# Copyright 2015 Google Inc. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. require 'google/apis/core/base_service' require 'google/apis/core/json_representation' require 'google/apis/core/hashable' require 'google/apis/errors' module Google module Apis module GenomicsV1 # Genomics API # # An API to store, process, explore, and share genomic data. It supports # reference-based alignements, genetic variants, and reference genomes. This API # provides an implementation of the Global Alliance for Genomics and Health ( # GA4GH) v0.5.1 API as well as several extensions. # # @example # require 'google/apis/genomics_v1' # # Genomics = Google::Apis::GenomicsV1 # Alias the module # service = Genomics::GenomicsService.new # # @see class GenomicsService < Google::Apis::Core::BaseService # @return [String] # API key. Your API key identifies your project and provides you with API access, # quota, and reports. Required unless you provide an OAuth 2.0 token. attr_accessor :key # @return [String] # 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. attr_accessor :quota_user def initialize super('https://genomics.googleapis.com/', '') end # 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) # @param [String] project_id # Required. The project to list datasets for. # @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] 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] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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 list_datasets(project_id: nil, page_size: nil, page_token: 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['projectId'] = project_id unless project_id.nil? command.query['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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::Dataset] dataset_object # @param [String] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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) # @param [String] dataset_id # The ID of the dataset. # @param [String] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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) 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. # @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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # Deletes 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) # @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. # @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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.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 [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. # @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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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 [ # Fundamentals of Google Genomics](https://cloud.google.com/genomics/ # fundamentals-of-google-genomics) See Setting a Policy for more information. # @param [String] resource # REQUIRED: The resource for which policy is being specified. Format is ` # datasets/`. # @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] 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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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 Getting a Policy 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] resource # REQUIRED: The resource for which policy is being specified. Format is ` # datasets/`. # @param [Google::Apis::GenomicsV1::GetIamPolicyRequest] get_iam_policy_request_object # @param [String] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # Returns permissions that a caller has on the specified resource. See Testing # Permissions 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] resource # REQUIRED: The resource for which policy is being specified. Format is ` # datasets/`. # @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] 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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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. # @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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.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: * # projectId: Required. Corresponds to OperationMetadata.projectId. * createTime: # The time this job was created, in seconds from the [epoch](http://en. # wikipedia.org/wiki/Unix_time). Can use `>=` and/or `= 1432140000` * `projectId # = my-project AND createTime >= 1432140000 AND createTime <= 1432150000 AND # status = RUNNING` # @param [Fixnum] page_size # The maximum number of results to return. If unspecified, defaults to 256. The # maximum value is 2048. # @param [String] page_token # The standard list page token. # @param [String] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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 list_operations(name, filter: nil, page_size: nil, page_token: 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['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.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. # @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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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 [ # 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 (and # "BQ" tag, 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] 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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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 [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](google.genomics.v1.ReadServiceV1.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] 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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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 [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] 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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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 # @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. # @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 [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 err [StandardError] error object if request failed # # @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 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? 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? execute_or_queue_command(command, &block) end # 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] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.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. # @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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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] reference_name # The name of the reference to query, within the reference set associated with # this query. Optional. # @param [String] start # The start position of the range on the reference, 0-based inclusive. If # specified, `referenceName` must also be specified. Defaults to 0. # @param [String] 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] 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] 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 [String] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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 list_coverage_buckets(read_group_set_id, reference_name: nil, start: nil, end_: nil, target_bucket_width: nil, page_token: nil, page_size: 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['referenceName'] = reference_name unless reference_name.nil? command.query['start'] = start unless start.nil? command.query['end'] = end_ unless end_.nil? command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.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? command.query['quotaUser'] = quota_user unless quota_user.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 [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. # @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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # Returns a stream of all the reads matching the search request, ordered by # reference name, position, and ID. # @param [Google::Apis::GenomicsV1::StreamReadsRequest] stream_reads_request_object # @param [String] fields # Selector specifying which fields to include in a partial 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 [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1::StreamReadsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1::StreamReadsResponse] # # @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 stream_reads(stream_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/reads:stream', options) command.request_representation = Google::Apis::GenomicsV1::StreamReadsRequest::Representation command.request_object = stream_reads_request_object command.response_representation = Google::Apis::GenomicsV1::StreamReadsResponse::Representation command.response_class = Google::Apis::GenomicsV1::StreamReadsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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.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. # @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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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. # 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. # @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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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.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. # @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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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. # 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. # @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 [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 err [StandardError] error object if request failed # # @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(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? command.query['quotaUser'] = quota_user unless quota_user.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 [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] start_position # The start position (0-based) of this query. Defaults to 0. # @param [String] 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 [String] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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 list_reference_bases(reference_id, start_position: nil, end_position: nil, page_token: nil, page_size: 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['start'] = start_position unless start_position.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['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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) 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 other fields (such as key/value # pairs) are discarded. In particular, this means for merged VCF variants that # have conflicting INFO fields, some data will be arbitrarily discarded. 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. # @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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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. # @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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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 [Google::Apis::GenomicsV1::Variant] variant_object # @param [String] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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. # @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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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_id # The ID of the variant to be deleted. # @param [String] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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) 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.query['quotaUser'] = quota_user unless quota_user.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. # @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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # Returns a stream of all the variants matching the search request, ordered by # reference name, position, and ID. # @param [Google::Apis::GenomicsV1::StreamVariantsRequest] stream_variants_request_object # @param [String] fields # Selector specifying which fields to include in a partial 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 [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1::StreamVariantsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1::StreamVariantsResponse] # # @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 stream_variants(stream_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variants:stream', options) command.request_representation = Google::Apis::GenomicsV1::StreamVariantsRequest::Representation command.request_object = stream_variants_request_object command.response_representation = Google::Apis::GenomicsV1::StreamVariantsResponse::Representation command.response_class = Google::Apis::GenomicsV1::StreamVariantsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.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. # @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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.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 [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. # @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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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 [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] 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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # Returns a list of all variant sets matching search criteria. For the # definitions of variant sets and other genomics resources, see [Fundamentals of # Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google- # genomics) Implements [GlobalAllianceApi.searchVariantSets](https://github.com/ # ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49). # @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_request_object # @param [String] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # Deletes the contents of a variant set. The variant set object is not deleted. # 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. # @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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.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 [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. Leaving `updateMask` unset is equivalent to specifying all mutable # fields. # @param [String] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.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 [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. # @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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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::CallSet] call_set_object # @param [String] fields # Selector specifying which fields to include in a partial 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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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) 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] 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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end # 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) # @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] 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 [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 err [StandardError] error object if request failed # # @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_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? command.query['quotaUser'] = quota_user unless quota_user.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 [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. # @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 [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 err [StandardError] error object if request failed # # @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 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? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end protected def apply_command_defaults(command) command.query['key'] = key unless key.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? end end end end end