class Google::Apis::GenomicsV1::GenomicsService
Genomics API
Stores, processes, explores and shares genomic data. This API implements the
Global Alliance for Genomics and Health (GA4GH) v0.5.1 API as well as several extensions.
@example
require 'google/apis/genomics_v1' Genomics = Google::Apis::GenomicsV1 # Alias the module service = Genomics::GenomicsService.new
Attributes
@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.
@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.
Public Class Methods
# File generated/google/apis/genomics_v1/service.rb, line 47 def initialize super('https://genomics.googleapis.com/', '') end
Public Instance Methods
Creates one or more new annotations atomically. All annotations must belong to the same annotation set. Caller must have WRITE permission for this annotation set. For optimal performance, batch positionally adjacent annotations together. If the request has a systemic issue, such as an attempt to write to an inaccessible annotation set, the entire RPC will fail accordingly. For lesser data issues, when possible an error will be isolated to the corresponding batch entry in the response; the remaining well formed annotations will be created normally. For details on the requirements for each individual annotation resource, see CreateAnnotation. @param [Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest] batch_create_annotations_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 283 def batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/annotations:batchCreate', options) command.request_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest::Representation command.request_object = batch_create_annotations_request_object command.response_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse::Representation command.response_class = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Starts asynchronous cancellation on a long-running operation. The server makes a best effort to cancel the operation, but success is not guaranteed. Clients may use Operations.GetOperation or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite cancellation. @param [String] name
The name of the operation resource to be cancelled.
@param [Google::Apis::GenomicsV1::CancelOperationRequest] cancel_operation_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Empty]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 860 def cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/{+name}:cancel', options) command.request_representation = Google::Apis::GenomicsV1::CancelOperationRequest::Representation command.request_object = cancel_operation_request_object command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['name'] = name unless name.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Creates a new annotation. Caller must have WRITE permission for the associated annotation set. The following fields are required: * annotationSetId * referenceName or referenceId ### Transcripts For annotations of type TRANSCRIPT, the following fields of transcript must be provided: * exons.start
-
exons.end All other fields may be optionally specified, unless documented as
being server-generated (for example, the `id` field). The annotated range must be no longer than 100Mbp (mega base pairs). See the Annotation resource for additional restrictions on each field. @param [Google::Apis::GenomicsV1::Annotation] annotation_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Annotation]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 245 def create_annotation(annotation_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/annotations', options) command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation command.request_object = annotation_object command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation command.response_class = Google::Apis::GenomicsV1::Annotation command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Creates a new annotation set. Caller must have WRITE permission for the associated dataset. The following fields are required: * datasetId * referenceSetId All other fields may be optionally specified, unless documented as being server-generated (for example, the `id` field). @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::AnnotationSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 73 def create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/annotationsets', options) command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation command.request_object = annotation_set_object command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation command.response_class = Google::Apis::GenomicsV1::AnnotationSet command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Creates a new call set. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) @param [Google::Apis::GenomicsV1::CallSet] call_set_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::CallSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1987 def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/callsets', options) command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation command.request_object = call_set_object command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation command.response_class = Google::Apis::GenomicsV1::CallSet command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Creates a new dataset. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) @param [Google::Apis::GenomicsV1::Dataset] dataset_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Dataset]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 493 def create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/datasets', options) command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation command.request_object = dataset_object command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation command.response_class = Google::Apis::GenomicsV1::Dataset command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Creates a new variant. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) @param [Google::Apis::GenomicsV1::Variant] variant_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Variant]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1521 def create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variants', options) command.request_representation = Google::Apis::GenomicsV1::Variant::Representation command.request_object = variant_object command.response_representation = Google::Apis::GenomicsV1::Variant::Representation command.response_class = Google::Apis::GenomicsV1::Variant command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Creates a new variant set. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google. com/genomics/fundamentals-of-google-genomics) The provided variant set must have a valid `datasetId` set - all other fields are optional. Note that the ` id` field will be ignored, as this is assigned by the server. @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::VariantSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1746 def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variantsets', options) command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation command.request_object = variant_set_object command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation command.response_class = Google::Apis::GenomicsV1::VariantSet command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Deletes an annotation. Caller must have WRITE permission for the associated annotation set. @param [String] annotation_id
The ID of the annotation to be deleted.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Empty]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 385 def delete_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/annotations/{annotationId}', options) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.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.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Empty]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 175 def delete_annotationset(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/annotationsets/{annotationSetId}', options) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Deletes a call set. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) @param [String] call_set_id
The ID of the call set to be deleted.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Empty]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 2060 def delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/callsets/{callSetId}', options) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['callSetId'] = call_set_id unless call_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Deletes a dataset and all of its contents (all read group sets, reference sets, variant sets, call sets, annotation sets, etc.) This is reversible (up to one week after the deletion) via the datasets.undelete operation. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google- genomics) @param [String] dataset_id
The ID of the dataset to be deleted.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Empty]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 601 def delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/datasets/{datasetId}', options) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['datasetId'] = dataset_id unless dataset_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Deletes a read group set. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google. com/genomics/fundamentals-of-google-genomics) @param [String] read_group_set_id
The ID of the read group set to be deleted. The caller must have WRITE permissions to the dataset associated with this read group set.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Empty]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1051 def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/readgroupsets/{readGroupSetId}', options) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Deletes a variant. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) @param [String] variant_id
The ID of the variant to be deleted.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Empty]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1595 def delete_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/variants/{variantId}', options) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['variantId'] = variant_id unless variant_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Deletes a variant set including all variants, call sets, and calls within. This is not reversible. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) @param [String] variant_set_id
The ID of the variant set to be deleted.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Empty]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1882 def delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/variantsets/{variantSetId}', options) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Exports a read group set to a BAM file in Google Cloud Storage. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google- genomics) Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. See [ ImportReadGroupSets](google.genomics.v1.ReadServiceV1.ImportReadGroupSets) for caveats. @param [String] read_group_set_id
Required. The ID of the read group set to export. The caller must have READ access to this read group set.
@param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Operation]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 940 def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/readgroupsets/{readGroupSetId}:export', options) command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation command.request_object = export_read_group_set_request_object command.response_representation = Google::Apis::GenomicsV1::Operation::Representation command.response_class = Google::Apis::GenomicsV1::Operation command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Exports variant set data to an external destination. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google-genomics) @param [String] variant_set_id
Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ access to this variant set.
@param [Google::Apis::GenomicsV1::ExportVariantSetRequest] export_variant_set_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Operation]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1781 def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variantsets/{variantSetId}:export', options) command.request_representation = Google::Apis::GenomicsV1::ExportVariantSetRequest::Representation command.request_object = export_variant_set_request_object command.response_representation = Google::Apis::GenomicsV1::Operation::Representation command.response_class = Google::Apis::GenomicsV1::Operation command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets an annotation. Caller must have READ permission for the associated annotation set. @param [String] annotation_id
The ID of the annotation to be retrieved.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Annotation]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 315 def get_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/annotations/{annotationId}', options) command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation command.response_class = Google::Apis::GenomicsV1::Annotation command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.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.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::AnnotationSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 105 def get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/annotationsets/{annotationSetId}', options) command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation command.response_class = Google::Apis::GenomicsV1::AnnotationSet command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets a call set by ID. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) @param [String] call_set_id
The ID of the call set.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::CallSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 2092 def get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/callsets/{callSetId}', options) command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation command.response_class = Google::Apis::GenomicsV1::CallSet command.params['callSetId'] = call_set_id unless call_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets a dataset by ID. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) @param [String] dataset_id
The ID of the dataset.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Dataset]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 526 def get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/datasets/{datasetId}', options) command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation command.response_class = Google::Apis::GenomicsV1::Dataset command.params['datasetId'] = dataset_id unless dataset_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets the access control policy for the dataset. This is empty if the policy or resource does not exist. See Getting a Policy for more information. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google- genomics) @param [String] resource
REQUIRED: The resource for which policy is being specified. Format is ` datasets/`.
@param [Google::Apis::GenomicsV1::GetIamPolicyRequest] get_iam_policy_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Policy]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 711 def get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/{+resource}:getIamPolicy', options) command.request_representation = Google::Apis::GenomicsV1::GetIamPolicyRequest::Representation command.request_object = get_iam_policy_request_object command.response_representation = Google::Apis::GenomicsV1::Policy::Representation command.response_class = Google::Apis::GenomicsV1::Policy command.params['resource'] = resource unless resource.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets the latest state of a long-running operation. Clients can use this method to poll the operation result at intervals as recommended by the API service. @param [String] name
The name of the operation resource.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Operation]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 781 def get_operation(name, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/{+name}', options) command.response_representation = Google::Apis::GenomicsV1::Operation::Representation command.response_class = Google::Apis::GenomicsV1::Operation command.params['name'] = name unless name.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets a read group set by ID. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google. com/genomics/fundamentals-of-google-genomics) @param [String] read_group_set_id
The ID of the read group set.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::ReadGroupSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1083 def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}', options) command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation command.response_class = Google::Apis::GenomicsV1::ReadGroupSet command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets a reference. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi. getReference](github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/ avro/referencemethods.avdl#L158). @param [String] reference_id
The ID of the reference.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Reference] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Reference]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1364 def get_reference(reference_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/references/{referenceId}', options) command.response_representation = Google::Apis::GenomicsV1::Reference::Representation command.response_class = Google::Apis::GenomicsV1::Reference command.params['referenceId'] = reference_id unless reference_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets a reference set. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi. getReferenceSet](github.com/ga4gh/schemas/blob/v0.5.1/src/main/ resources/avro/referencemethods.avdl#L83). @param [String] reference_set_id
The ID of the reference set.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::ReferenceSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::ReferenceSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1296 def get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/referencesets/{referenceSetId}', options) command.response_representation = Google::Apis::GenomicsV1::ReferenceSet::Representation command.response_class = Google::Apis::GenomicsV1::ReferenceSet command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets a variant by ID. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) @param [String] variant_id
The ID of the variant.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Variant]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1627 def get_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/variants/{variantId}', options) command.response_representation = Google::Apis::GenomicsV1::Variant::Representation command.response_class = Google::Apis::GenomicsV1::Variant command.params['variantId'] = variant_id unless variant_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets a variant set by ID. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google. com/genomics/fundamentals-of-google-genomics) @param [String] variant_set_id
Required. The ID of the variant set.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::VariantSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1815 def get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/variantsets/{variantSetId}', options) command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation command.response_class = Google::Apis::GenomicsV1::VariantSet command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Creates read group sets by asynchronously importing the provided information. For the definitions of read group sets and other genomics resources, see [ Fundamentals of Google Genomics](cloud.google.com/genomics/ fundamentals-of-google-genomics) The caller must have WRITE permissions to the dataset. ## Notes on [BAM](samtools.github.io/hts-specs/SAMv1.pdf) import - Tags will be converted to strings - tag types are not preserved - Comments (`@CO`) in the input file header will not be preserved - Original header order of references (`@SQ`) will not be preserved - Any reverse stranded unmapped reads will be reverse complemented, and their qualities ( also the “BQ” and “OQ” tags, if any) will be reversed - Unmapped reads will be stripped of positional information (reference name and position) @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Operation]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 901 def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/readgroupsets:import', options) command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation command.request_object = import_read_group_sets_request_object command.response_representation = Google::Apis::GenomicsV1::Operation::Representation command.response_class = Google::Apis::GenomicsV1::Operation command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Creates variant data by asynchronously importing the provided information. For the definitions of variant sets and other genomics resources, see [ Fundamentals of Google Genomics](cloud.google.com/genomics/ fundamentals-of-google-genomics) The variants for import will be merged with any existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant, and Variant info fields are merged as specified in infoMergeConfig. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set. @param [Google::Apis::GenomicsV1::ImportVariantsRequest] import_variants_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Operation]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1455 def import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variants:import', options) command.request_representation = Google::Apis::GenomicsV1::ImportVariantsRequest::Representation command.request_object = import_variants_request_object command.response_representation = Google::Apis::GenomicsV1::Operation::Representation command.response_class = Google::Apis::GenomicsV1::Operation command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Lists fixed width coverage buckets for a read group set, each of which correspond to a range of a reference sequence. Each bucket summarizes coverage information across its corresponding genomic range. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google-genomics) Coverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several precomputed bucket widths, enabling retrieval of various coverage 'zoom levels' . The caller must have READ permissions for the target read group set. @param [String] read_group_set_id
Required. The ID of the read group set over which coverage is requested.
@param [String] reference_name
The name of the reference to query, within the reference set associated with this query. Optional.
@param [String] start
The start position of the range on the reference, 0-based inclusive. If specified, `referenceName` must also be specified. Defaults to 0.
@param [String] end_
The end position of the range on the reference, 0-based exclusive. If specified, `referenceName` must also be specified. If unset or 0, defaults to the length of the reference.
@param [String] target_bucket_width
The desired width of each reported coverage bucket in base pairs. This will be rounded down to the nearest precomputed bucket width; the value of which is returned as `bucketWidth` in the response. Defaults to infinity (each bucket spans an entire reference sequence) or the length of the target range, if specified. The smallest precomputed `bucketWidth` is currently 2048 base pairs; this is subject to change.
@param [String] page_token
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of ` nextPageToken` from the previous response.
@param [Fixnum] page_size
The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 2048.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1145 def list_coverage_buckets(read_group_set_id, reference_name: nil, start: nil, end_: nil, target_bucket_width: nil, page_token: nil, page_size: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', options) command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['referenceName'] = reference_name unless reference_name.nil? command.query['start'] = start unless start.nil? command.query['end'] = end_ unless end_.nil? command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['pageSize'] = page_size unless page_size.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Lists datasets within a project. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google. com/genomics/fundamentals-of-google-genomics) @param [String] project_id
Required. The project to list datasets for.
@param [Fixnum] page_size
The maximum number of results to return in a single page. If unspecified, defaults to 50. The maximum value is 1024.
@param [String] page_token
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of ` nextPageToken` from the previous response.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::ListDatasetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::ListDatasetsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 460 def list_datasets(project_id: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/datasets', options) command.response_representation = Google::Apis::GenomicsV1::ListDatasetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::ListDatasetsResponse command.query['projectId'] = project_id unless project_id.nil? command.query['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Lists operations that match the specified filter in the request. @param [String] name
The name of the operation collection.
@param [String] filter
A string for filtering Operations. The following filter fields are supported: * projectId: Required. Corresponds to OperationMetadata.projectId. * createTime: The time this job was created, in seconds from the [epoch](http://en. wikipedia.org/wiki/Unix_time). Can use `>=` and/or `= 1432140000` * `projectId = my-project AND createTime >= 1432140000 AND createTime <= 1432150000 AND status = RUNNING`
@param [Fixnum] page_size
The maximum number of results to return. If unspecified, defaults to 256. The maximum value is 2048.
@param [String] page_token
The standard list page token.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::ListOperationsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::ListOperationsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 823 def list_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/{+name}', options) command.response_representation = Google::Apis::GenomicsV1::ListOperationsResponse::Representation command.response_class = Google::Apis::GenomicsV1::ListOperationsResponse command.params['name'] = name unless name.nil? command.query['filter'] = filter unless filter.nil? command.query['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Lists the bases in a reference, optionally restricted to a range. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google- genomics) Implements [GlobalAllianceApi.getReferenceBases](github.com/ ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221). @param [String] reference_id
The ID of the reference.
@param [String] start_position
The start position (0-based) of this query. Defaults to 0.
@param [String] end_position
The end position (0-based, exclusive) of this query. Defaults to the length of this reference.
@param [String] page_token
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of ` nextPageToken` from the previous response.
@param [Fixnum] page_size
The maximum number of bases to return in a single page. If unspecified, defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base pairs).
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::ListBasesResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::ListBasesResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1411 def list_reference_bases(reference_id, start_position: nil, end_position: nil, page_token: nil, page_size: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/references/{referenceId}/bases', options) command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation command.response_class = Google::Apis::GenomicsV1::ListBasesResponse command.params['referenceId'] = reference_id unless reference_id.nil? command.query['start'] = start_position unless start_position.nil? command.query['end'] = end_position unless end_position.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['pageSize'] = page_size unless page_size.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Merges the given variants with existing variants. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics]( cloud.google.com/genomics/fundamentals-of-google-genomics) Each variant will be merged with an existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant. Variant info fields are merged as specified in the infoMergeConfig field of the MergeVariantsRequest. Please exercise caution when using this method! It is easy to introduce mistakes in existing variants and difficult to back out of them. For example, suppose you were trying to merge a new variant with an existing one and both variants contain calls that belong to callsets with the same callset ID. // Existing variant - irrelevant fields trimmed for clarity ` “variantSetId”: “10473108253681171589”, “referenceName”: “1”, “start”: “10582”, “referenceBases”: “G”, “alternateBases”: [ “A” ], “calls”: [ ` “callSetId”: “ 10473108253681171589-0”, “callSetName”: “CALLSET0”, “genotype”: [ 0, 1 ], ` ] ` // New variant with conflicting call information ` “variantSetId”: “ 10473108253681171589”, “referenceName”: “1”, “start”: “10582”, “referenceBases” : “G”, “alternateBases”: [ “A” ], “calls”: [ ` “callSetId”: “ 10473108253681171589-0”, “callSetName”: “CALLSET0”, “genotype”: [ 1, 1 ], ` ] ` The resulting merged variant would overwrite the existing calls with those from the new variant: ` “variantSetId”: “10473108253681171589”, “referenceName” : “1”, “start”: “10582”, “referenceBases”: “G”, “alternateBases”: [ “A” ], “ calls”: [ ` “callSetId”: “10473108253681171589-0”, “callSetName”: “CALLSET0”, “ genotype”: [ 1, 1 ], ` ] ` This may be the desired outcome, but it is up to the user to determine if if that is indeed the case. @param [Google::Apis::GenomicsV1::MergeVariantsRequest] merge_variants_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Empty]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1681 def merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variants:merge', options) command.request_representation = Google::Apis::GenomicsV1::MergeVariantsRequest::Representation command.request_object = merge_variants_request_object command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Updates a call set. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) This method supports patch semantics. @param [String] call_set_id
The ID of the call set to be updated.
@param [Google::Apis::GenomicsV1::CallSet] call_set_object @param [String] update_mask
An optional mask specifying which fields to update. At this time, the only mutable field is name. The only acceptable value is "name". If unspecified, all mutable fields will be updated.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::CallSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 2025 def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:patch, 'v1/callsets/{callSetId}', options) command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation command.request_object = call_set_object command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation command.response_class = Google::Apis::GenomicsV1::CallSet command.params['callSetId'] = call_set_id unless call_set_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Updates a dataset. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) This method supports patch semantics. @param [String] dataset_id
The ID of the dataset to be updated.
@param [Google::Apis::GenomicsV1::Dataset] dataset_object @param [String] update_mask
An optional mask specifying which fields to update. At this time, the only mutable field is name. The only acceptable value is "name". If unspecified, all mutable fields will be updated.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Dataset]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 563 def patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:patch, 'v1/datasets/{datasetId}', options) command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation command.request_object = dataset_object command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation command.response_class = Google::Apis::GenomicsV1::Dataset command.params['datasetId'] = dataset_id unless dataset_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Updates a read group set. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google. com/genomics/fundamentals-of-google-genomics) This method supports patch semantics. @param [String] read_group_set_id
The ID of the read group set to be updated. The caller must have WRITE permissions to the dataset associated with this read group set.
@param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object @param [String] update_mask
An optional mask specifying which fields to update. Supported fields: * name. * referenceSetId. Leaving `updateMask` unset is equivalent to specifying all mutable fields.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::ReadGroupSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1015 def patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:patch, 'v1/readgroupsets/{readGroupSetId}', options) command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation command.request_object = read_group_set_object command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation command.response_class = Google::Apis::GenomicsV1::ReadGroupSet command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Updates a variant. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/ genomics/fundamentals-of-google-genomics) This method supports patch semantics. Returns the modified variant without its calls. @param [String] variant_id
The ID of the variant to be updated.
@param [Google::Apis::GenomicsV1::Variant] variant_object @param [String] update_mask
An optional mask specifying which fields to update. At this time, mutable fields are names and info. Acceptable values are "names" and "info". If unspecified, all mutable fields will be updated.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Variant]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1560 def patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:patch, 'v1/variants/{variantId}', options) command.request_representation = Google::Apis::GenomicsV1::Variant::Representation command.request_object = variant_object command.response_representation = Google::Apis::GenomicsV1::Variant::Representation command.response_class = Google::Apis::GenomicsV1::Variant command.params['variantId'] = variant_id unless variant_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Updates a variant set using patch semantics. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https: //cloud.google.com/genomics/fundamentals-of-google-genomics) @param [String] variant_set_id
The ID of the variant to be updated (must already exist).
@param [Google::Apis::GenomicsV1::VariantSet] variant_set_object @param [String] update_mask
An optional mask specifying which fields to update. Supported fields: * metadata. Leaving `updateMask` unset is equivalent to specifying all mutable fields.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::VariantSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1919 def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:patch, 'v1/variantsets/{variantSetId}', options) command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation command.request_object = variant_set_object command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation command.response_class = Google::Apis::GenomicsV1::VariantSet command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Searches for annotations that match the given criteria. Results are ordered by genomic coordinate (by reference sequence, then position). Annotations with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotations in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried annotation sets. @param [Google::Apis::GenomicsV1::SearchAnnotationsRequest] search_annotations_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::SearchAnnotationsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 420 def search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/annotations/search', options) command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationsRequest::Representation command.request_object = search_annotations_request_object command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchAnnotationsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Searches for annotation sets that match the given criteria. Annotation sets are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotation sets in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried datasets. @param [Google::Apis::GenomicsV1::SearchAnnotationSetsRequest] search_annotation_sets_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 208 def search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/annotationsets/search', options) command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsRequest::Representation command.request_object = search_annotation_sets_request_object command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets a list of call sets matching the criteria. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https: //cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [ GlobalAllianceApi.searchCallSets](github.com/ga4gh/schemas/blob/v0.5.1/ src/main/resources/avro/variantmethods.avdl#L178). @param [Google::Apis::GenomicsV1::SearchCallSetsRequest] search_call_sets_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::SearchCallSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::SearchCallSetsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1955 def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/callsets/search', options) command.request_representation = Google::Apis::GenomicsV1::SearchCallSetsRequest::Representation command.request_object = search_call_sets_request_object command.response_representation = Google::Apis::GenomicsV1::SearchCallSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchCallSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Searches for read group sets matching the criteria. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchReadGroupSets](github.com/ga4gh/ schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135). @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 975 def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/readgroupsets/search', options) command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation command.request_object = search_read_group_sets_request_object command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets a list of reads for one or more read group sets. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google-genomics) Reads search operates over a genomic coordinate space of reference sequence & position defined over the reference sequences to which the requested read group sets are aligned. If a target positional range is specified, search returns all reads whose alignment to the reference genome overlap the range. A query which specifies only read group set IDs yields all reads in those read group sets, including unmapped reads. All reads returned (including reads on subsequent pages) are ordered by genomic coordinate (by reference sequence, then position). Reads with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield reads in the same order across their respective streams of paginated responses. Implements [GlobalAllianceApi. searchReads](github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/ avro/readmethods.avdl#L85). @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::SearchReadsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::SearchReadsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1195 def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/reads/search', options) command.request_representation = Google::Apis::GenomicsV1::SearchReadsRequest::Representation command.request_object = search_reads_request_object command.response_representation = Google::Apis::GenomicsV1::SearchReadsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchReadsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Searches for reference sets which match the given criteria. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google- genomics) Implements [GlobalAllianceApi.searchReferenceSets](github. com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl# L71) @param [Google::Apis::GenomicsV1::SearchReferenceSetsRequest] search_reference_sets_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::SearchReferenceSetsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1261 def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/referencesets/search', options) command.request_representation = Google::Apis::GenomicsV1::SearchReferenceSetsRequest::Representation command.request_object = search_reference_sets_request_object command.response_representation = Google::Apis::GenomicsV1::SearchReferenceSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchReferenceSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Searches for references which match the given criteria. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics]( cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [ GlobalAllianceApi.searchReferences](github.com/ga4gh/schemas/blob/v0.5. 1/src/main/resources/avro/referencemethods.avdl#L146). @param [Google::Apis::GenomicsV1::SearchReferencesRequest] search_references_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::SearchReferencesResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::SearchReferencesResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1329 def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/references/search', options) command.request_representation = Google::Apis::GenomicsV1::SearchReferencesRequest::Representation command.request_object = search_references_request_object command.response_representation = Google::Apis::GenomicsV1::SearchReferencesResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchReferencesResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Returns a list of all variant sets matching search criteria. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google- genomics) Implements [GlobalAllianceApi.searchVariantSets](github.com/ ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49). @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::SearchVariantSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::SearchVariantSetsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1848 def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variantsets/search', options) command.request_representation = Google::Apis::GenomicsV1::SearchVariantSetsRequest::Representation command.request_object = search_variant_sets_request_object command.response_representation = Google::Apis::GenomicsV1::SearchVariantSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchVariantSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Gets a list of variants matching the criteria. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https:// cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [ GlobalAllianceApi.searchVariants](github.com/ga4gh/schemas/blob/v0.5.1/ src/main/resources/avro/variantmethods.avdl#L126). @param [Google::Apis::GenomicsV1::SearchVariantsRequest] search_variants_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::SearchVariantsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::SearchVariantsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1489 def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variants/search', options) command.request_representation = Google::Apis::GenomicsV1::SearchVariantsRequest::Representation command.request_object = search_variants_request_object command.response_representation = Google::Apis::GenomicsV1::SearchVariantsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchVariantsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Sets the access control policy on the specified dataset. Replaces any existing policy. For the definitions of datasets and other genomics resources, see [ Fundamentals of Google Genomics](cloud.google.com/genomics/ fundamentals-of-google-genomics) See Setting a Policy for more information. @param [String] resource
REQUIRED: The resource for which policy is being specified. Format is ` datasets/`.
@param [Google::Apis::GenomicsV1::SetIamPolicyRequest] set_iam_policy_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Policy]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 673 def set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/{+resource}:setIamPolicy', options) command.request_representation = Google::Apis::GenomicsV1::SetIamPolicyRequest::Representation command.request_object = set_iam_policy_request_object command.response_representation = Google::Apis::GenomicsV1::Policy::Representation command.response_class = Google::Apis::GenomicsV1::Policy command.params['resource'] = resource unless resource.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Returns a stream of all the reads matching the search request, ordered by reference name, position, and ID. @param [Google::Apis::GenomicsV1::StreamReadsRequest] stream_reads_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::StreamReadsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::StreamReadsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1226 def stream_reads(stream_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/reads:stream', options) command.request_representation = Google::Apis::GenomicsV1::StreamReadsRequest::Representation command.request_object = stream_reads_request_object command.response_representation = Google::Apis::GenomicsV1::StreamReadsResponse::Representation command.response_class = Google::Apis::GenomicsV1::StreamReadsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Returns a stream of all the variants matching the search request, ordered by reference name, position, and ID. @param [Google::Apis::GenomicsV1::StreamVariantsRequest] stream_variants_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::StreamVariantsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::StreamVariantsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 1712 def stream_variants(stream_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variants:stream', options) command.request_representation = Google::Apis::GenomicsV1::StreamVariantsRequest::Representation command.request_object = stream_variants_request_object command.response_representation = Google::Apis::GenomicsV1::StreamVariantsResponse::Representation command.response_class = Google::Apis::GenomicsV1::StreamVariantsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Returns permissions that a caller has on the specified resource. See Testing Permissions for more information. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google. com/genomics/fundamentals-of-google-genomics) @param [String] resource
REQUIRED: The resource for which policy is being specified. Format is ` datasets/`.
@param [Google::Apis::GenomicsV1::TestIamPermissionsRequest] test_iam_permissions_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::TestIamPermissionsResponse] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::TestIamPermissionsResponse]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 748 def test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/{+resource}:testIamPermissions', options) command.request_representation = Google::Apis::GenomicsV1::TestIamPermissionsRequest::Representation command.request_object = test_iam_permissions_request_object command.response_representation = Google::Apis::GenomicsV1::TestIamPermissionsResponse::Representation command.response_class = Google::Apis::GenomicsV1::TestIamPermissionsResponse command.params['resource'] = resource unless resource.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Undeletes a dataset by restoring a dataset which was deleted via this API. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google- genomics) This operation is only possible for a week after the deletion occurred. @param [String] dataset_id
The ID of the dataset to be undeleted.
@param [Google::Apis::GenomicsV1::UndeleteDatasetRequest] undelete_dataset_request_object @param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Dataset]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 636 def undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/datasets/{datasetId}:undelete', options) command.request_representation = Google::Apis::GenomicsV1::UndeleteDatasetRequest::Representation command.request_object = undelete_dataset_request_object command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation command.response_class = Google::Apis::GenomicsV1::Dataset command.params['datasetId'] = dataset_id unless dataset_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Updates an annotation. Caller must have WRITE permission for the associated dataset. @param [String] annotation_id
The ID of the annotation to be updated.
@param [Google::Apis::GenomicsV1::Annotation] annotation_object @param [String] update_mask
An optional mask specifying which fields to update. Mutable fields are name, variant, transcript, and info. If unspecified, all mutable fields will be updated.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::Annotation]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 351 def update_annotation(annotation_id, annotation_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:put, 'v1/annotations/{annotationId}', options) command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation command.request_object = annotation_object command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation command.response_class = Google::Apis::GenomicsV1::Annotation command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Updates an annotation set. The update must respect all mutability restrictions and other invariants described on the annotation set resource. Caller must have WRITE permission for the associated dataset. @param [String] annotation_set_id
The ID of the annotation set to be updated.
@param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object @param [String] update_mask
An optional mask specifying which fields to update. Mutable fields are name, source_uri, and info. If unspecified, all mutable fields will be updated.
@param [String] fields
Selector specifying which fields to include in a partial response.
@param [String] #quota_user
Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
@param [Google::Apis::RequestOptions] options
Request-specific options
@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object @yieldparam err [StandardError] error object if request failed
@return [Google::Apis::GenomicsV1::AnnotationSet]
@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required
# File generated/google/apis/genomics_v1/service.rb, line 141 def update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:put, 'v1/annotationsets/{annotationSetId}', options) command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation command.request_object = annotation_set_object command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation command.response_class = Google::Apis::GenomicsV1::AnnotationSet command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end
Protected Instance Methods
# File generated/google/apis/genomics_v1/service.rb, line 2104 def apply_command_defaults(command) command.query['key'] = key unless key.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? end