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

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

Overview

Genomics API

Upload, process, query, and search 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

Constructor Details

#initialize ⇒ GenomicsService

Returns a new instance of GenomicsService



45
46
47
 
# File 'generated/google/apis/genomics_v1/service.rb', line 45

def initialize
  super('https://genomics.googleapis.com/', '')
end

Instance Attribute Details

#key ⇒ String

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.



38
39
40
 
# File 'generated/google/apis/genomics_v1/service.rb', line 38

def key
  @key
end

#quota_user ⇒ String

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.



43
44
45
 
# 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, quota_user: nil, fields: 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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1852
1853
1854
1855
1856
1857
1858
1859
1860
1861
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1852

def batch_create_annotations(batch_create_annotations_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#cancel_operation(name, cancel_operation_request_object = nil, quota_user: nil, fields: 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.

Parameters:

  • name (String) —

    The name of the operation resource to be cancelled.

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



2027
2028
2029
2030
2031
2032
2033
2034
2035
2036
2037
 
# File 'generated/google/apis/genomics_v1/service.rb', line 2027

def cancel_operation(name, cancel_operation_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#create_annotation(annotation_object = nil, quota_user: nil, fields: 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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1811
1812
1813
1814
1815
1816
1817
1818
1819
1820
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1811

def create_annotation(annotation_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#create_annotation_set(annotation_set_object = nil, quota_user: nil, fields: 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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



604
605
606
607
608
609
610
611
612
613
 
# File 'generated/google/apis/genomics_v1/service.rb', line 604

def create_annotation_set(annotation_set_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Creates a new call set. For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



568
569
570
571
572
573
574
575
576
577
 
# File 'generated/google/apis/genomics_v1/service.rb', line 568

def create_call_set(call_set_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Creates a new dataset. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1506

def create_dataset(dataset_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Creates a new variant. For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



963
964
965
966
967
968
969
970
971
972
 
# File 'generated/google/apis/genomics_v1/service.rb', line 963

def create_variant(variant_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Creates a new variant set. For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics The provided variant set must have a valid datasetId set - all other fields are optional. Note that the id field will be ignored, as this is assigned by the server.

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1616

def create_variantset(variant_set_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#delete_annotation(annotation_id, quota_user: nil, fields: 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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1993
1994
1995
1996
1997
1998
1999
2000
2001
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1993

def delete_annotation(annotation_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#delete_annotationset(annotation_set_id, quota_user: nil, fields: 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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



636
637
638
639
640
641
642
643
644
 
# File 'generated/google/apis/genomics_v1/service.rb', line 636

def delete_annotationset(annotation_set_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Deletes a call set. For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics

Parameters:

  • call_set_id (String) —

    The ID of the call set to be deleted.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



424
425
426
427
428
429
430
431
432
 
# File 'generated/google/apis/genomics_v1/service.rb', line 424

def delete_call_set(call_set_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#delete_dataset(dataset_id, quota_user: nil, fields: 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. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics

Parameters:

  • dataset_id (String) —

    The ID of the dataset to be deleted.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1432
1433
1434
1435
1436
1437
1438
1439
1440
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1432

def delete_dataset(dataset_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Deletes a read group set. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics

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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



73
74
75
76
77
78
79
80
81
 
# File 'generated/google/apis/genomics_v1/service.rb', line 73

def delete_read_group_set(read_group_set_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Deletes a variant. For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics

Parameters:

  • variant_id (String) —

    The ID of the variant to be deleted.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



776
777
778
779
780
781
782
783
784
 
# File 'generated/google/apis/genomics_v1/service.rb', line 776

def delete_variant(variant_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#delete_variantset(variant_set_id, quota_user: nil, fields: 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. For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics

Parameters:

  • variant_set_id (String) —

    The ID of the variant set to be deleted.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1581
1582
1583
1584
1585
1586
1587
1588
1589
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1581

def delete_variantset(variant_set_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Exports a read group set to a BAM file in Google Cloud Storage. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics 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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



155
156
157
158
159
160
161
162
163
164
165
 
# File 'generated/google/apis/genomics_v1/service.rb', line 155

def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Exports variant set data to an external destination. For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics

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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1652

def export_variant_set(variant_set_id, export_variant_set_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#get_annotation(annotation_id, quota_user: nil, fields: 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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1920
1921
1922
1923
1924
1925
1926
1927
1928
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1920

def get_annotation(annotation_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#get_annotation_set(annotation_set_id, quota_user: nil, fields: 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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



701
702
703
704
705
706
707
708
709
 
# File 'generated/google/apis/genomics_v1/service.rb', line 701

def get_annotation_set(annotation_set_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Gets a call set by ID. For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics

Parameters:

  • call_set_id (String) —

    The ID of the call set.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



536
537
538
539
540
541
542
543
544
 
# File 'generated/google/apis/genomics_v1/service.rb', line 536

def get_call_set(call_set_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Gets a dataset by ID. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics

Parameters:

  • dataset_id (String) —

    The ID of the dataset.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1312
1313
1314
1315
1316
1317
1318
1319
1320
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1312

def get_dataset(dataset_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, quota_user: nil, fields: 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. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics

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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1240

def get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#get_operation(name, quota_user: nil, fields: 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.

Parameters:

  • name (String) —

    The name of the operation resource.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



2116
2117
2118
2119
2120
2121
2122
2123
2124
 
# File 'generated/google/apis/genomics_v1/service.rb', line 2116

def get_operation(name, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Gets a read group set by ID. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics

Parameters:

  • read_group_set_id (String) —

    The ID of the read group set.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



271
272
273
274
275
276
277
278
279
 
# File 'generated/google/apis/genomics_v1/service.rb', line 271

def get_read_group_set(read_group_set_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Gets a reference. For the definitions of references and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.getReference.

Parameters:

  • reference_id (String) —

    The ID of the reference.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1149
1150
1151
1152
1153
1154
1155
1156
1157
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1149

def get_reference(reference_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Gets a reference set. For the definitions of references and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.getReferenceSet.

Parameters:

  • reference_set_id (String) —

    The ID of the reference set.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



2188
2189
2190
2191
2192
2193
2194
2195
2196
 
# File 'generated/google/apis/genomics_v1/service.rb', line 2188

def get_reference_set(reference_set_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Gets a variant by ID. For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics

Parameters:

  • variant_id (String) —

    The ID of the variant.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1033
1034
1035
1036
1037
1038
1039
1040
1041
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1033

def get_variant(variant_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Gets a variant set by ID. For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics

Parameters:

  • variant_set_id (String) —

    Required. The ID of the variant set.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1767
1768
1769
1770
1771
1772
1773
1774
1775
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1767

def get_variantset(variant_set_id, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Creates read group sets by asynchronously importing the provided information. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics 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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



115
116
117
118
119
120
121
122
123
124
 
# File 'generated/google/apis/genomics_v1/service.rb', line 115

def import_read_group_sets(import_read_group_sets_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

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

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



819
820
821
822
823
824
825
826
827
828
 
# File 'generated/google/apis/genomics_v1/service.rb', line 819

def import_variants(import_variants_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#list_coverage_buckets(read_group_set_id, reference_name: nil, end_: nil, page_token: nil, page_size: nil, start: nil, target_bucket_width: nil, quota_user: nil, fields: 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. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics Coverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several precomputed bucket widths, enabling retrieval of various coverage 'zoom levels'. The caller must have READ permissions for the target read group set.

Parameters:

  • read_group_set_id (String) —

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

  • reference_name (String) —

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

  • end_ (String) —

    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_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.

  • page_size (Fixnum) —

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

  • start (String) —

    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 (String) —

    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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
 
# File 'generated/google/apis/genomics_v1/service.rb', line 336

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

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

Lists datasets within a project. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics

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.

  • project_id (String) —

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

  • 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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1472

def list_datasets(page_size: nil, project_id: nil, page_token: nil, quota_user: nil, fields: 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['projectId'] = project_id unless project_id.nil?
  command.query['pageToken'] = page_token unless page_token.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Lists operations that match the specified filter in the request.

Parameters:

  • name (String) —

    The name of the operation collection.

  • page_size (Fixnum) —

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

    1. The maximum value is 2048.
  • filter (String) —

    A string for filtering Operations. The following filter fields are supported:

    • projectId: Required. Corresponds to OperationMetadata.projectId.
    • createTime: The time this job was created, in seconds from the epoch. 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_token (String) —

    The standard list page token.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



2081
2082
2083
2084
2085
2086
2087
2088
2089
2090
2091
2092
 
# File 'generated/google/apis/genomics_v1/service.rb', line 2081

def list_operations(name, page_size: nil, filter: nil, page_token: nil, quota_user: nil, fields: 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['pageSize'] = page_size unless page_size.nil?
  command.query['filter'] = filter unless filter.nil?
  command.query['pageToken'] = page_token unless page_token.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Lists the bases in a reference, optionally restricted to a range. For the definitions of references and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.getReferenceBases.

Parameters:

  • reference_id (String) —

    The ID of the reference.

  • end_position (String) —

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

  • 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.

  • 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).

  • start_position (String) —

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

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1198

def list_reference_bases(reference_id, end_position: nil, page_token: nil, page_size: nil, start_position: nil, quota_user: nil, fields: 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['pageToken'] = page_token unless page_token.nil?
  command.query['pageSize'] = page_size unless page_size.nil?
  command.query['start'] = start_position unless start_position.nil?
  command.query['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Merges the given variants with existing variants. For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics Each variant will be merged with an existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant. Variant info fields are merged as specified in the infoMergeConfig field of the MergeVariantsRequest. Please exercise caution when using this method! It is easy to introduce mistakes in existing variants and difficult to back out of them. For example, suppose you were trying to merge a new variant with an existing one and both variants contain calls that belong to callsets with the same callset ID. // Existing variant - irrelevant fields trimmed for clarity "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 0, 1 ], ] // New variant with conflicting call information "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], ] The resulting merged variant would overwrite the existing calls with those from the new variant: "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], ] This may be the desired outcome, but it is up to the user to determine if if that is indeed the case.

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



930
931
932
933
934
935
936
937
938
939
 
# File 'generated/google/apis/genomics_v1/service.rb', line 930

def merge_variants(merge_variants_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Updates a call set. For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics 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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



500
501
502
503
504
505
506
507
508
509
510
511
 
# File 'generated/google/apis/genomics_v1/service.rb', line 500

def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Updates a dataset. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics 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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1352

def patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Updates a read group set. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics 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.
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



235
236
237
238
239
240
241
242
243
244
245
246
 
# File 'generated/google/apis/genomics_v1/service.rb', line 235

def patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Updates a variant. For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics 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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1074

def patch_variant(variant_id, variant_object = nil, update_mask: nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Updates a variant set using patch semantics. For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics

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.
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1731
1732
1733
1734
1735
1736
1737
1738
1739
1740
1741
1742
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1731

def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#search_annotations(search_annotations_request_object = nil, quota_user: nil, fields: 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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1888
1889
1890
1891
1892
1893
1894
1895
1896
1897
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1888

def search_annotations(search_annotations_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, quota_user: nil, fields: 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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



669
670
671
672
673
674
675
676
677
678
 
# File 'generated/google/apis/genomics_v1/service.rb', line 669

def search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Gets a list of call sets matching the criteria. For the definitions of call sets and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.searchCallSets.

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



459
460
461
462
463
464
465
466
467
468
 
# File 'generated/google/apis/genomics_v1/service.rb', line 459

def search_call_sets(search_call_sets_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Searches for read group sets matching the criteria. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.searchReadGroupSets.

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



192
193
194
195
196
197
198
199
200
201
 
# File 'generated/google/apis/genomics_v1/service.rb', line 192

def search_read_group_sets(search_read_group_sets_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Gets a list of reads for one or more read group sets. For the definitions of read group sets and other genomics resources, see Fundamentals of Google Genomics 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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



390
391
392
393
394
395
396
397
398
399
 
# File 'generated/google/apis/genomics_v1/service.rb', line 390

def search_reads(search_reads_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Searches for reference sets which match the given criteria. For the definitions of references and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.searchReferenceSets

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



2151
2152
2153
2154
2155
2156
2157
2158
2159
2160
 
# File 'generated/google/apis/genomics_v1/service.rb', line 2151

def search_reference_sets(search_reference_sets_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Searches for references which match the given criteria. For the definitions of references and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.searchReferences.

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1112

def search_references(search_references_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Returns a list of all variant sets matching search criteria. For the definitions of variant sets and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.searchVariantSets.

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1689

def search_variant_sets(search_variant_sets_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Gets a list of variants matching the criteria. For the definitions of variants and other genomics resources, see Fundamentals of Google Genomics Implements GlobalAllianceApi.searchVariants.

Parameters:

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

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



999
1000
1001
1002
1003
1004
1005
1006
1007
1008
 
# File 'generated/google/apis/genomics_v1/service.rb', line 999

def search_variants(search_variants_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Sets the access control policy on the specified dataset. Replaces any existing policy. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics 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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1545

def set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, quota_user: nil, fields: 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. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics

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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1392

def test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

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

Undeletes a dataset by restoring a dataset which was deleted via this API. For the definitions of datasets and other genomics resources, see Fundamentals of Google Genomics 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)
  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1277

def undelete_dataset(dataset_id, undelete_dataset_request_object = nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#update_annotation(annotation_id, annotation_object = nil, update_mask: nil, quota_user: nil, fields: 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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



1959
1960
1961
1962
1963
1964
1965
1966
1967
1968
1969
1970
 
# File 'generated/google/apis/genomics_v1/service.rb', line 1959

def update_annotation(annotation_id, annotation_object = nil, update_mask: nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end

#update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, quota_user: nil, fields: 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.

  • 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.

  • fields (String) —

    Selector specifying which fields to include in a partial response.

  • options (Google::Apis::RequestOptions) —

    Request-specific options

Yields:

  • (result, err) —

    Result & error if block supplied

Yield Parameters:

Returns:

Raises:



740
741
742
743
744
745
746
747
748
749
750
751
 
# File 'generated/google/apis/genomics_v1/service.rb', line 740

def update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, quota_user: nil, fields: 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['quotaUser'] = quota_user unless quota_user.nil?
  command.query['fields'] = fields unless fields.nil?
  execute_or_queue_command(command, &block)
end