method supports patch semantics. - # @param [String] read_group_set_id - # The ID of the read group set to be updated. The caller must have WRITE - # permissions to the dataset associated with this read group set. - # @param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object + # Updates an annotation. Caller must have + # WRITE permission for the associated dataset. + # @param [String] annotation_id + # The ID of the annotation to be updated. + # @param [Google::Apis::GenomicsV1::Annotation] annotation_object # @param [String] update_mask - # An optional mask specifying which fields to update. Supported fields: - # * name. - # * referenceSetId. - # Leaving `updateMask` unset is equivalent to specifying all mutable - # fields. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # An optional mask specifying which fields to update. Mutable fields are + # name, + # variant, + # transcript, and + # info. If unspecified, all mutable + # fields will be updated. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::ReadGroupSet] + # @return [Google::Apis::GenomicsV1::Annotation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:patch, 'v1/readgroupsets/{readGroupSetId}', options) - command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation - command.request_object = read_group_set_object - command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation - command.response_class = Google::Apis::GenomicsV1::ReadGroupSet - command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? + def update_annotation(annotation_id, annotation_object = nil, update_mask: nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:put, 'v1/annotations/{annotationId}', options) + command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation + command.request_object = annotation_object + command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation + command.response_class = Google::Apis::GenomicsV1::Annotation + command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Lists fixed width coverage buckets for a read group set, each of which - # correspond to a range of a reference sequence. Each bucket summarizes - # coverage information across its corresponding genomic range. - # For the definitions of read group sets and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Coverage is defined as the number of reads which are aligned to a given - # base in the reference sequence. Coverage buckets are available at several - # precomputed bucket widths, enabling retrieval of various coverage 'zoom - # levels'. The caller must have READ permissions for the target read group - # set. - # @param [String] read_group_set_id - # Required. The ID of the read group set over which coverage is requested. - # @param [String] page_token - # 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. - # @param [Fixnum] page_size - # The maximum number of results to return in a single page. If unspecified, - # defaults to 1024. The maximum value is 2048. - # @param [Fixnum] start - # The start position of the range on the reference, 0-based inclusive. If - # specified, `referenceName` must also be specified. Defaults to 0. - # @param [Fixnum] target_bucket_width - # The desired width of each reported coverage bucket in base pairs. This - # will be rounded down to the nearest precomputed bucket width; the value - # of which is returned as `bucketWidth` in the response. Defaults - # to infinity (each bucket spans an entire reference sequence) or the length - # of the target range, if specified. The smallest precomputed - # `bucketWidth` is currently 2048 base pairs; this is subject to - # change. - # @param [String] reference_name - # The name of the reference to query, within the reference set associated - # with this query. Optional. - # @param [Fixnum] end_ - # The end position of the range on the reference, 0-based exclusive. If - # specified, `referenceName` must also be specified. If unset or 0, defaults - # to the length of the reference. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Deletes an annotation. Caller must have WRITE permission for + # the associated annotation set. + # @param [String] annotation_id + # The ID of the annotation to be deleted. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] + # @return [Google::Apis::GenomicsV1::Empty] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def list_coverage_buckets(read_group_set_id, page_token: nil, page_size: nil, start: nil, target_bucket_width: nil, reference_name: nil, end_: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', options) - command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse - command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? - command.query['pageToken'] = page_token unless page_token.nil? - command.query['pageSize'] = page_size unless page_size.nil? - command.query['start'] = start unless start.nil? - command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil? - command.query['referenceName'] = reference_name unless reference_name.nil? - command.query['end'] = end_ unless end_.nil? - command.query['fields'] = fields unless fields.nil? + def delete_annotation(annotation_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:delete, 'v1/annotations/{annotationId}', options) + command.response_representation = Google::Apis::GenomicsV1::Empty::Representation + command.response_class = Google::Apis::GenomicsV1::Empty + command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets a list of variants matching the criteria. - # For the definitions of variants and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Implements - # [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5. - # 1/src/main/resources/avro/variantmethods.avdl#L126). - # @param [Google::Apis::GenomicsV1::SearchVariantsRequest] search_variants_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Creates a new annotation. Caller must have WRITE permission + # for the associated annotation set. + # The following fields are required: + # * annotationSetId + # * referenceName or + # referenceId + # ### Transcripts + # For annotations of type TRANSCRIPT, the following fields of + # transcript must be provided: + # * exons.start + # * exons.end + # All other fields may be optionally specified, unless documented as being + # server-generated (for example, the `id` field). The annotated + # range must be no longer than 100Mbp (mega base pairs). See the + # Annotation resource + # for additional restrictions on each field. + # @param [Google::Apis::GenomicsV1::Annotation] annotation_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::SearchVariantsResponse] + # @return [Google::Apis::GenomicsV1::Annotation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variants/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchVariantsRequest::Representation - command.request_object = search_variants_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchVariantsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchVariantsResponse - command.query['fields'] = fields unless fields.nil? + def create_annotation(annotation_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/annotations', options) + command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation + command.request_object = annotation_object + command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation + command.response_class = Google::Apis::GenomicsV1::Annotation command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets a variant by ID. - # For the definitions of variants and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_id - # The ID of the variant. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Creates one or more new annotations atomically. All annotations must + # belong to the same annotation set. Caller must have WRITE + # permission for this annotation set. For optimal performance, batch + # positionally adjacent annotations together. + # If the request has a systemic issue, such as an attempt to write to + # an inaccessible annotation set, the entire RPC will fail accordingly. For + # lesser data issues, when possible an error will be isolated to the + # corresponding batch entry in the response; the remaining well formed + # annotations will be created normally. + # For details on the requirements for each individual annotation resource, + # see + # CreateAnnotation. + # @param [Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest] batch_create_annotations_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Variant] + # @return [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/variants/{variantId}', options) - command.response_representation = Google::Apis::GenomicsV1::Variant::Representation - command.response_class = Google::Apis::GenomicsV1::Variant - command.params['variantId'] = variant_id unless variant_id.nil? - command.query['fields'] = fields unless fields.nil? + def batch_create_annotations(batch_create_annotations_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/annotations:batchCreate', options) + command.request_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest::Representation + command.request_object = batch_create_annotations_request_object + command.response_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Updates a variant. - # For the definitions of variants and other genomics resources, see - # [Fundamentals of Google - # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # This method supports patch semantics. Returns the modified variant without - # its calls. - # @param [String] variant_id - # The ID of the variant to be updated. - # @param [Google::Apis::GenomicsV1::Variant] variant_object - # @param [String] update_mask - # An optional mask specifying which fields to update. At this time, mutable - # fields are names and - # info. Acceptable values are "names" and - # "info". If unspecified, all mutable fields will be updated. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Searches for annotations that match the given criteria. Results are + # ordered by genomic coordinate (by reference sequence, then position). + # Annotations with equivalent genomic coordinates are returned in an + # unspecified order. This order is consistent, such that two queries for the + # same content (regardless of page size) yield annotations in the same order + # across their respective streams of paginated responses. Caller must have + # READ permission for the queried annotation sets. + # @param [Google::Apis::GenomicsV1::SearchAnnotationsRequest] search_annotations_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Variant] + # @return [Google::Apis::GenomicsV1::SearchAnnotationsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:patch, 'v1/variants/{variantId}', options) - command.request_representation = Google::Apis::GenomicsV1::Variant::Representation - command.request_object = variant_object - command.response_representation = Google::Apis::GenomicsV1::Variant::Representation - command.response_class = Google::Apis::GenomicsV1::Variant - command.params['variantId'] = variant_id unless variant_id.nil? - command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? + def search_annotations(search_annotations_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/annotations/search', options) + command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationsRequest::Representation + command.request_object = search_annotations_request_object + command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::SearchAnnotationsResponse command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Deletes a variant. - # For the definitions of variants and other genomics resources, see + # Deletes a variant set including all variants, call sets, and calls within. + # This is not reversible. + # For the definitions of variant sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [String] variant_id - # The ID of the variant to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] variant_set_id + # The ID of the variant set to be deleted. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object @@ -1822,378 +1875,325 @@ # @return [Google::Apis::GenomicsV1::Empty] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/variants/{variantId}', options) + def delete_variantset(variant_set_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:delete, 'v1/variantsets/{variantSetId}', options) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty - command.params['variantId'] = variant_id unless variant_id.nil? - command.query['fields'] = fields unless fields.nil? + command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Creates variant data by asynchronously importing the provided information. + # Creates a new variant set. # For the definitions of variant sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # The variants for import will be merged with any existing variant that - # matches its reference sequence, start, end, reference bases, and - # alternative bases. If no such variant exists, a new one will be created. - # When variants are merged, the call information from the new variant - # is added to the existing variant, and Variant info fields are merged - # as specified in - # infoMergeConfig. - # As a special case, for single-sample VCF files, QUAL and FILTER fields will - # be moved to the call level; these are sometimes interpreted in a - # call-specific context. - # Imported VCF headers are appended to the metadata already in a variant set. - # @param [Google::Apis::GenomicsV1::ImportVariantsRequest] import_variants_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # The provided variant set must have a valid `datasetId` set - all other + # fields are optional. Note that the `id` field will be ignored, as this is + # assigned by the server. + # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Operation] + # @return [Google::Apis::GenomicsV1::VariantSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variants:import', options) - command.request_representation = Google::Apis::GenomicsV1::ImportVariantsRequest::Representation - command.request_object = import_variants_request_object - command.response_representation = Google::Apis::GenomicsV1::Operation::Representation - command.response_class = Google::Apis::GenomicsV1::Operation - command.query['fields'] = fields unless fields.nil? + def create_variantset(variant_set_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/variantsets', options) + command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation + command.request_object = variant_set_object + command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation + command.response_class = Google::Apis::GenomicsV1::VariantSet command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Merges the given variants with existing variants. - # For the definitions of variants and other genomics resources, see + # Exports variant set data to an external destination. + # For the definitions of variant sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # Each variant will be - # merged with an existing variant that matches its reference sequence, - # start, end, reference bases, and alternative bases. If no such variant - # exists, a new one will be created. - # When variants are merged, the call information from the new variant - # is added to the existing variant. Variant info fields are merged as - # specified in the - # infoMergeConfig - # field of the MergeVariantsRequest. - # Please exercise caution when using this method! It is easy to introduce - # mistakes in existing variants and difficult to back out of them. For - # example, - # suppose you were trying to merge a new variant with an existing one and - # both - # variants contain calls that belong to callsets with the same callset ID. - # // Existing variant - irrelevant fields trimmed for clarity - # ` - # "variantSetId": "10473108253681171589", - # "referenceName": "1", - # "start": "10582", - # "referenceBases": "G", - # "alternateBases": [ - # "A" - # ], - # "calls": [ - # ` - # "callSetId": "10473108253681171589-0", - # "callSetName": "CALLSET0", - # "genotype": [ - # 0, - # 1 - # ], - # ` - # ] - # ` - # // New variant with conflicting call information - # ` - # "variantSetId": "10473108253681171589", - # "referenceName": "1", - # "start": "10582", - # "referenceBases": "G", - # "alternateBases": [ - # "A" - # ], - # "calls": [ - # ` - # "callSetId": "10473108253681171589-0", - # "callSetName": "CALLSET0", - # "genotype": [ - # 1, - # 1 - # ], - # ` - # ] - # ` - # The resulting merged variant would overwrite the existing calls with those - # from the new variant: - # ` - # "variantSetId": "10473108253681171589", - # "referenceName": "1", - # "start": "10582", - # "referenceBases": "G", - # "alternateBases": [ - # "A" - # ], - # "calls": [ - # ` - # "callSetId": "10473108253681171589-0", - # "callSetName": "CALLSET0", - # "genotype": [ - # 1, - # 1 - # ], - # ` - # ] - # ` - # This may be the desired outcome, but it is up to the user to determine if - # if that is indeed the case. - # @param [Google::Apis::GenomicsV1::MergeVariantsRequest] merge_variants_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # @param [String] variant_set_id + # Required. The ID of the variant set that contains variant data which + # should be exported. The caller must have READ access to this variant set. + # @param [Google::Apis::GenomicsV1::ExportVariantSetRequest] export_variant_set_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Empty] + # @return [Google::Apis::GenomicsV1::Operation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variants:merge', options) - command.request_representation = Google::Apis::GenomicsV1::MergeVariantsRequest::Representation - command.request_object = merge_variants_request_object - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.query['fields'] = fields unless fields.nil? + def export_variant_set(variant_set_id, export_variant_set_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/variantsets/{variantSetId}:export', options) + command.request_representation = Google::Apis::GenomicsV1::ExportVariantSetRequest::Representation + command.request_object = export_variant_set_request_object + command.response_representation = Google::Apis::GenomicsV1::Operation::Representation + command.response_class = Google::Apis::GenomicsV1::Operation + command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Creates a new variant. - # For the definitions of variants and other genomics resources, see + # Returns a list of all variant sets matching search criteria. + # For the definitions of variant sets and other genomics resources, see # [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) - # @param [Google::Apis::GenomicsV1::Variant] variant_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Implements + # [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0. + # 5.1/src/main/resources/avro/variantmethods.avdl#L49). + # @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Variant] + # @return [Google::Apis::GenomicsV1::SearchVariantSetsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/variants', options) - command.request_representation = Google::Apis::GenomicsV1::Variant::Representation - command.request_object = variant_object - command.response_representation = Google::Apis::GenomicsV1::Variant::Representation - command.response_class = Google::Apis::GenomicsV1::Variant - command.query['fields'] = fields unless fields.nil? + def search_variant_sets(search_variant_sets_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/variantsets/search', options) + command.request_representation = Google::Apis::GenomicsV1::SearchVariantSetsRequest::Representation + command.request_object = search_variant_sets_request_object + command.response_representation = Google::Apis::GenomicsV1::SearchVariantSetsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::SearchVariantSetsResponse command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Updates an annotation set. The update must respect all mutability - # restrictions and other invariants described on the annotation set resource. - # Caller must have WRITE permission for the associated dataset. - # @param [String] annotation_set_id - # The ID of the annotation set to be updated. - # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object + # Updates a variant set using patch semantics. + # For the definitions of variant sets and other genomics resources, see + # [Fundamentals of Google + # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) + # @param [String] variant_set_id + # The ID of the variant to be updated (must already exist). + # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object # @param [String] update_mask - # An optional mask specifying which fields to update. Mutable fields are - # name, - # source_uri, and - # info. If unspecified, all - # mutable fields will be updated. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # An optional mask specifying which fields to update. Supported fields: + # * metadata. + # * name. + # * description. + # Leaving `updateMask` unset is equivalent to specifying all mutable + # fields. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::AnnotationSet] + # @return [Google::Apis::GenomicsV1::VariantSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:put, 'v1/annotationsets/{annotationSetId}', options) - command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation - command.request_object = annotation_set_object - command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation - command.response_class = Google::Apis::GenomicsV1::AnnotationSet - command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? + def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:patch, 'v1/variantsets/{variantSetId}', options) + command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation + command.request_object = variant_set_object + command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation + command.response_class = Google::Apis::GenomicsV1::VariantSet + command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? - command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Creates a new annotation set. Caller must have WRITE permission for the - # associated dataset. - # The following fields are required: - # * datasetId - # * referenceSetId - # All other fields may be optionally specified, unless documented as being - # server-generated (for example, the `id` field). - # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Gets a variant set by ID. + # For the definitions of variant sets and other genomics resources, see + # [Fundamentals of Google + # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) + # @param [String] variant_set_id + # Required. The ID of the variant set. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::AnnotationSet] + # @return [Google::Apis::GenomicsV1::VariantSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/annotationsets', options) - command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation - command.request_object = annotation_set_object - command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation - command.response_class = Google::Apis::GenomicsV1::AnnotationSet - command.query['fields'] = fields unless fields.nil? + def get_variantset(variant_set_id, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/variantsets/{variantSetId}', options) + command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation + command.response_class = Google::Apis::GenomicsV1::VariantSet + command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Deletes an annotation set. Caller must have WRITE permission - # for the associated annotation set. - # @param [String] annotation_set_id - # The ID of the annotation set to be deleted. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Lists operations that match the specified filter in the request. + # @param [String] name + # The name of the operation's parent resource. + # @param [String] filter + # A string for filtering Operations. + # The following filter fields are supported&#58; + # * projectId&#58; Required. Corresponds to + # OperationMetadata.projectId. + # * createTime&#58; The time this job was created, in seconds from the + # [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=` + # operators. + # * status&#58; Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only + # one status may be specified. + # * labels.key where key is a label key. + # Examples&#58; + # * `projectId = my-project AND createTime >= 1432140000` + # * `projectId = my-project AND createTime >= 1432140000 AND createTime <= + # 1432150000 AND status = RUNNING` + # * `projectId = my-project AND labels.color = *` + # * `projectId = my-project AND labels.color = red` + # @param [String] page_token + # The standard list page token. + # @param [Fixnum] page_size + # The maximum number of results to return. If unspecified, defaults to + # 256. The maximum value is 2048. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::ListOperationsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::Empty] + # @return [Google::Apis::GenomicsV1::ListOperationsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def delete_annotationset(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:delete, 'v1/annotationsets/{annotationSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::Empty::Representation - command.response_class = Google::Apis::GenomicsV1::Empty - command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? - command.query['fields'] = fields unless fields.nil? + def list_operations(name, filter: nil, page_token: nil, page_size: nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/{+name}', options) + command.response_representation = Google::Apis::GenomicsV1::ListOperationsResponse::Representation + command.response_class = Google::Apis::GenomicsV1::ListOperationsResponse + command.params['name'] = name unless name.nil? + command.query['filter'] = filter unless filter.nil? + command.query['pageToken'] = page_token unless page_token.nil? + command.query['pageSize'] = page_size unless page_size.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Searches for annotation sets that match the given criteria. Annotation sets - # are returned in an unspecified order. This order is consistent, such that - # two queries for the same content (regardless of page size) yield annotation - # sets in the same order across their respective streams of paginated - # responses. Caller must have READ permission for the queried datasets. - # @param [Google::Apis::GenomicsV1::SearchAnnotationSetsRequest] search_annotation_sets_request_object - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Gets the latest state of a long-running operation. Clients can use this + # method to poll the operation result at intervals as recommended by the API + # service. + # @param [String] name + # The name of the operation resource. # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse] + # @return [Google::Apis::GenomicsV1::Operation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:post, 'v1/annotationsets/search', options) - command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsRequest::Representation - command.request_object = search_annotation_sets_request_object - command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse::Representation - command.response_class = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse - command.query['fields'] = fields unless fields.nil? + def get_operation(name, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:get, 'v1/{+name}', options) + command.response_representation = Google::Apis::GenomicsV1::Operation::Representation + command.response_class = Google::Apis::GenomicsV1::Operation + command.params['name'] = name unless name.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end - # Gets an annotation set. Caller must have READ permission for - # the associated dataset. - # @param [String] annotation_set_id - # The ID of the annotation set to be retrieved. - # @param [String] fields - # Selector specifying which fields to include in a partial response. + # Starts asynchronous cancellation on a long-running operation. The server makes + # a best effort to cancel the operation, but success is not guaranteed. Clients + # may use Operations.GetOperation or Operations.ListOperations to check whether + # the cancellation succeeded or the operation completed despite cancellation. + # @param [String] name + # The name of the operation resource to be cancelled. + # @param [Google::Apis::GenomicsV1::CancelOperationRequest] cancel_operation_request_object # @param [String] quota_user # Available to use for quota purposes for server-side applications. Can be any # arbitrary string assigned to a user, but should not exceed 40 characters. + # @param [String] fields + # Selector specifying which fields to include in a partial response. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied - # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object + # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object # @yieldparam err [StandardError] error object if request failed # - # @return [Google::Apis::GenomicsV1::AnnotationSet] + # @return [Google::Apis::GenomicsV1::Empty] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required - def get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block) - command = make_simple_command(:get, 'v1/annotationsets/{annotationSetId}', options) - command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation - command.response_class = Google::Apis::GenomicsV1::AnnotationSet - command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? - command.query['fields'] = fields unless fields.nil? + def cancel_operation(name, cancel_operation_request_object = nil, quota_user: nil, fields: nil, options: nil, &block) + command = make_simple_command(:post, 'v1/{+name}:cancel', options) + command.request_representation = Google::Apis::GenomicsV1::CancelOperationRequest::Representation + command.request_object = cancel_operation_request_object + command.response_representation = Google::Apis::GenomicsV1::Empty::Representation + command.response_class = Google::Apis::GenomicsV1::Empty + command.params['name'] = name unless name.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? + command.query['fields'] = fields unless fields.nil? execute_or_queue_command(command, &block) end protected