Class: Google::Apis::GenomicsV1::GenomicsService

Inherits:
Core::BaseService show all
Defined in:
generated/google/apis/genomics_v1/service.rb

Overview

Genomics API

Uploads, processes, queries, and searches Genomics data in the cloud.

Examples:

require 'google/apis/genomics_v1'

Genomics = Google::Apis::GenomicsV1 # Alias the module
service = Genomics::GenomicsService.new

See Also:

Instance Attribute Summary collapse

Attributes inherited from Core::BaseService

#authorization, #base_path, #batch_path, #client, #client_options, #request_options, #root_url, #upload_path

Instance Method Summary collapse

Methods inherited from Core::BaseService

#batch, #batch_upload, #fetch_all, #http

Methods included from Core::Logging

#logger

Constructor Details

#initializeGenomicsService

Returns a new instance of GenomicsService


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# File 'generated/google/apis/genomics_v1/service.rb', line 45

def initialize
  super('https://genomics.googleapis.com/', '')
  @batch_path = 'batch'
end

Instance Attribute Details

#keyString

Returns 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.

Returns:

  • (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.


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# File 'generated/google/apis/genomics_v1/service.rb', line 38

def key
  @key
end

#quota_userString

Returns Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.

Returns:

  • (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.


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# File 'generated/google/apis/genomics_v1/service.rb', line 43

def quota_user
  @quota_user
end

Instance Method Details

#batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse

Creates one or more new annotations atomically. All annotations must belong to the same annotation set. Caller must have WRITE permission for this annotation set. For optimal performance, batch positionally adjacent annotations together. If the request has a systemic issue, such as an attempt to write to an inaccessible annotation set, the entire RPC will fail accordingly. For lesser data issues, when possible an error will be isolated to the corresponding batch entry in the response; the remaining well formed annotations will be created normally. For details on the requirements for each individual annotation resource, see CreateAnnotation.

Parameters:

  • batch_create_annotations_request_object (Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 80

def batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/annotations:batchCreate', options)
  command.request_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest::Representation
  command.request_object = batch_create_annotations_request_object
  command.response_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty

Starts asynchronous cancellation on a long-running operation. The server makes a best effort to cancel the operation, but success is not guaranteed. Clients may use Operations.GetOperation or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite cancellation. Authorization requires the following Google IAM permission:

  • genomics.operations.cancel

Parameters:

  • name (String)

    The name of the operation resource to be cancelled.

  • cancel_operation_request_object (Google::Apis::GenomicsV1::CancelOperationRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 960

def cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/{+name}:cancel', options)
  command.request_representation = Google::Apis::GenomicsV1::CancelOperationRequest::Representation
  command.request_object = cancel_operation_request_object
  command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
  command.response_class = Google::Apis::GenomicsV1::Empty
  command.params['name'] = name unless name.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#create_annotation(annotation_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Annotation

Creates a new annotation. Caller must have WRITE permission for the associated annotation set. The following fields are required:

  • annotationSetId
  • referenceName or referenceId ### Transcripts For annotations of type TRANSCRIPT, the following fields of transcript must be provided:
  • exons.start
  • exons.end All other fields may be optionally specified, unless documented as being server-generated (for example, the id field). The annotated range must be no longer than 100Mbp (mega base pairs). See the Annotation resource for additional restrictions on each field.

Parameters:

  • annotation_object (Google::Apis::GenomicsV1::Annotation) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 125

def create_annotation(annotation_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/annotations', options)
  command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation
  command.request_object = annotation_object
  command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation
  command.response_class = Google::Apis::GenomicsV1::Annotation
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::AnnotationSet

Creates a new annotation set. Caller must have WRITE permission for the associated dataset. The following fields are required:

  • datasetId
  • referenceSetId All other fields may be optionally specified, unless documented as being server-generated (for example, the id field).

Parameters:

  • annotation_set_object (Google::Apis::GenomicsV1::AnnotationSet) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 301

def create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/annotationsets', options)
  command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
  command.request_object = annotation_set_object
  command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
  command.response_class = Google::Apis::GenomicsV1::AnnotationSet
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::CallSet

Creates a new call set.

Parameters:

  • call_set_object (Google::Apis::GenomicsV1::CallSet) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 469

def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/callsets', options)
  command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
  command.request_object = call_set_object
  command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
  command.response_class = Google::Apis::GenomicsV1::CallSet
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset

Creates a new dataset.

Parameters:

  • dataset_object (Google::Apis::GenomicsV1::Dataset) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 632

def create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/datasets', options)
  command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation
  command.request_object = dataset_object
  command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
  command.response_class = Google::Apis::GenomicsV1::Dataset
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Variant

Creates a new variant.

Parameters:

  • variant_object (Google::Apis::GenomicsV1::Variant) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1604

def create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/variants', options)
  command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
  command.request_object = variant_object
  command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
  command.response_class = Google::Apis::GenomicsV1::Variant
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::VariantSet

Creates a new variant set. The provided variant set must have a valid datasetId set - all other fields are optional. Note that the id field will be ignored, as this is assigned by the server.

Parameters:

  • variant_set_object (Google::Apis::GenomicsV1::VariantSet) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1920

def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/variantsets', options)
  command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
  command.request_object = variant_set_object
  command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
  command.response_class = Google::Apis::GenomicsV1::VariantSet
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#delete_annotation(annotation_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty

Deletes an annotation. Caller must have WRITE permission for the associated annotation set.

Parameters:

  • annotation_id (String)

    The ID of the annotation to be deleted.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 157

def delete_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:delete, 'v1/annotations/{annotationId}', options)
  command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
  command.response_class = Google::Apis::GenomicsV1::Empty
  command.params['annotationId'] = annotation_id unless annotation_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#delete_annotationset(annotation_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty

Deletes an annotation set. Caller must have WRITE permission for the associated annotation set.

Parameters:

  • annotation_set_id (String)

    The ID of the annotation set to be deleted.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 333

def delete_annotationset(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:delete, 'v1/annotationsets/{annotationSetId}', options)
  command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
  command.response_class = Google::Apis::GenomicsV1::Empty
  command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty

Deletes a call set.

Parameters:

  • call_set_id (String)

    The ID of the call set to be deleted.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 500

def delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:delete, 'v1/callsets/{callSetId}', options)
  command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
  command.response_class = Google::Apis::GenomicsV1::Empty
  command.params['callSetId'] = call_set_id unless call_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty

Deletes a dataset and all of its contents (all read group sets, reference sets, variant sets, call sets, annotation sets, etc.) This is reversible (up to one week after the deletion) via the datasets.undelete operation.

Parameters:

  • dataset_id (String)

    The ID of the dataset to be deleted.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 668

def delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:delete, 'v1/datasets/{datasetId}', options)
  command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
  command.response_class = Google::Apis::GenomicsV1::Empty
  command.params['datasetId'] = dataset_id unless dataset_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty

Deletes a read group set.

Parameters:

  • read_group_set_id (String)

    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.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1096

def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:delete, 'v1/readgroupsets/{readGroupSetId}', options)
  command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
  command.response_class = Google::Apis::GenomicsV1::Empty
  command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#delete_variant(variant_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty

Deletes a variant.

Parameters:

  • variant_id (String)

    The ID of the variant to be deleted.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1635

def delete_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:delete, 'v1/variants/{variantId}', options)
  command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
  command.response_class = Google::Apis::GenomicsV1::Empty
  command.params['variantId'] = variant_id unless variant_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty

Deletes a variant set including all variants, call sets, and calls within. This is not reversible.

Parameters:

  • variant_set_id (String)

    The ID of the variant set to be deleted.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1952

def delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:delete, 'v1/variantsets/{variantSetId}', options)
  command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
  command.response_class = Google::Apis::GenomicsV1::Empty
  command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation

Exports a read group set 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. See ImportReadGroupSets for caveats.

Parameters:

  • read_group_set_id (String)

    Required. The ID of the read group set to export. The caller must have READ access to this read group set.

  • export_read_group_set_request_object (Google::Apis::GenomicsV1::ExportReadGroupSetRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1132

def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/readgroupsets/{readGroupSetId}:export', options)
  command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation
  command.request_object = export_read_group_set_request_object
  command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
  command.response_class = Google::Apis::GenomicsV1::Operation
  command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation

Exports variant set data to an external destination.

Parameters:

  • variant_set_id (String)

    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.

  • export_variant_set_request_object (Google::Apis::GenomicsV1::ExportVariantSetRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1984

def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/variantsets/{variantSetId}:export', options)
  command.request_representation = Google::Apis::GenomicsV1::ExportVariantSetRequest::Representation
  command.request_object = export_variant_set_request_object
  command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
  command.response_class = Google::Apis::GenomicsV1::Operation
  command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#get_annotation(annotation_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Annotation

Gets an annotation. Caller must have READ permission for the associated annotation set.

Parameters:

  • annotation_id (String)

    The ID of the annotation to be retrieved.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 188

def get_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/annotations/{annotationId}', options)
  command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation
  command.response_class = Google::Apis::GenomicsV1::Annotation
  command.params['annotationId'] = annotation_id unless annotation_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::AnnotationSet

Gets an annotation set. Caller must have READ permission for the associated dataset.

Parameters:

  • annotation_set_id (String)

    The ID of the annotation set to be retrieved.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 364

def get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/annotationsets/{annotationSetId}', options)
  command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
  command.response_class = Google::Apis::GenomicsV1::AnnotationSet
  command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::CallSet

Gets a call set by ID.

Parameters:

  • call_set_id (String)

    The ID of the call set.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 530

def get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/callsets/{callSetId}', options)
  command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
  command.response_class = Google::Apis::GenomicsV1::CallSet
  command.params['callSetId'] = call_set_id unless call_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset

Gets a dataset by ID.

Parameters:

  • dataset_id (String)

    The ID of the dataset.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 698

def get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/datasets/{datasetId}', options)
  command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
  command.response_class = Google::Apis::GenomicsV1::Dataset
  command.params['datasetId'] = dataset_id unless dataset_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Policy

Gets the access control policy for the dataset. This is empty if the policy or resource does not exist. See Getting a Policy for more information.

Parameters:

  • resource (String)

    REQUIRED: The resource for which policy is being specified. Format is datasets/<dataset ID>.

  • get_iam_policy_request_object (Google::Apis::GenomicsV1::GetIamPolicyRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 733

def get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/{+resource}:getIamPolicy', options)
  command.request_representation = Google::Apis::GenomicsV1::GetIamPolicyRequest::Representation
  command.request_object = get_iam_policy_request_object
  command.response_representation = Google::Apis::GenomicsV1::Policy::Representation
  command.response_class = Google::Apis::GenomicsV1::Policy
  command.params['resource'] = resource unless resource.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#get_operation(name, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation

Gets the latest state of a long-running operation. Clients can use this method to poll the operation result at intervals as recommended by the API service. Authorization requires the following Google IAM permission:

  • genomics.operations.get

Parameters:

  • name (String)

    The name of the operation resource.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 997

def get_operation(name, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/{+name}', options)
  command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
  command.response_class = Google::Apis::GenomicsV1::Operation
  command.params['name'] = name unless name.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ReadGroupSet

Gets a read group set by ID.

Parameters:

  • read_group_set_id (String)

    The ID of the read group set.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1164

def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}', options)
  command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
  command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
  command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#get_reference(reference_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Reference

Gets a reference. Implements GlobalAllianceApi.getReference.

Parameters:

  • reference_id (String)

    The ID of the reference.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1426

def get_reference(reference_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/references/{referenceId}', options)
  command.response_representation = Google::Apis::GenomicsV1::Reference::Representation
  command.response_class = Google::Apis::GenomicsV1::Reference
  command.params['referenceId'] = reference_id unless reference_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ReferenceSet

Gets a reference set. Implements GlobalAllianceApi.getReferenceSet.

Parameters:

  • reference_set_id (String)

    The ID of the reference set.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1542

def get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/referencesets/{referenceSetId}', options)
  command.response_representation = Google::Apis::GenomicsV1::ReferenceSet::Representation
  command.response_class = Google::Apis::GenomicsV1::ReferenceSet
  command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#get_variant(variant_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Variant

Gets a variant by ID.

Parameters:

  • variant_id (String)

    The ID of the variant.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1665

def get_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/variants/{variantId}', options)
  command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
  command.response_class = Google::Apis::GenomicsV1::Variant
  command.params['variantId'] = variant_id unless variant_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::VariantSet

Gets a variant set by ID.

Parameters:

  • variant_set_id (String)

    Required. The ID of the variant set.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 2016

def get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/variantsets/{variantSetId}', options)
  command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
  command.response_class = Google::Apis::GenomicsV1::VariantSet
  command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation

Creates read group sets by asynchronously importing the provided information. The caller must have WRITE permissions to the dataset.

Notes on BAM import

  • Tags will be converted to strings - tag types are not preserved
  • Comments (@CO) in the input file header will not be preserved
  • Original header order of references (@SQ) will not be preserved
  • Any reverse stranded unmapped reads will be reverse complemented, and their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
  • Unmapped reads will be stripped of positional information (reference name and position)

Parameters:

  • import_read_group_sets_request_object (Google::Apis::GenomicsV1::ImportReadGroupSetsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1203

def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/readgroupsets:import', options)
  command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation
  command.request_object = import_read_group_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
  command.response_class = Google::Apis::GenomicsV1::Operation
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation

Creates variant data by asynchronously importing the provided information. The variants for import will be merged with any existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant, and Variant info fields are merged as specified in infoMergeConfig. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set.

Parameters:

  • import_variants_request_object (Google::Apis::GenomicsV1::ImportVariantsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1705

def import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/variants:import', options)
  command.request_representation = Google::Apis::GenomicsV1::ImportVariantsRequest::Representation
  command.request_object = import_variants_request_object
  command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
  command.response_class = Google::Apis::GenomicsV1::Operation
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#list_coverage_buckets(read_group_set_id, end_: nil, page_size: nil, page_token: nil, reference_name: nil, start: nil, target_bucket_width: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListCoverageBucketsResponse

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.

Parameters:

  • read_group_set_id (String)

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

  • end_ (Fixnum)

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

  • page_size (Fixnum)

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

  • page_token (String)

    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.

  • reference_name (String)

    The name of the reference to query, within the reference set associated with this query. Optional.

  • start (Fixnum)

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

  • target_bucket_width (Fixnum)

    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.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1341

def list_coverage_buckets(read_group_set_id, end_: nil, page_size: nil, page_token: nil, reference_name: nil, start: nil, target_bucket_width: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', options)
  command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse
  command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
  command.query['end'] = end_ unless end_.nil?
  command.query['pageSize'] = page_size unless page_size.nil?
  command.query['pageToken'] = page_token unless page_token.nil?
  command.query['referenceName'] = reference_name unless reference_name.nil?
  command.query['start'] = start unless 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?
  execute_or_queue_command(command, &block)
end

#list_datasets(page_size: nil, page_token: nil, project_id: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListDatasetsResponse

Lists datasets within a project.

Parameters:

  • page_size (Fixnum)

    The maximum number of results to return in a single page. If unspecified, defaults to 50. The maximum value is 1024.

  • page_token (String)

    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.

  • project_id (String)

    Required. The Google Cloud project ID to list datasets for.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 772

def list_datasets(page_size: nil, page_token: nil, project_id: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/datasets', options)
  command.response_representation = Google::Apis::GenomicsV1::ListDatasetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::ListDatasetsResponse
  command.query['pageSize'] = page_size unless page_size.nil?
  command.query['pageToken'] = page_token unless page_token.nil?
  command.query['projectId'] = project_id unless project_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#list_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListOperationsResponse

Lists operations that match the specified filter in the request. Authorization requires the following Google IAM permission:

  • genomics.operations.list

Parameters:

  • name (String)

    The name of the operation's parent resource.

  • filter (String)

    A string for filtering Operations. In v2alpha1, the following filter fields are supported:

    • createTime: The time this job was created
    • events: The set of event (names) that have occurred while running the pipeline. The : operator can be used to determine if a particular event has occurred.
    • error: If the pipeline is running, this value is NULL. Once the pipeline finishes, the value is the standard Google error code.
    • labels.key or labels."key with space" where key is a label key.
    • done: If the pipeline is running, this value is false. Once the pipeline finishes, the value is true. In v1 and v1alpha2, the following filter fields are supported:
    • projectId: Required. Corresponds to OperationMetadata.projectId.
    • createTime: The time this job was created, in seconds from the epoch. Can use >= and/or <= operators.
    • status: Can be RUNNING, SUCCESS, FAILURE, or CANCELED. Only one status may be specified.
    • labels.key where key is a label key. Examples:
    • projectId = my-project AND createTime >= 1432140000
    • projectId = my-project AND createTime >= 1432140000 AND createTime <= 1432150000 AND status = RUNNING
    • projectId = my-project AND labels.color = *
    • projectId = my-project AND labels.color = red
  • page_size (Fixnum)

    The maximum number of results to return. If unspecified, defaults to

    1. The maximum value is 2048.
  • page_token (String)

    The standard list page token.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1062

def list_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/{+name}', options)
  command.response_representation = Google::Apis::GenomicsV1::ListOperationsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::ListOperationsResponse
  command.params['name'] = name unless name.nil?
  command.query['filter'] = filter unless filter.nil?
  command.query['pageSize'] = page_size unless page_size.nil?
  command.query['pageToken'] = page_token unless page_token.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#list_reference_bases(reference_id, end_position: nil, page_size: nil, page_token: nil, start_position: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListBasesResponse

Lists the bases in a reference, optionally restricted to a range. Implements GlobalAllianceApi.getReferenceBases.

Parameters:

  • reference_id (String)

    The ID of the reference.

  • end_position (Fixnum)

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

  • page_size (Fixnum)

    The maximum number of bases to return in a single page. If unspecified, defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base pairs).

  • page_token (String)

    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.

  • start_position (Fixnum)

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

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1505

def list_reference_bases(reference_id, end_position: nil, page_size: nil, page_token: nil, start_position: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:get, 'v1/references/{referenceId}/bases', options)
  command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::ListBasesResponse
  command.params['referenceId'] = reference_id unless reference_id.nil?
  command.query['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?
  execute_or_queue_command(command, &block)
end

#merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty

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. Variant info fields are merged as specified in the infoMergeConfig field of the MergeVariantsRequest. Please exercise caution when using this method! It is easy to introduce mistakes in existing variants and difficult to back out of them. For example, suppose you were trying to merge a new variant with an existing one and both variants contain calls that belong to callsets with the same callset ID. // Existing variant - irrelevant fields trimmed for clarity "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 0, 1 ], ] // New variant with conflicting call information "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], ] The resulting merged variant would overwrite the existing calls with those from the new variant: "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], ] This may be the desired outcome, but it is up to the user to determine if if that is indeed the case.

Parameters:

  • merge_variants_request_object (Google::Apis::GenomicsV1::MergeVariantsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1813

def merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/variants:merge', options)
  command.request_representation = Google::Apis::GenomicsV1::MergeVariantsRequest::Representation
  command.request_object = merge_variants_request_object
  command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
  command.response_class = Google::Apis::GenomicsV1::Empty
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::CallSet

Updates a call set. This method supports patch semantics.

Parameters:

  • call_set_id (String)

    The ID of the call set to be updated.

  • call_set_object (Google::Apis::GenomicsV1::CallSet) (defaults to: nil)
  • update_mask (String)

    An optional mask specifying which fields to update. At this time, the only mutable field is name. The only acceptable value is "name". If unspecified, all mutable fields will be updated.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 567

def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:patch, 'v1/callsets/{callSetId}', options)
  command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
  command.request_object = call_set_object
  command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
  command.response_class = Google::Apis::GenomicsV1::CallSet
  command.params['callSetId'] = call_set_id unless call_set_id.nil?
  command.query['updateMask'] = update_mask unless update_mask.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset

Updates a dataset. This method supports patch semantics.

Parameters:

  • dataset_id (String)

    The ID of the dataset to be updated.

  • dataset_object (Google::Apis::GenomicsV1::Dataset) (defaults to: nil)
  • update_mask (String)

    An optional mask specifying which fields to update. At this time, the only mutable field is name. The only acceptable value is "name". If unspecified, all mutable fields will be updated.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 811

def patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:patch, 'v1/datasets/{datasetId}', options)
  command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation
  command.request_object = dataset_object
  command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
  command.response_class = Google::Apis::GenomicsV1::Dataset
  command.params['datasetId'] = dataset_id unless dataset_id.nil?
  command.query['updateMask'] = update_mask unless update_mask.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ReadGroupSet

Updates a read group set. This method supports patch semantics.

Parameters:

  • read_group_set_id (String)

    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.

  • read_group_set_object (Google::Apis::GenomicsV1::ReadGroupSet) (defaults to: nil)
  • update_mask (String)

    An optional mask specifying which fields to update. Supported fields:

    • name.
    • referenceSetId. Leaving updateMask unset is equivalent to specifying all mutable fields.
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1243

def patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:patch, 'v1/readgroupsets/{readGroupSetId}', options)
  command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
  command.request_object = read_group_set_object
  command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
  command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
  command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
  command.query['updateMask'] = update_mask unless update_mask.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Variant

Updates a variant. This method supports patch semantics. Returns the modified variant without its calls.

Parameters:

  • variant_id (String)

    The ID of the variant to be updated.

  • variant_object (Google::Apis::GenomicsV1::Variant) (defaults to: nil)
  • update_mask (String)

    An optional mask specifying which fields to update. At this time, mutable fields are names and info. Acceptable values are "names" and "info". If unspecified, all mutable fields will be updated.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1852

def patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:patch, 'v1/variants/{variantId}', options)
  command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
  command.request_object = variant_object
  command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
  command.response_class = Google::Apis::GenomicsV1::Variant
  command.params['variantId'] = variant_id unless variant_id.nil?
  command.query['updateMask'] = update_mask unless update_mask.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::VariantSet

Updates a variant set using patch semantics.

Parameters:

  • variant_set_id (String)

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

  • variant_set_object (Google::Apis::GenomicsV1::VariantSet) (defaults to: nil)
  • update_mask (String)

    An optional mask specifying which fields to update. Supported fields:

    • metadata.
    • name.
    • description. Leaving updateMask unset is equivalent to specifying all mutable fields.
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 2054

def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:patch, 'v1/variantsets/{variantSetId}', options)
  command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
  command.request_object = variant_set_object
  command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
  command.response_class = Google::Apis::GenomicsV1::VariantSet
  command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
  command.query['updateMask'] = update_mask unless update_mask.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchAnnotationsResponse

Searches for annotations that match the given criteria. Results are ordered by genomic coordinate (by reference sequence, then position). Annotations with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotations in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried annotation sets.

Parameters:

  • search_annotations_request_object (Google::Apis::GenomicsV1::SearchAnnotationsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 223

def search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/annotations/search', options)
  command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationsRequest::Representation
  command.request_object = search_annotations_request_object
  command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::SearchAnnotationsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchAnnotationSetsResponse

Searches for annotation sets that match the given criteria. Annotation sets are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotation sets in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried datasets.

Parameters:

  • search_annotation_sets_request_object (Google::Apis::GenomicsV1::SearchAnnotationSetsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 397

def search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/annotationsets/search', options)
  command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsRequest::Representation
  command.request_object = search_annotation_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchCallSetsResponse

Gets a list of call sets matching the criteria. Implements GlobalAllianceApi.searchCallSets.

Parameters:

  • search_call_sets_request_object (Google::Apis::GenomicsV1::SearchCallSetsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 602

def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/callsets/search', options)
  command.request_representation = Google::Apis::GenomicsV1::SearchCallSetsRequest::Representation
  command.request_object = search_call_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1::SearchCallSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::SearchCallSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReadGroupSetsResponse

Searches for read group sets matching the criteria. Implements GlobalAllianceApi.searchReadGroupSets.

Parameters:

  • search_read_group_sets_request_object (Google::Apis::GenomicsV1::SearchReadGroupSetsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1278

def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/readgroupsets/search', options)
  command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation
  command.request_object = search_read_group_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReadsResponse

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 (by reference sequence, then position). Reads with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield reads in the same order across their respective streams of paginated responses. Implements GlobalAllianceApi.searchReads.

Parameters:

  • search_reads_request_object (Google::Apis::GenomicsV1::SearchReadsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1392

def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/reads/search', options)
  command.request_representation = Google::Apis::GenomicsV1::SearchReadsRequest::Representation
  command.request_object = search_reads_request_object
  command.response_representation = Google::Apis::GenomicsV1::SearchReadsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::SearchReadsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReferenceSetsResponse

Searches for reference sets which match the given criteria. Implements GlobalAllianceApi.searchReferenceSets

Parameters:

  • search_reference_sets_request_object (Google::Apis::GenomicsV1::SearchReferenceSetsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1574

def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/referencesets/search', options)
  command.request_representation = Google::Apis::GenomicsV1::SearchReferenceSetsRequest::Representation
  command.request_object = search_reference_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1::SearchReferenceSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::SearchReferenceSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReferencesResponse

Searches for references which match the given criteria. Implements GlobalAllianceApi.searchReferences.

Parameters:

  • search_references_request_object (Google::Apis::GenomicsV1::SearchReferencesRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1458

def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/references/search', options)
  command.request_representation = Google::Apis::GenomicsV1::SearchReferencesRequest::Representation
  command.request_object = search_references_request_object
  command.response_representation = Google::Apis::GenomicsV1::SearchReferencesResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::SearchReferencesResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchVariantSetsResponse

Returns a list of all variant sets matching search criteria. Implements GlobalAllianceApi.searchVariantSets.

Parameters:

  • search_variant_sets_request_object (Google::Apis::GenomicsV1::SearchVariantSetsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 2089

def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/variantsets/search', options)
  command.request_representation = Google::Apis::GenomicsV1::SearchVariantSetsRequest::Representation
  command.request_object = search_variant_sets_request_object
  command.response_representation = Google::Apis::GenomicsV1::SearchVariantSetsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::SearchVariantSetsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchVariantsResponse

Gets a list of variants matching the criteria. Implements GlobalAllianceApi.searchVariants.

Parameters:

  • search_variants_request_object (Google::Apis::GenomicsV1::SearchVariantsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 1887

def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/variants/search', options)
  command.request_representation = Google::Apis::GenomicsV1::SearchVariantsRequest::Representation
  command.request_object = search_variants_request_object
  command.response_representation = Google::Apis::GenomicsV1::SearchVariantsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::SearchVariantsResponse
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Policy

Sets the access control policy on the specified dataset. Replaces any existing policy. See Setting a Policy for more information.

Parameters:

  • resource (String)

    REQUIRED: The resource for which policy is being specified. Format is datasets/<dataset ID>.

  • set_iam_policy_request_object (Google::Apis::GenomicsV1::SetIamPolicyRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 849

def set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/{+resource}:setIamPolicy', options)
  command.request_representation = Google::Apis::GenomicsV1::SetIamPolicyRequest::Representation
  command.request_object = set_iam_policy_request_object
  command.response_representation = Google::Apis::GenomicsV1::Policy::Representation
  command.response_class = Google::Apis::GenomicsV1::Policy
  command.params['resource'] = resource unless resource.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::TestIamPermissionsResponse

Returns permissions that a caller has on the specified resource. See Testing Permissions for more information.

Parameters:

  • resource (String)

    REQUIRED: The resource for which policy is being specified. Format is datasets/<dataset ID>.

  • test_iam_permissions_request_object (Google::Apis::GenomicsV1::TestIamPermissionsRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 885

def test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/{+resource}:testIamPermissions', options)
  command.request_representation = Google::Apis::GenomicsV1::TestIamPermissionsRequest::Representation
  command.request_object = test_iam_permissions_request_object
  command.response_representation = Google::Apis::GenomicsV1::TestIamPermissionsResponse::Representation
  command.response_class = Google::Apis::GenomicsV1::TestIamPermissionsResponse
  command.params['resource'] = resource unless resource.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset

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.

Parameters:

  • dataset_id (String)

    The ID of the dataset to be undeleted.

  • undelete_dataset_request_object (Google::Apis::GenomicsV1::UndeleteDatasetRequest) (defaults to: nil)
  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 919

def undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:post, 'v1/datasets/{datasetId}:undelete', options)
  command.request_representation = Google::Apis::GenomicsV1::UndeleteDatasetRequest::Representation
  command.request_object = undelete_dataset_request_object
  command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
  command.response_class = Google::Apis::GenomicsV1::Dataset
  command.params['datasetId'] = dataset_id unless dataset_id.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#update_annotation(annotation_id, annotation_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Annotation

Updates an annotation. Caller must have WRITE permission for the associated dataset.

Parameters:

  • annotation_id (String)

    The ID of the annotation to be updated.

  • annotation_object (Google::Apis::GenomicsV1::Annotation) (defaults to: nil)
  • update_mask (String)

    An optional mask specifying which fields to update. Mutable fields are name, variant, transcript, and info. If unspecified, all mutable fields will be updated.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 263

def update_annotation(annotation_id, annotation_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:put, 'v1/annotations/{annotationId}', options)
  command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation
  command.request_object = annotation_object
  command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation
  command.response_class = Google::Apis::GenomicsV1::Annotation
  command.params['annotationId'] = annotation_id unless annotation_id.nil?
  command.query['updateMask'] = update_mask unless update_mask.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end

#update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::AnnotationSet

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.

Parameters:

  • annotation_set_id (String)

    The ID of the annotation set to be updated.

  • annotation_set_object (Google::Apis::GenomicsV1::AnnotationSet) (defaults to: nil)
  • update_mask (String)

    An optional mask specifying which fields to update. Mutable fields are name, source_uri, and info. If unspecified, all mutable fields will be updated.

  • fields (String)

    Selector specifying which fields to include in a partial response.

  • quota_user (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.

  • options (Google::Apis::RequestOptions)

    Request-specific options

Yields:

  • (result, err)

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:


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# File 'generated/google/apis/genomics_v1/service.rb', line 437

def update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
  command =  make_simple_command(:put, 'v1/annotationsets/{annotationSetId}', options)
  command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
  command.request_object = annotation_set_object
  command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
  command.response_class = Google::Apis::GenomicsV1::AnnotationSet
  command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
  command.query['updateMask'] = update_mask unless update_mask.nil?
  command.query['fields'] = fields unless fields.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  execute_or_queue_command(command, &block)
end