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

@see cloud.google.com/genomics/

Attributes

key[RW]

@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.
quota_user[RW]

@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

new() click to toggle source
Calls superclass method Google::Apis::Core::BaseService.new
# File generated/google/apis/genomics_v1/service.rb, line 47
def initialize
  super('https://genomics.googleapis.com/', '')
end

Public Instance Methods

batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
create_annotation(annotation_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
delete_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
delete_annotationset(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
delete_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_operation(name, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_reference(reference_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
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) click to toggle source

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
list_datasets(project_id: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
list_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
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) click to toggle source

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
merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
stream_reads(stream_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
stream_variants(stream_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
update_annotation(annotation_id, annotation_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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
update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) click to toggle source

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

apply_command_defaults(command) click to toggle source
# 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