class Google::Apis::GenomicsV1beta2::GenomicsService

Genomics API

Provides access to Genomics data.

@example

require 'google/apis/genomics_v1beta2'

Genomics = Google::Apis::GenomicsV1beta2 # Alias the module
service = Genomics::GenomicsService.new

@see developers.google.com/genomics/v1beta2/reference

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.
Overrides userIp if both are provided.
user_ip[RW]

@return [String]

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

Public Class Methods

new() click to toggle source
Calls superclass method Google::Apis::Core::BaseService.new
# File generated/google/apis/genomics_v1beta2/service.rb, line 51
def initialize
  super('https://www.googleapis.com/', 'genomics/v1beta2/')
end

Public Instance Methods

align_read_group_sets(align_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Aligns read data from existing read group sets or files from Google Cloud Storage. See the alignment and variant calling documentation for more details. @param [Google::Apis::GenomicsV1beta2::AlignReadGroupSetsRequest] align_read_group_sets_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1213
def align_read_group_sets(align_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'readgroupsets/align'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::AlignReadGroupSetsRequest::Representation
  command.request_object = align_read_group_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::AlignReadGroupSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, user_ip: 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. @param [Google::Apis::GenomicsV1beta2::BatchCreateAnnotationsRequest] batch_create_annotations_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::BatchAnnotationsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::BatchAnnotationsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 315
def batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotations:batchCreate'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::BatchCreateAnnotationsRequest::Representation
  command.request_object = batch_create_annotations_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::BatchAnnotationsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::BatchAnnotationsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
call_read_group_sets(call_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Calls variants on read data from existing read group sets or files from Google Cloud Storage. See the alignment and variant calling documentation for more details. @param [Google::Apis::GenomicsV1beta2::CallReadGroupSetsRequest] call_read_group_sets_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1251
def call_read_group_sets(call_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'readgroupsets/call'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::CallReadGroupSetsRequest::Representation
  command.request_object = call_read_group_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::CallReadGroupSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
cancel_job(job_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Cancels a job by ID. Note that it is possible for partial results to be generated and stored for cancelled jobs. @param [String] job_id

Required. The ID of the job.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [NilClass] No result returned for this method @yieldparam err [StandardError] error object if request failed

@return [void]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1107
def cancel_job(job_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'jobs/{jobId}/cancel'
  command =  make_simple_command(:post, path, options)
  command.params['jobId'] = job_id unless job_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
create_annotation(annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Creates a new annotation. Caller must have WRITE permission for the associated annotation set. @param [Google::Apis::GenomicsV1beta2::Annotation] annotation_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Annotation] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Annotation]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 352
def create_annotation(annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotations'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
  command.request_object = annotation_object
  command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Annotation
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Creates a new annotation set. Caller must have WRITE permission for the associated dataset. @param [Google::Apis::GenomicsV1beta2::AnnotationSet] annotation_set_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::AnnotationSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::AnnotationSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 79
def create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotationSets'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
  command.request_object = annotation_set_object
  command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
create_call_set(call_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Creates a new call set. @param [Google::Apis::GenomicsV1beta2::CallSet] call_set_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::CallSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 581
def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'callsets'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
  command.request_object = call_set_object
  command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::CallSet
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
create_dataset(dataset_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Creates a new dataset. @param [Google::Apis::GenomicsV1beta2::Dataset] dataset_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Dataset]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 802
def create_dataset(dataset_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'datasets'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
  command.request_object = dataset_object
  command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Dataset
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
create_experimental_job(experimental_create_job_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Creates and asynchronously runs an ad-hoc job. This is an experimental call and may be removed or changed at any time. @param [Google::Apis::GenomicsV1beta2::ExperimentalCreateJobRequest] experimental_create_job_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1069
def create_experimental_job(experimental_create_job_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'experimental/jobs/create'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::ExperimentalCreateJobRequest::Representation
  command.request_object = experimental_create_job_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ExperimentalCreateJobResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
create_variant(variant_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Creates a new variant. @param [Google::Apis::GenomicsV1beta2::Variant] variant_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Variant] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Variant]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1871
def create_variant(variant_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variants'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::Variant::Representation
  command.request_object = variant_object
  command.response_representation = Google::Apis::GenomicsV1beta2::Variant::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Variant
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Creates a new variant set (only necessary in v1). @param [Google::Apis::GenomicsV1beta2::VariantSet] variant_set_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::VariantSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::VariantSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 2054
def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variantsets'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
  command.request_object = variant_set_object
  command.response_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::VariantSet
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
delete_annotation(annotation_id, fields: nil, quota_user: nil, user_ip: 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 set to be deleted.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [NilClass] No result returned for this method @yieldparam err [StandardError] error object if request failed

@return [void]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 390
def delete_annotation(annotation_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotations/{annotationId}'
  command =  make_simple_command(:delete, path, options)
  command.params['annotationId'] = annotation_id unless annotation_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
delete_annotation_set(annotation_set_id, fields: nil, quota_user: nil, user_ip: 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.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [NilClass] No result returned for this method @yieldparam err [StandardError] error object if request failed

@return [void]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 117
def delete_annotation_set(annotation_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotationSets/{annotationSetId}'
  command =  make_simple_command(:delete, path, options)
  command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
delete_call_set(call_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Deletes a call set. @param [String] call_set_id

The ID of the call set to be deleted.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [NilClass] No result returned for this method @yieldparam err [StandardError] error object if request failed

@return [void]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 618
def delete_call_set(call_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'callsets/{callSetId}'
  command =  make_simple_command(:delete, path, options)
  command.params['callSetId'] = call_set_id unless call_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
delete_dataset(dataset_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Deletes a dataset. @param [String] dataset_id

The ID of the dataset to be deleted.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [NilClass] No result returned for this method @yieldparam err [StandardError] error object if request failed

@return [void]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 839
def delete_dataset(dataset_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'datasets/{datasetId}'
  command =  make_simple_command(:delete, path, options)
  command.params['datasetId'] = dataset_id unless dataset_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Deletes a read group set. @param [String] read_group_set_id

The ID of the read group set to be deleted. The caller must have WRITE
permissions to the dataset associated with this read group set.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [NilClass] No result returned for this method @yieldparam err [StandardError] error object if request failed

@return [void]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1289
def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'readgroupsets/{readGroupSetId}'
  command =  make_simple_command(:delete, path, options)
  command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
delete_variant(variant_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Deletes a variant. @param [String] variant_id

The ID of the variant to be deleted.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [NilClass] No result returned for this method @yieldparam err [StandardError] error object if request failed

@return [void]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1908
def delete_variant(variant_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variants/{variantId}'
  command =  make_simple_command(:delete, path, options)
  command.params['variantId'] = variant_id unless variant_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
delete_variantset(variant_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Deletes the contents of a variant set. The variant set object is not deleted. @param [String] variant_set_id

The ID of the variant set to be deleted.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [NilClass] No result returned for this method @yieldparam err [StandardError] error object if request failed

@return [void]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 2091
def delete_variantset(variant_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variantsets/{variantSetId}'
  command =  make_simple_command(:delete, path, options)
  command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
export_read_group_sets(export_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Exports read group sets to a BAM file in Google Cloud Storage. Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. In particular, comments in the input file header will not be preserved, some custom tags will be converted to strings, and original reference sequence order is not necessarily preserved. @param [Google::Apis::GenomicsV1beta2::ExportReadGroupSetsRequest] export_read_group_sets_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1327
def export_read_group_sets(export_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'readgroupsets/export'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::ExportReadGroupSetsRequest::Representation
  command.request_object = export_read_group_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ExportReadGroupSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Exports variant set data to an external destination. @param [String] variant_set_id

Required. The ID of the variant set that contains variant data which should be
exported. The caller must have READ access to this variant set.

@param [Google::Apis::GenomicsV1beta2::ExportVariantSetRequest] export_variant_set_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ExportVariantSetResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ExportVariantSetResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 2127
def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variantsets/{variantSetId}/export'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::ExportVariantSetRequest::Representation
  command.request_object = export_variant_set_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::ExportVariantSetResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ExportVariantSetResponse
  command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
get_annotation(annotation_id, fields: nil, quota_user: nil, user_ip: 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 set to be retrieved.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Annotation] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Annotation]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 425
def get_annotation(annotation_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotations/{annotationId}'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Annotation
  command.params['annotationId'] = annotation_id unless annotation_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, user_ip: 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.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::AnnotationSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::AnnotationSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 152
def get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotationSets/{annotationSetId}'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet
  command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
get_call_set(call_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a call set by ID. @param [String] call_set_id

The ID of the call set.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::CallSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 652
def get_call_set(call_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'callsets/{callSetId}'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::CallSet
  command.params['callSetId'] = call_set_id unless call_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
get_dataset(dataset_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a dataset by ID. @param [String] dataset_id

The ID of the dataset.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Dataset]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 873
def get_dataset(dataset_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'datasets/{datasetId}'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Dataset
  command.params['datasetId'] = dataset_id unless dataset_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
get_job(job_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a job by ID. @param [String] job_id

Required. The ID of the job.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Job] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Job]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1141
def get_job(job_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'jobs/{jobId}'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::Job::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Job
  command.params['jobId'] = job_id unless job_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a read group set by ID. @param [String] read_group_set_id

The ID of the read group set.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ReadGroupSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ReadGroupSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1364
def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'readgroupsets/{readGroupSetId}'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ReadGroupSet
  command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
get_reference(reference_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a reference. Implements GlobalAllianceApi.getReference. @param [String] reference_id

The ID of the reference.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Reference] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Reference]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1673
def get_reference(reference_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'references/{referenceId}'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::Reference::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Reference
  command.params['referenceId'] = reference_id unless reference_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
get_reference_set(reference_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a reference set. Implements GlobalAllianceApi.getReferenceSet. @param [String] reference_set_id

The ID of the reference set.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ReferenceSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ReferenceSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1799
def get_reference_set(reference_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'referencesets/{referenceSetId}'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::ReferenceSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ReferenceSet
  command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
get_variant(variant_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a variant by ID. @param [String] variant_id

The ID of the variant.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Variant] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Variant]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1942
def get_variant(variant_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variants/{variantId}'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::Variant::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Variant
  command.params['variantId'] = variant_id unless variant_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
get_variantset(variant_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a variant set by ID. @param [String] variant_set_id

Required. The ID of the variant set.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::VariantSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::VariantSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 2165
def get_variantset(variant_set_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variantsets/{variantSetId}'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::VariantSet
  command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Creates read group sets by asynchronously importing the provided information. Note that currently comments in the input file header are not imported and some custom tags will be converted to strings, rather than preserving tag types. The caller must have WRITE permissions to the dataset. @param [Google::Apis::GenomicsV1beta2::ImportReadGroupSetsRequest] import_read_group_sets_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1402
def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'readgroupsets/import'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::ImportReadGroupSetsRequest::Representation
  command.request_object = import_read_group_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ImportReadGroupSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
import_variants(variant_set_id, import_variants_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Creates variant data by asynchronously importing the provided information. The variants for import will be merged with any existing data and each other according to the behavior of mergeVariants. In particular, this means for merged VCF variants that have conflicting INFO fields, some data will be arbitrarily discarded. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set. @param [String] variant_set_id

Required. The variant set to which variant data should be imported.

@param [Google::Apis::GenomicsV1beta2::ImportVariantsRequest] import_variants_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ImportVariantsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ImportVariantsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 2209
def import_variants(variant_set_id, import_variants_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variantsets/{variantSetId}/importVariants'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::ImportVariantsRequest::Representation
  command.request_object = import_variants_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::ImportVariantsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ImportVariantsResponse
  command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
list_coverage_buckets(read_group_set_id, page_size: nil, page_token: nil, range_end: nil, range_reference_name: nil, range_start: nil, target_bucket_width: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) 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. Coverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several precomputed bucket widths, enabling retrieval of various coverage 'zoom levels' . The caller must have READ permissions for the target read group set. @param [String] read_group_set_id

Required. The ID of the read group set over which coverage is requested.

@param [Fixnum] page_size

The maximum number of results to return in a single page. If unspecified,
defaults to 1024. The maximum value is 2048.

@param [String] page_token

The continuation token, which is used to page through large result sets. To
get the next page of results, set this parameter to the value of nextPageToken
from the previous response.

@param [String] range_end

The end position of the range on the reference, 0-based exclusive. If
specified, referenceName must also be specified.

@param [String] range_reference_name

The reference sequence name, for example chr1, 1, or chrX.

@param [String] range_start

The start position of the range on the reference, 0-based inclusive. If
specified, referenceName must also be specified.

@param [String] target_bucket_width

The desired width of each reported coverage bucket in base pairs. This will be
rounded down to the nearest precomputed bucket width; the value of which is
returned as bucketWidth in the response. Defaults to infinity (each bucket
spans an entire reference sequence) or the length of the target range, if
specified. The smallest precomputed bucketWidth is currently 2048 base pairs;
this is subject to change.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ListCoverageBucketsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ListCoverageBucketsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1584
def list_coverage_buckets(read_group_set_id, page_size: nil, page_token: nil, range_end: nil, range_reference_name: nil, range_start: nil, target_bucket_width: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'readgroupsets/{readGroupSetId}/coveragebuckets'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::ListCoverageBucketsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ListCoverageBucketsResponse
  command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
  command.query['pageSize'] = page_size unless page_size.nil?
  command.query['pageToken'] = page_token unless page_token.nil?
  command.query['range.end'] = range_end unless range_end.nil?
  command.query['range.referenceName'] = range_reference_name unless range_reference_name.nil?
  command.query['range.start'] = range_start unless range_start.nil?
  command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
list_datasets(page_size: nil, page_token: nil, project_number: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Lists datasets within a project. @param [Fixnum] page_size

The maximum number of results returned by this request. If unspecified,
defaults to 50.

@param [String] page_token

The continuation token, which is used to page through large result sets. To
get the next page of results, set this parameter to the value of nextPageToken
from the previous response.

@param [String] project_number

Required. The project to list datasets for.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ListDatasetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ListDatasetsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 916
def list_datasets(page_size: nil, page_token: nil, project_number: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'datasets'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::ListDatasetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ListDatasetsResponse
  command.query['pageSize'] = page_size unless page_size.nil?
  command.query['pageToken'] = page_token unless page_token.nil?
  command.query['projectNumber'] = project_number unless project_number.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
list_reference_bases(reference_id, end_position: nil, page_size: nil, page_token: nil, start_position: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Lists the bases in a reference, optionally restricted to a range. Implements GlobalAllianceApi.getReferenceBases. @param [String] reference_id

The ID of the reference.

@param [String] end_position

The end position (0-based, exclusive) of this query. Defaults to the length of
this reference.

@param [Fixnum] page_size

Specifies the maximum number of bases to return in a single page.

@param [String] page_token

The continuation token, which is used to page through large result sets. To
get the next page of results, set this parameter to the value of nextPageToken
from the previous response.

@param [String] start_position

The start position (0-based) of this query. Defaults to 0.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ListBasesResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ListBasesResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1758
def list_reference_bases(reference_id, end_position: nil, page_size: nil, page_token: nil, start_position: nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'references/{referenceId}/bases'
  command =  make_simple_command(:get, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::ListBasesResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ListBasesResponse
  command.params['referenceId'] = reference_id unless reference_id.nil?
  command.query['end'] = end_position unless end_position.nil?
  command.query['pageSize'] = page_size unless page_size.nil?
  command.query['pageToken'] = page_token unless page_token.nil?
  command.query['start'] = start_position unless start_position.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
merge_variants(variant_set_id, merge_variants_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Merges the given variants with existing variants. Each variant will be merged with an existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant, and other fields (such as key/value pairs) are discarded. @param [String] variant_set_id

The destination variant set.

@param [Google::Apis::GenomicsV1beta2::MergeVariantsRequest] merge_variants_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [NilClass] No result returned for this method @yieldparam err [StandardError] error object if request failed

@return [void]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 2254
def merge_variants(variant_set_id, merge_variants_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variantsets/{variantSetId}/mergeVariants'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::MergeVariantsRequest::Representation
  command.request_object = merge_variants_request_object
  command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
patch_annotation(annotation_id, annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Updates an annotation. The update must respect all mutability restrictions and other invariants described on the annotation resource. Caller must have WRITE permission for the associated dataset. This method supports patch semantics. @param [String] annotation_id

The ID of the annotation set to be updated.

@param [Google::Apis::GenomicsV1beta2::Annotation] annotation_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Annotation] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Annotation]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 464
def patch_annotation(annotation_id, annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotations/{annotationId}'
  command =  make_simple_command(:patch, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
  command.request_object = annotation_object
  command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Annotation
  command.params['annotationId'] = annotation_id unless annotation_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
patch_annotation_set(annotation_set_id, annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: 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. This method supports patch semantics. @param [String] annotation_set_id

The ID of the annotation set to be updated.

@param [Google::Apis::GenomicsV1beta2::AnnotationSet] annotation_set_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::AnnotationSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::AnnotationSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 192
def patch_annotation_set(annotation_set_id, annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotationSets/{annotationSetId}'
  command =  make_simple_command(:patch, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
  command.request_object = annotation_set_object
  command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet
  command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
patch_call_set(call_set_id, call_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Updates a call set. This method supports patch semantics. @param [String] call_set_id

The ID of the call set to be updated.

@param [Google::Apis::GenomicsV1beta2::CallSet] call_set_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::CallSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 689
def patch_call_set(call_set_id, call_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'callsets/{callSetId}'
  command =  make_simple_command(:patch, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
  command.request_object = call_set_object
  command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::CallSet
  command.params['callSetId'] = call_set_id unless call_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
patch_dataset(dataset_id, dataset_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Updates a dataset. This method supports patch semantics. @param [String] dataset_id

The ID of the dataset to be updated.

@param [Google::Apis::GenomicsV1beta2::Dataset] dataset_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Dataset]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 955
def patch_dataset(dataset_id, dataset_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'datasets/{datasetId}'
  command =  make_simple_command(:patch, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
  command.request_object = dataset_object
  command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Dataset
  command.params['datasetId'] = dataset_id unless dataset_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
patch_read_group_set(read_group_set_id, read_group_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Updates a read group set. This method supports patch semantics. @param [String] read_group_set_id

The ID of the read group set to be updated. The caller must have WRITE
permissions to the dataset associated with this read group set.

@param [Google::Apis::GenomicsV1beta2::ReadGroupSet] read_group_set_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ReadGroupSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ReadGroupSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1441
def patch_read_group_set(read_group_set_id, read_group_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'readgroupsets/{readGroupSetId}'
  command =  make_simple_command(:patch, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation
  command.request_object = read_group_set_object
  command.response_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ReadGroupSet
  command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
patch_variantset(variant_set_id, variant_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Updates a variant set's metadata. All other modifications are silently ignored. This method supports patch semantics. @param [String] variant_set_id

The ID of the variant to be updated (must already exist).

@param [Google::Apis::GenomicsV1beta2::VariantSet] variant_set_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::VariantSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::VariantSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 2292
def patch_variantset(variant_set_id, variant_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variantsets/{variantSetId}'
  command =  make_simple_command(:patch, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
  command.request_object = variant_set_object
  command.response_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::VariantSet
  command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
search_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Searches for annotation sets that match the given criteria. Results are returned in a deterministic order. Caller must have READ permission for the queried datasets. @param [Google::Apis::GenomicsV1beta2::SearchAnnotationSetsRequest] search_annotation_sets_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::SearchAnnotationSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::SearchAnnotationSetsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 231
def search_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotationSets/search'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationSetsRequest::Representation
  command.request_object = search_annotation_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::SearchAnnotationSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Searches for annotations that match the given criteria. Results are returned ordered by start position. Annotations that have matching start positions are ordered deterministically. Caller must have READ permission for the queried annotation sets. @param [Google::Apis::GenomicsV1beta2::SearchAnnotationsRequest] search_annotations_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 504
def search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotations/search'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationsRequest::Representation
  command.request_object = search_annotations_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::SearchAnnotationsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a list of call sets matching the criteria. Implements GlobalAllianceApi.searchCallSets. @param [Google::Apis::GenomicsV1beta2::SearchCallSetsRequest] search_call_sets_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::SearchCallSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::SearchCallSetsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 727
def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'callsets/search'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::SearchCallSetsRequest::Representation
  command.request_object = search_call_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::SearchCallSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::SearchCallSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
search_jobs(search_jobs_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a list of jobs matching the criteria. @param [Google::Apis::GenomicsV1beta2::SearchJobsRequest] search_jobs_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::SearchJobsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::SearchJobsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1176
def search_jobs(search_jobs_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'jobs/search'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::SearchJobsRequest::Representation
  command.request_object = search_jobs_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::SearchJobsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::SearchJobsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Searches for read group sets matching the criteria. Implements GlobalAllianceApi.searchReadGroupSets. @param [Google::Apis::GenomicsV1beta2::SearchReadGroupSetsRequest] search_read_group_sets_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReadGroupSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::SearchReadGroupSetsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1479
def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'readgroupsets/search'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::SearchReadGroupSetsRequest::Representation
  command.request_object = search_read_group_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::SearchReadGroupSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::SearchReadGroupSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a list of reads for one or more read group sets. Reads search operates over a genomic coordinate space of reference sequence & position defined over the reference sequences to which the requested read group sets are aligned. If a target positional range is specified, search returns all reads whose alignment to the reference genome overlap the range. A query which specifies only read group set IDs yields all reads in those read group sets, including unmapped reads. All reads returned (including reads on subsequent pages) are ordered by genomic coordinate (reference sequence & position). Reads with equivalent genomic coordinates are returned in a deterministic order. Implements GlobalAllianceApi.searchReads. @param [Google::Apis::GenomicsV1beta2::SearchReadsRequest] search_reads_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReadsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::SearchReadsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1635
def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'reads/search'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::SearchReadsRequest::Representation
  command.request_object = search_reads_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::SearchReadsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::SearchReadsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Searches for reference sets which match the given criteria. Implements GlobalAllianceApi.searchReferenceSets. @param [Google::Apis::GenomicsV1beta2::SearchReferenceSetsRequest] search_reference_sets_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReferenceSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::SearchReferenceSetsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1835
def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'referencesets/search'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::SearchReferenceSetsRequest::Representation
  command.request_object = search_reference_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::SearchReferenceSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::SearchReferenceSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
search_references(search_references_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Searches for references which match the given criteria. Implements GlobalAllianceApi.searchReferences. @param [Google::Apis::GenomicsV1beta2::SearchReferencesRequest] search_references_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::SearchReferencesResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::SearchReferencesResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1709
def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'references/search'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::SearchReferencesRequest::Representation
  command.request_object = search_references_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::SearchReferencesResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::SearchReferencesResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Returns a list of all variant sets matching search criteria. Implements GlobalAllianceApi.searchVariantSets. @param [Google::Apis::GenomicsV1beta2::SearchVariantSetsRequest] search_variant_sets_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::SearchVariantSetsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::SearchVariantSetsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 2330
def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variantsets/search'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::SearchVariantSetsRequest::Representation
  command.request_object = search_variant_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::SearchVariantSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::SearchVariantSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Gets a list of variants matching the criteria. Implements GlobalAllianceApi.searchVariants. @param [Google::Apis::GenomicsV1beta2::SearchVariantsRequest] search_variants_request_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::SearchVariantsResponse] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::SearchVariantsResponse]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1978
def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variants/search'
  command =  make_simple_command(:post, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::SearchVariantsRequest::Representation
  command.request_object = search_variants_request_object
  command.response_representation = Google::Apis::GenomicsV1beta2::SearchVariantsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::SearchVariantsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
undelete_dataset(dataset_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Undeletes a dataset by restoring a dataset which was deleted via this API. This operation is only possible for a week after the deletion occurred. @param [String] dataset_id

The ID of the dataset to be undeleted.

@param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Dataset]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 994
def undelete_dataset(dataset_id, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'datasets/{datasetId}/undelete'
  command =  make_simple_command(:post, path, options)
  command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Dataset
  command.params['datasetId'] = dataset_id unless dataset_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
update_annotation(annotation_id, annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Updates an annotation. The update must respect all mutability restrictions and other invariants described on the annotation resource. Caller must have WRITE permission for the associated dataset. @param [String] annotation_id

The ID of the annotation set to be updated.

@param [Google::Apis::GenomicsV1beta2::Annotation] annotation_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Annotation] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Annotation]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 544
def update_annotation(annotation_id, annotation_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotations/{annotationId}'
  command =  make_simple_command(:put, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
  command.request_object = annotation_object
  command.response_representation = Google::Apis::GenomicsV1beta2::Annotation::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Annotation
  command.params['annotationId'] = annotation_id unless annotation_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
update_annotation_set(annotation_set_id, annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: 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::GenomicsV1beta2::AnnotationSet] annotation_set_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::AnnotationSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::AnnotationSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 271
def update_annotation_set(annotation_set_id, annotation_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'annotationSets/{annotationSetId}'
  command =  make_simple_command(:put, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
  command.request_object = annotation_set_object
  command.response_representation = Google::Apis::GenomicsV1beta2::AnnotationSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::AnnotationSet
  command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
update_call_set(call_set_id, call_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Updates a call set. @param [String] call_set_id

The ID of the call set to be updated.

@param [Google::Apis::GenomicsV1beta2::CallSet] call_set_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::CallSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::CallSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 765
def update_call_set(call_set_id, call_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'callsets/{callSetId}'
  command =  make_simple_command(:put, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
  command.request_object = call_set_object
  command.response_representation = Google::Apis::GenomicsV1beta2::CallSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::CallSet
  command.params['callSetId'] = call_set_id unless call_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
update_dataset(dataset_id, dataset_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Updates a dataset. @param [String] dataset_id

The ID of the dataset to be updated.

@param [Google::Apis::GenomicsV1beta2::Dataset] dataset_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Dataset] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Dataset]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1031
def update_dataset(dataset_id, dataset_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'datasets/{datasetId}'
  command =  make_simple_command(:put, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
  command.request_object = dataset_object
  command.response_representation = Google::Apis::GenomicsV1beta2::Dataset::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Dataset
  command.params['datasetId'] = dataset_id unless dataset_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
update_read_group_set(read_group_set_id, read_group_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Updates a read group set. @param [String] read_group_set_id

The ID of the read group set to be updated. The caller must have WRITE
permissions to the dataset associated with this read group set.

@param [Google::Apis::GenomicsV1beta2::ReadGroupSet] read_group_set_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::ReadGroupSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::ReadGroupSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 1518
def update_read_group_set(read_group_set_id, read_group_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'readgroupsets/{readGroupSetId}'
  command =  make_simple_command(:put, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation
  command.request_object = read_group_set_object
  command.response_representation = Google::Apis::GenomicsV1beta2::ReadGroupSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::ReadGroupSet
  command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
update_variant(variant_id, variant_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Updates a variant's names and info fields. All other modifications are silently ignored. Returns the modified variant without its calls. @param [String] variant_id

The ID of the variant to be updated.

@param [Google::Apis::GenomicsV1beta2::Variant] variant_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::Variant] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::Variant]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 2017
def update_variant(variant_id, variant_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variants/{variantId}'
  command =  make_simple_command(:put, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::Variant::Representation
  command.request_object = variant_object
  command.response_representation = Google::Apis::GenomicsV1beta2::Variant::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::Variant
  command.params['variantId'] = variant_id unless variant_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end
update_variantset(variant_set_id, variant_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block) click to toggle source

Updates a variant set's metadata. All other modifications are silently ignored. @param [String] variant_set_id

The ID of the variant to be updated (must already exist).

@param [Google::Apis::GenomicsV1beta2::VariantSet] variant_set_object @param [String] fields

Selector specifying which fields to include in a partial response.

@param [String] #quota_user

Available to use for quota purposes for server-side applications. Can be any
arbitrary string assigned to a user, but should not exceed 40 characters.
Overrides userIp if both are provided.

@param [String] #user_ip

IP address of the site where the request originates. Use this if you want to
enforce per-user limits.

@param [Google::Apis::RequestOptions] options

Request-specific options

@yield [result, err] Result & error if block supplied @yieldparam result [Google::Apis::GenomicsV1beta2::VariantSet] parsed result object @yieldparam err [StandardError] error object if request failed

@return [Google::Apis::GenomicsV1beta2::VariantSet]

@raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification @raise [Google::Apis::AuthorizationError] Authorization is required

# File generated/google/apis/genomics_v1beta2/service.rb, line 2368
def update_variantset(variant_set_id, variant_set_object = nil, fields: nil, quota_user: nil, user_ip: nil, options: nil, &block)
  path = 'variantsets/{variantSetId}'
  command =  make_simple_command(:put, path, options)
  command.request_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
  command.request_object = variant_set_object
  command.response_representation = Google::Apis::GenomicsV1beta2::VariantSet::Representation
  command.response_class = Google::Apis::GenomicsV1beta2::VariantSet
  command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
  execute_or_queue_command(command, &block)
end

Protected Instance Methods

apply_command_defaults(command) click to toggle source
# File generated/google/apis/genomics_v1beta2/service.rb, line 2384
def apply_command_defaults(command)
  command.query['key'] = key unless key.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['userIp'] = user_ip unless user_ip.nil?
end