# 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 GenomicsV1beta2 # Genomics API # # Provides access to Genomics data. # # @example # require 'google/apis/genomics_v1beta2' # # Genomics = Google::Apis::GenomicsV1beta2 # Alias the module # service = Genomics::GenomicsService.new # # @see https://developers.google.com/genomics/v1beta2/reference 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. # Overrides userIp if both are provided. attr_accessor :quota_user # @return [String] # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. attr_accessor :user_ip def initialize super('https://www.googleapis.com/', 'genomics/v1beta2/') end # Creates a new annotation set. Caller must have WRITE permission for the # associated dataset. # @param [Google::Apis::GenomicsV1beta2::AnnotationSet] annotation_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::AnnotationSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::AnnotationSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotationSets' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation command.request_object = annotation_set_object command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Deletes an annotation set. Caller must have WRITE permission for the # associated annotation set. # @param [String] annotation_set_id # The ID of the annotation set to be deleted. # @param [String] fields # Selector specifying which fields to include in a partial response. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [NilClass] No result returned for this method # @yieldparam err [StandardError] error object if request failed # # @return [void] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def delete_annotation_set(annotation_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotationSets/{annotationSetId}' command = make_simple_command(:delete, path, options) command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets an annotation set. Caller must have READ permission for the associated # dataset. # @param [String] annotation_set_id # The ID of the annotation set to be retrieved. # @param [String] fields # Selector specifying which fields to include in a partial response. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::AnnotationSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::AnnotationSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotationSets/{annotationSetId}' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates an annotation set. The update must respect all mutability restrictions # and other invariants described on the annotation set resource. Caller must # have WRITE permission for the associated dataset. This method supports patch # semantics. # @param [String] annotation_set_id # The ID of the annotation set to be updated. # @param [Google::Apis::GenomicsV1beta2::AnnotationSet] annotation_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::AnnotationSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::AnnotationSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def patch_annotation_set(annotation_set_id, annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotationSets/{annotationSetId}' command = make_simple_command(:patch, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation command.request_object = annotation_set_object command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Searches for annotation sets that match the given criteria. Results are # returned in a deterministic order. Caller must have READ permission for the # queried datasets. # @param [Google::Apis::GenomicsV1beta2::SearchAnnotationSetsRequest] search_annotation_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::SearchAnnotationSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::SearchAnnotationSetsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def search_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotationSets/search' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationSetsRequest::Representation command.request_object = search_annotation_sets_request_object command.response_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::SearchAnnotationSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates an annotation set. The update must respect all mutability restrictions # and other invariants described on the annotation set resource. Caller must # have WRITE permission for the associated dataset. # @param [String] annotation_set_id # The ID of the annotation set to be updated. # @param [Google::Apis::GenomicsV1beta2::AnnotationSet] annotation_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::AnnotationSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::AnnotationSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def update_annotation_set(annotation_set_id, annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotationSets/{annotationSetId}' command = make_simple_command(:put, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation command.request_object = annotation_set_object command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Creates one or more new annotations atomically. All annotations must belong to # the same annotation set. Caller must have WRITE permission for this annotation # set. For optimal performance, batch positionally adjacent annotations together. # If the request has a systemic issue, such as an attempt to write to an # inaccessible annotation set, the entire RPC will fail accordingly. For lesser # data issues, when possible an error will be isolated to the corresponding # batch entry in the response; the remaining well formed annotations will be # created normally. # @param [Google::Apis::GenomicsV1beta2::BatchCreateAnnotationsRequest] batch_create_annotations_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::BatchAnnotationsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::BatchAnnotationsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotations:batchCreate' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::BatchCreateAnnotationsRequest::Representation command.request_object = batch_create_annotations_request_object command.response_representation = Google::Apis::GenomicsV1beta2::BatchAnnotationsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::BatchAnnotationsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Creates a new annotation. Caller must have WRITE permission for the associated # annotation set. # @param [Google::Apis::GenomicsV1beta2::Annotation] annotation_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Annotation] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::Annotation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def create_annotation(annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotations' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation command.request_object = annotation_object command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation command.response_class = Google::Apis::GenomicsV1beta2::Annotation command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Deletes an annotation. Caller must have WRITE permission for the associated # annotation set. # @param [String] annotation_id # The ID of the annotation 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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [NilClass] No result returned for this method # @yieldparam err [StandardError] error object if request failed # # @return [void] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def delete_annotation(annotation_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotations/{annotationId}' command = make_simple_command(:delete, path, options) command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets an annotation. Caller must have READ permission for the associated # annotation set. # @param [String] annotation_id # The ID of the annotation set to be retrieved. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Annotation] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::Annotation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def get_annotation(annotation_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotations/{annotationId}' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation command.response_class = Google::Apis::GenomicsV1beta2::Annotation command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates an annotation. The update must respect all mutability restrictions and # other invariants described on the annotation resource. Caller must have WRITE # permission for the associated dataset. This method supports patch semantics. # @param [String] annotation_id # The ID of the annotation set to be updated. # @param [Google::Apis::GenomicsV1beta2::Annotation] annotation_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Annotation] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::Annotation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def patch_annotation(annotation_id, annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotations/{annotationId}' command = make_simple_command(:patch, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation command.request_object = annotation_object command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation command.response_class = Google::Apis::GenomicsV1beta2::Annotation command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Searches for annotations that match the given criteria. Results are returned # ordered by start position. Annotations that have matching start positions are # ordered deterministically. Caller must have READ permission for the queried # annotation sets. # @param [Google::Apis::GenomicsV1beta2::SearchAnnotationsRequest] search_annotations_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotations/search' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationsRequest::Representation command.request_object = search_annotations_request_object command.response_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates an annotation. The update must respect all mutability restrictions and # other invariants described on the annotation resource. Caller must have WRITE # permission for the associated dataset. # @param [String] annotation_id # The ID of the annotation set to be updated. # @param [Google::Apis::GenomicsV1beta2::Annotation] annotation_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Annotation] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::Annotation] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def update_annotation(annotation_id, annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'annotations/{annotationId}' command = make_simple_command(:put, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation command.request_object = annotation_object command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation command.response_class = Google::Apis::GenomicsV1beta2::Annotation command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Creates a new call set. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'callsets' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation command.request_object = call_set_object command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::CallSet command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Deletes a call set. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [NilClass] No result returned for this method # @yieldparam err [StandardError] error object if request failed # # @return [void] # # @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, user_ip: nil, options: nil, &block) path = 'callsets/{callSetId}' command = make_simple_command(:delete, path, options) 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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a call set by ID. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'callsets/{callSetId}' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates a call set. This method supports patch semantics. # @param [String] call_set_id # The ID of the call set to be updated. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'callsets/{callSetId}' command = make_simple_command(:patch, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation command.request_object = call_set_object command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a list of call sets matching the criteria. # Implements GlobalAllianceApi.searchCallSets. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::SearchCallSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'callsets/search' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::SearchCallSetsRequest::Representation command.request_object = search_call_sets_request_object command.response_representation = Google::Apis::GenomicsV1beta2::SearchCallSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::SearchCallSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates a call set. # @param [String] call_set_id # The ID of the call set to be updated. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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 update_call_set(call_set_id, call_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'callsets/{callSetId}' command = make_simple_command(:put, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation command.request_object = call_set_object command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Creates a new dataset. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'datasets' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation command.request_object = dataset_object command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation command.response_class = Google::Apis::GenomicsV1beta2::Dataset command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Deletes a dataset. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [NilClass] No result returned for this method # @yieldparam err [StandardError] error object if request failed # # @return [void] # # @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, user_ip: nil, options: nil, &block) path = 'datasets/{datasetId}' command = make_simple_command(:delete, path, options) 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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a dataset by ID. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'datasets/{datasetId}' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Lists datasets within a project. # @param [Fixnum] page_size # The maximum number of results returned by this request. If unspecified, # defaults to 50. # @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] project_number # The project to list datasets for. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ListDatasetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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(page_size: nil, page_token: nil, project_number: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'datasets' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::ListDatasetsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::ListDatasetsResponse command.query['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['projectNumber'] = project_number unless project_number.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates a dataset. This method supports patch semantics. # @param [String] dataset_id # The ID of the dataset to be updated. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'datasets/{datasetId}' command = make_simple_command(:patch, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation command.request_object = dataset_object command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Undeletes a dataset by restoring a dataset which was deleted via this API. # 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 [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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'datasets/{datasetId}/undelete' command = make_simple_command(:post, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates a dataset. # @param [String] dataset_id # The ID of the dataset to be updated. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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 update_dataset(dataset_id, dataset_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'datasets/{datasetId}' command = make_simple_command(:put, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation command.request_object = dataset_object command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Creates and asynchronously runs an ad-hoc job. This is an experimental call # and may be removed or changed at any time. # @param [Google::Apis::GenomicsV1beta2::ExperimentalCreateJobRequest] experimental_create_job_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse] # # @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_experimental_job(experimental_create_job_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'experimental/jobs/create' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::ExperimentalCreateJobRequest::Representation command.request_object = experimental_create_job_request_object command.response_representation = Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Cancels a job by ID. Note that it is possible for partial results to be # generated and stored for cancelled jobs. # @param [String] job_id # Required. The ID of the job. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [NilClass] No result returned for this method # @yieldparam err [StandardError] error object if request failed # # @return [void] # # @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_job(job_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'jobs/{jobId}/cancel' command = make_simple_command(:post, path, options) command.params['jobId'] = job_id unless job_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a job by ID. # @param [String] job_id # Required. The ID of the job. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Job] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::Job] # # @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_job(job_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'jobs/{jobId}' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::Job::Representation command.response_class = Google::Apis::GenomicsV1beta2::Job command.params['jobId'] = job_id unless job_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a list of jobs matching the criteria. # @param [Google::Apis::GenomicsV1beta2::SearchJobsRequest] search_jobs_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::SearchJobsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::SearchJobsResponse] # # @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_jobs(search_jobs_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'jobs/search' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::SearchJobsRequest::Representation command.request_object = search_jobs_request_object command.response_representation = Google::Apis::GenomicsV1beta2::SearchJobsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::SearchJobsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Aligns read data from existing read group sets or files from Google Cloud # Storage. See the alignment and variant calling documentation for more details. # @param [Google::Apis::GenomicsV1beta2::AlignReadGroupSetsRequest] align_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse] # # @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 align_read_group_sets(align_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'readgroupsets/align' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::AlignReadGroupSetsRequest::Representation command.request_object = align_read_group_sets_request_object command.response_representation = Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Calls variants on read data from existing read group sets or files from Google # Cloud Storage. See the alignment and variant calling documentation for more # details. # @param [Google::Apis::GenomicsV1beta2::CallReadGroupSetsRequest] call_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse] # # @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 call_read_group_sets(call_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'readgroupsets/call' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::CallReadGroupSetsRequest::Representation command.request_object = call_read_group_sets_request_object command.response_representation = Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Deletes a read group set. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [NilClass] No result returned for this method # @yieldparam err [StandardError] error object if request failed # # @return [void] # # @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, user_ip: nil, options: nil, &block) path = 'readgroupsets/{readGroupSetId}' command = make_simple_command(:delete, path, options) 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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Exports read group sets to a BAM file in Google Cloud Storage. # Note that currently there may be some differences between exported BAM files # and the original BAM file at the time of import. In particular, comments in # the input file header will not be preserved, some custom tags will be # converted to strings, and original reference sequence order is not necessarily # preserved. # @param [Google::Apis::GenomicsV1beta2::ExportReadGroupSetsRequest] export_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse] # # @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(export_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'readgroupsets/export' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::ExportReadGroupSetsRequest::Representation command.request_object = export_read_group_sets_request_object command.response_representation = Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a read group set by ID. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ReadGroupSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'readgroupsets/{readGroupSetId}' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Creates read group sets by asynchronously importing the provided information. # Note that currently comments in the input file header are not imported and # some custom tags will be converted to strings, rather than preserving tag # types. The caller must have WRITE permissions to the dataset. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse] # # @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, user_ip: nil, options: nil, &block) path = 'readgroupsets/import' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::ImportReadGroupSetsRequest::Representation command.request_object = import_read_group_sets_request_object command.response_representation = Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates a read group set. 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::GenomicsV1beta2::ReadGroupSet] read_group_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ReadGroupSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'readgroupsets/{readGroupSetId}' command = make_simple_command(:patch, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation command.request_object = read_group_set_object command.response_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Searches for read group sets matching the criteria. # Implements GlobalAllianceApi.searchReadGroupSets. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReadGroupSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'readgroupsets/search' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::SearchReadGroupSetsRequest::Representation command.request_object = search_read_group_sets_request_object command.response_representation = Google::Apis::GenomicsV1beta2::SearchReadGroupSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::SearchReadGroupSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates a read group set. # @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::GenomicsV1beta2::ReadGroupSet] read_group_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ReadGroupSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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 update_read_group_set(read_group_set_id, read_group_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'readgroupsets/{readGroupSetId}' command = make_simple_command(:put, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation command.request_object = read_group_set_object command.response_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.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. # Coverage is defined as the number of reads which are aligned to a given base # in the reference sequence. Coverage buckets are available at several # precomputed bucket widths, enabling retrieval of various coverage 'zoom levels' # . The caller must have READ permissions for the target read group set. # @param [String] read_group_set_id # Required. The ID of the read group set over which coverage is requested. # @param [Fixnum] page_size # The maximum number of results to return in a single page. If unspecified, # defaults to 1024. The maximum value is 2048. # @param [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] range_end # The end position of the range on the reference, 0-based exclusive. If # specified, referenceName must also be specified. # @param [String] range_reference_name # The reference sequence name, for example chr1, 1, or chrX. # @param [String] range_start # The start position of the range on the reference, 0-based inclusive. If # specified, referenceName must also be specified. # @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] 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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ListCoverageBucketsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, page_size: nil, page_token: nil, range_end: nil, range_reference_name: nil, range_start: nil, target_bucket_width: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'readgroupsets/{readGroupSetId}/coveragebuckets' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::ListCoverageBucketsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::ListCoverageBucketsResponse command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['range.end'] = range_end unless range_end.nil? command.query['range.referenceName'] = range_reference_name unless range_reference_name.nil? command.query['range.start'] = range_start unless range_start.nil? command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a list of reads for one or more read group sets. 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 (reference sequence & position). Reads with equivalent # genomic coordinates are returned in a deterministic order. # Implements GlobalAllianceApi.searchReads. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReadsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'reads/search' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::SearchReadsRequest::Representation command.request_object = search_reads_request_object command.response_representation = Google::Apis::GenomicsV1beta2::SearchReadsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::SearchReadsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a reference. # Implements GlobalAllianceApi.getReference. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Reference] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'references/{referenceId}' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::Reference::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Searches for references which match the given criteria. # Implements GlobalAllianceApi.searchReferences. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReferencesResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'references/search' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::SearchReferencesRequest::Representation command.request_object = search_references_request_object command.response_representation = Google::Apis::GenomicsV1beta2::SearchReferencesResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::SearchReferencesResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Lists the bases in a reference, optionally restricted to a range. # Implements GlobalAllianceApi.getReferenceBases. # @param [String] reference_id # The ID of the reference. # @param [String] end_position # The end position (0-based, exclusive) of this query. Defaults to the length of # this reference. # @param [Fixnum] page_size # Specifies the maximum number of bases to return in a single page. # @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] start_position # The start position (0-based) of this query. Defaults to 0. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ListBasesResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, end_position: nil, page_size: nil, page_token: nil, start_position: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'references/{referenceId}/bases' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::ListBasesResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::ListBasesResponse command.params['referenceId'] = reference_id unless reference_id.nil? command.query['end'] = end_position unless end_position.nil? command.query['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['start'] = start_position unless start_position.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a reference set. # Implements GlobalAllianceApi.getReferenceSet. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ReferenceSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'referencesets/{referenceSetId}' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::ReferenceSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Searches for reference sets which match the given criteria. # Implements GlobalAllianceApi.searchReferenceSets. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReferenceSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'referencesets/search' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::SearchReferenceSetsRequest::Representation command.request_object = search_reference_sets_request_object command.response_representation = Google::Apis::GenomicsV1beta2::SearchReferenceSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::SearchReferenceSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Creates a new variant. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Variant] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'variants' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::Variant::Representation command.request_object = variant_object command.response_representation = Google::Apis::GenomicsV1beta2::Variant::Representation command.response_class = Google::Apis::GenomicsV1beta2::Variant command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Deletes a variant. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [NilClass] No result returned for this method # @yieldparam err [StandardError] error object if request failed # # @return [void] # # @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, user_ip: nil, options: nil, &block) path = 'variants/{variantId}' command = make_simple_command(:delete, path, options) 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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a variant by ID. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Variant] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'variants/{variantId}' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::Variant::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a list of variants matching the criteria. # Implements GlobalAllianceApi.searchVariants. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::SearchVariantsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'variants/search' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::SearchVariantsRequest::Representation command.request_object = search_variants_request_object command.response_representation = Google::Apis::GenomicsV1beta2::SearchVariantsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::SearchVariantsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates a variant's names and info fields. All other modifications are # silently ignored. Returns the modified variant without its calls. # @param [String] variant_id # The ID of the variant to be updated. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::Variant] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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 update_variant(variant_id, variant_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'variants/{variantId}' command = make_simple_command(:put, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::Variant::Representation command.request_object = variant_object command.response_representation = Google::Apis::GenomicsV1beta2::Variant::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Deletes the contents of a variant set. The variant set object is not deleted. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [NilClass] No result returned for this method # @yieldparam err [StandardError] error object if request failed # # @return [void] # # @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, user_ip: nil, options: nil, &block) path = 'variantsets/{variantSetId}' command = make_simple_command(:delete, path, options) 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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Exports variant set data to an external destination. # @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::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ExportVariantSetResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::ExportVariantSetResponse] # # @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, user_ip: nil, options: nil, &block) path = 'variantsets/{variantSetId}/export' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::ExportVariantSetRequest::Representation command.request_object = export_variant_set_request_object command.response_representation = Google::Apis::GenomicsV1beta2::ExportVariantSetResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::ExportVariantSetResponse 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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Gets a variant set by ID. # @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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::VariantSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'variantsets/{variantSetId}' command = make_simple_command(:get, path, options) command.response_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Creates variant data by asynchronously importing the provided information. # The variants for import will be merged with any existing data and each other # according to the behavior of mergeVariants. 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 [String] variant_set_id # Required. The variant set to which variant data should be imported. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::ImportVariantsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::ImportVariantsResponse] # # @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(variant_set_id, import_variants_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'variantsets/{variantSetId}/importVariants' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::ImportVariantsRequest::Representation command.request_object = import_variants_request_object command.response_representation = Google::Apis::GenomicsV1beta2::ImportVariantsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::ImportVariantsResponse 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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Merges the given variants with existing variants. Each variant will be merged # with an existing variant that matches its reference sequence, start, end, # reference bases, and alternative bases. If no such variant exists, a new one # will be created. # When variants are merged, the call information from the new variant is added # to the existing variant, and other fields (such as key/value pairs) are # discarded. # @param [String] variant_set_id # The destination variant set. # @param [Google::Apis::GenomicsV1beta2::MergeVariantsRequest] merge_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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [NilClass] No result returned for this method # @yieldparam err [StandardError] error object if request failed # # @return [void] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def merge_variants(variant_set_id, merge_variants_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'variantsets/{variantSetId}/mergeVariants' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::MergeVariantsRequest::Representation command.request_object = merge_variants_request_object 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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates a variant set's metadata. All other modifications are silently ignored. # This method supports patch semantics. # @param [String] variant_set_id # The ID of the variant to be updated (must already exist). # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::VariantSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'variantsets/{variantSetId}' command = make_simple_command(:patch, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation command.request_object = variant_set_object command.response_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Returns a list of all variant sets matching search criteria. # Implements GlobalAllianceApi.searchVariantSets. # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::SearchVariantSetsResponse] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::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, user_ip: nil, options: nil, &block) path = 'variantsets/search' command = make_simple_command(:post, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::SearchVariantSetsRequest::Representation command.request_object = search_variant_sets_request_object command.response_representation = Google::Apis::GenomicsV1beta2::SearchVariantSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1beta2::SearchVariantSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? command.query['userIp'] = user_ip unless user_ip.nil? execute_or_queue_command(command, &block) end # Updates a variant set's metadata. All other modifications are silently ignored. # @param [String] variant_set_id # The ID of the variant to be updated (must already exist). # @param [Google::Apis::GenomicsV1beta2::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. # Overrides userIp if both are provided. # @param [String] user_ip # IP address of the site where the request originates. Use this if you want to # enforce per-user limits. # @param [Google::Apis::RequestOptions] options # Request-specific options # # @yield [result, err] Result & error if block supplied # @yieldparam result [Google::Apis::GenomicsV1beta2::VariantSet] parsed result object # @yieldparam err [StandardError] error object if request failed # # @return [Google::Apis::GenomicsV1beta2::VariantSet] # # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification # @raise [Google::Apis::AuthorizationError] Authorization is required def update_variantset(variant_set_id, variant_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) path = 'variantsets/{variantSetId}' command = make_simple_command(:put, path, options) command.request_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation command.request_object = variant_set_object command.response_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation command.response_class = Google::Apis::GenomicsV1beta2::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? command.query['userIp'] = user_ip unless user_ip.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? command.query['userIp'] = user_ip unless user_ip.nil? end end end end end