Class: Google::Apis::GenomicsV1::GenomicsService
- Inherits:
-
Core::BaseService
- Object
- Core::BaseService
- Google::Apis::GenomicsV1::GenomicsService
- Defined in:
- generated/google/apis/genomics_v1/service.rb
Overview
Genomics API
Upload, process, query, and search Genomics data in the cloud.
Instance Attribute Summary collapse
-
#key ⇒ String
API key.
-
#quota_user ⇒ String
Available to use for quota purposes for server-side applications.
Attributes inherited from Core::BaseService
#authorization, #base_path, #batch_path, #client, #client_options, #request_options, #root_url, #upload_path
Instance Method Summary collapse
-
#batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse
Creates one or more new annotations atomically.
-
#cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Starts asynchronous cancellation on a long-running operation.
-
#create_annotation(annotation_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Annotation
Creates a new annotation.
-
#create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::AnnotationSet
Creates a new annotation set.
-
#create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::CallSet
Creates a new call set.
-
#create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset
Creates a new dataset.
-
#create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Variant
Creates a new variant.
-
#create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::VariantSet
Creates a new variant set.
-
#delete_annotation(annotation_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes an annotation.
-
#delete_annotationset(annotation_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes an annotation set.
-
#delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes a call set.
-
#delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes a dataset and all of its contents (all read group sets, reference sets, variant sets, call sets, annotation sets, etc.) This is reversible (up to one week after the deletion) via the datasets.undelete operation.
-
#delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes a read group set.
-
#delete_variant(variant_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes a variant.
-
#delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes a variant set including all variants, call sets, and calls within.
-
#export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation
Exports a read group set to a BAM file in Google Cloud Storage.
-
#export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation
Exports variant set data to an external destination.
-
#get_annotation(annotation_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Annotation
Gets an annotation.
-
#get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::AnnotationSet
Gets an annotation set.
-
#get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::CallSet
Gets a call set by ID.
-
#get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset
Gets a dataset by ID.
-
#get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Policy
Gets the access control policy for the dataset.
-
#get_operation(name, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation
Gets the latest state of a long-running operation.
-
#get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ReadGroupSet
Gets a read group set by ID.
-
#get_reference(reference_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Reference
Gets a reference.
-
#get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ReferenceSet
Gets a reference set.
-
#get_variant(variant_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Variant
Gets a variant by ID.
-
#get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::VariantSet
Gets a variant set by ID.
-
#import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation
Creates read group sets by asynchronously importing the provided information.
-
#import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation
Creates variant data by asynchronously importing the provided information.
-
#initialize ⇒ GenomicsService
constructor
A new instance of GenomicsService.
-
#list_coverage_buckets(read_group_set_id, end_: nil, page_size: nil, page_token: nil, reference_name: nil, start: nil, target_bucket_width: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListCoverageBucketsResponse
Lists fixed width coverage buckets for a read group set, each of which correspond to a range of a reference sequence.
-
#list_datasets(page_size: nil, page_token: nil, project_id: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListDatasetsResponse
Lists datasets within a project.
-
#list_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListOperationsResponse
Lists operations that match the specified filter in the request.
-
#list_reference_bases(reference_id, end_position: nil, page_size: nil, page_token: nil, start_position: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListBasesResponse
Lists the bases in a reference, optionally restricted to a range.
-
#merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Merges the given variants with existing variants.
-
#patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::CallSet
Updates a call set.
-
#patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset
Updates a dataset.
-
#patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ReadGroupSet
Updates a read group set.
-
#patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Variant
Updates a variant.
-
#patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::VariantSet
Updates a variant set using patch semantics.
-
#search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchAnnotationsResponse
Searches for annotations that match the given criteria.
-
#search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchAnnotationSetsResponse
Searches for annotation sets that match the given criteria.
-
#search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchCallSetsResponse
Gets a list of call sets matching the criteria.
-
#search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReadGroupSetsResponse
Searches for read group sets matching the criteria.
-
#search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReadsResponse
Gets a list of reads for one or more read group sets.
-
#search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReferenceSetsResponse
Searches for reference sets which match the given criteria.
-
#search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReferencesResponse
Searches for references which match the given criteria.
-
#search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchVariantSetsResponse
Returns a list of all variant sets matching search criteria.
-
#search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchVariantsResponse
Gets a list of variants matching the criteria.
-
#set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Policy
Sets the access control policy on the specified dataset.
-
#test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::TestIamPermissionsResponse
Returns permissions that a caller has on the specified resource.
-
#undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset
Undeletes a dataset by restoring a dataset which was deleted via this API.
-
#update_annotation(annotation_id, annotation_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Annotation
Updates an annotation.
-
#update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::AnnotationSet
Updates an annotation set.
Methods inherited from Core::BaseService
#batch, #batch_upload, #fetch_all, #http
Methods included from Core::Logging
Constructor Details
#initialize ⇒ GenomicsService
Returns a new instance of GenomicsService
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# File 'generated/google/apis/genomics_v1/service.rb', line 45 def initialize super('https://genomics.googleapis.com/', '') @batch_path = 'batch' end |
Instance Attribute Details
#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.
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# 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.
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# File 'generated/google/apis/genomics_v1/service.rb', line 43 def quota_user @quota_user end |
Instance Method Details
#batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse
Creates one or more new annotations atomically. All annotations must belong to the same annotation set. Caller must have WRITE permission for this annotation set. For optimal performance, batch positionally adjacent annotations together. If the request has a systemic issue, such as an attempt to write to an inaccessible annotation set, the entire RPC will fail accordingly. For lesser data issues, when possible an error will be isolated to the corresponding batch entry in the response; the remaining well formed annotations will be created normally. For details on the requirements for each individual annotation resource, see CreateAnnotation.
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# File 'generated/google/apis/genomics_v1/service.rb', line 80 def batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/annotations:batchCreate', ) command.request_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest::Representation command.request_object = batch_create_annotations_request_object command.response_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse::Representation command.response_class = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Starts asynchronous cancellation on a long-running operation. The server makes a best effort to cancel the operation, but success is not guaranteed. Clients may use Operations.GetOperation or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite cancellation.
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# File 'generated/google/apis/genomics_v1/service.rb', line 955 def cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/{+name}:cancel', ) command.request_representation = Google::Apis::GenomicsV1::CancelOperationRequest::Representation command.request_object = cancel_operation_request_object command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['name'] = name unless name.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#create_annotation(annotation_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Annotation
Creates a new annotation. Caller must have WRITE permission for the associated annotation set. The following fields are required:
- annotationSetId
- referenceName or referenceId ### Transcripts For annotations of type TRANSCRIPT, the following fields of transcript must be provided:
- exons.start
- exons.end
All other fields may be optionally specified, unless documented as being
server-generated (for example, the
id
field). The annotated range must be no longer than 100Mbp (mega base pairs). See the Annotation resource for additional restrictions on each field.
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# File 'generated/google/apis/genomics_v1/service.rb', line 125 def create_annotation(annotation_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/annotations', ) command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation command.request_object = annotation_object command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation command.response_class = Google::Apis::GenomicsV1::Annotation command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::AnnotationSet
Creates a new annotation set. Caller must have WRITE permission for the associated dataset. The following fields are required:
- datasetId
- referenceSetId
All other fields may be optionally specified, unless documented as being
server-generated (for example, the
id
field).
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# File 'generated/google/apis/genomics_v1/service.rb', line 301 def create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/annotationsets', ) command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation command.request_object = annotation_set_object command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation command.response_class = Google::Apis::GenomicsV1::AnnotationSet command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::CallSet
Creates a new call set.
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# File 'generated/google/apis/genomics_v1/service.rb', line 469 def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/callsets', ) command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation command.request_object = call_set_object command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation command.response_class = Google::Apis::GenomicsV1::CallSet command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset
Creates a new dataset.
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# File 'generated/google/apis/genomics_v1/service.rb', line 632 def create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/datasets', ) command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation command.request_object = dataset_object command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation command.response_class = Google::Apis::GenomicsV1::Dataset command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Variant
Creates a new variant.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1591 def create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variants', ) command.request_representation = Google::Apis::GenomicsV1::Variant::Representation command.request_object = variant_object command.response_representation = Google::Apis::GenomicsV1::Variant::Representation command.response_class = Google::Apis::GenomicsV1::Variant command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::VariantSet
Creates a new variant set.
The provided variant set must have a valid datasetId
set - all other
fields are optional. Note that the id
field will be ignored, as this is
assigned by the server.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1907 def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variantsets', ) command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation command.request_object = variant_set_object command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation command.response_class = Google::Apis::GenomicsV1::VariantSet command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#delete_annotation(annotation_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes an annotation. Caller must have WRITE permission for the associated annotation set.
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# File 'generated/google/apis/genomics_v1/service.rb', line 157 def delete_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/annotations/{annotationId}', ) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#delete_annotationset(annotation_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes an annotation set. Caller must have WRITE permission for the associated annotation set.
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# File 'generated/google/apis/genomics_v1/service.rb', line 333 def delete_annotationset(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/annotationsets/{annotationSetId}', ) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes a call set.
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# File 'generated/google/apis/genomics_v1/service.rb', line 500 def delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/callsets/{callSetId}', ) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['callSetId'] = call_set_id unless call_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes a dataset and all of its contents (all read group sets, reference sets, variant sets, call sets, annotation sets, etc.) This is reversible (up to one week after the deletion) via the datasets.undelete operation.
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# File 'generated/google/apis/genomics_v1/service.rb', line 668 def delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/datasets/{datasetId}', ) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['datasetId'] = dataset_id unless dataset_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes a read group set.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1083 def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/readgroupsets/{readGroupSetId}', ) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#delete_variant(variant_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes a variant.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1622 def delete_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/variants/{variantId}', ) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['variantId'] = variant_id unless variant_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Deletes a variant set including all variants, call sets, and calls within. This is not reversible.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1939 def delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:delete, 'v1/variantsets/{variantSetId}', ) command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation
Exports a read group set to a BAM file in Google Cloud Storage. Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. See ImportReadGroupSets for caveats.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1119 def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/readgroupsets/{readGroupSetId}:export', ) command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation command.request_object = export_read_group_set_request_object command.response_representation = Google::Apis::GenomicsV1::Operation::Representation command.response_class = Google::Apis::GenomicsV1::Operation command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation
Exports variant set data to an external destination.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1971 def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variantsets/{variantSetId}:export', ) command.request_representation = Google::Apis::GenomicsV1::ExportVariantSetRequest::Representation command.request_object = export_variant_set_request_object command.response_representation = Google::Apis::GenomicsV1::Operation::Representation command.response_class = Google::Apis::GenomicsV1::Operation command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#get_annotation(annotation_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Annotation
Gets an annotation. Caller must have READ permission for the associated annotation set.
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# File 'generated/google/apis/genomics_v1/service.rb', line 188 def get_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/annotations/{annotationId}', ) command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation command.response_class = Google::Apis::GenomicsV1::Annotation command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::AnnotationSet
Gets an annotation set. Caller must have READ permission for the associated dataset.
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# File 'generated/google/apis/genomics_v1/service.rb', line 364 def get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/annotationsets/{annotationSetId}', ) command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation command.response_class = Google::Apis::GenomicsV1::AnnotationSet command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::CallSet
Gets a call set by ID.
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# File 'generated/google/apis/genomics_v1/service.rb', line 530 def get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/callsets/{callSetId}', ) command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation command.response_class = Google::Apis::GenomicsV1::CallSet command.params['callSetId'] = call_set_id unless call_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset
Gets a dataset by ID.
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# File 'generated/google/apis/genomics_v1/service.rb', line 698 def get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/datasets/{datasetId}', ) command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation command.response_class = Google::Apis::GenomicsV1::Dataset command.params['datasetId'] = dataset_id unless dataset_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Policy
Gets the access control policy for the dataset. This is empty if the policy or resource does not exist. See Getting a Policy for more information.
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# File 'generated/google/apis/genomics_v1/service.rb', line 733 def get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/{+resource}:getIamPolicy', ) command.request_representation = Google::Apis::GenomicsV1::GetIamPolicyRequest::Representation command.request_object = get_iam_policy_request_object command.response_representation = Google::Apis::GenomicsV1::Policy::Representation command.response_class = Google::Apis::GenomicsV1::Policy command.params['resource'] = resource unless resource.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#get_operation(name, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation
Gets the latest state of a long-running operation. Clients can use this method to poll the operation result at intervals as recommended by the API service.
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# File 'generated/google/apis/genomics_v1/service.rb', line 989 def get_operation(name, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/{+name}', ) command.response_representation = Google::Apis::GenomicsV1::Operation::Representation command.response_class = Google::Apis::GenomicsV1::Operation command.params['name'] = name unless name.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ReadGroupSet
Gets a read group set by ID.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1151 def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}', ) command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation command.response_class = Google::Apis::GenomicsV1::ReadGroupSet command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#get_reference(reference_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Reference
Gets a reference. Implements GlobalAllianceApi.getReference.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1413 def get_reference(reference_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/references/{referenceId}', ) command.response_representation = Google::Apis::GenomicsV1::Reference::Representation command.response_class = Google::Apis::GenomicsV1::Reference command.params['referenceId'] = reference_id unless reference_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ReferenceSet
Gets a reference set. Implements GlobalAllianceApi.getReferenceSet.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1529 def get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/referencesets/{referenceSetId}', ) command.response_representation = Google::Apis::GenomicsV1::ReferenceSet::Representation command.response_class = Google::Apis::GenomicsV1::ReferenceSet command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#get_variant(variant_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Variant
Gets a variant by ID.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1652 def get_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/variants/{variantId}', ) command.response_representation = Google::Apis::GenomicsV1::Variant::Representation command.response_class = Google::Apis::GenomicsV1::Variant command.params['variantId'] = variant_id unless variant_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::VariantSet
Gets a variant set by ID.
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# File 'generated/google/apis/genomics_v1/service.rb', line 2003 def get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/variantsets/{variantSetId}', ) command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation command.response_class = Google::Apis::GenomicsV1::VariantSet command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation
Creates read group sets by asynchronously importing the provided information. The caller must have WRITE permissions to the dataset.
Notes on BAM import
- Tags will be converted to strings - tag types are not preserved
- Comments (
@CO
) in the input file header will not be preserved - Original header order of references (
@SQ
) will not be preserved - Any reverse stranded unmapped reads will be reverse complemented, and their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
- Unmapped reads will be stripped of positional information (reference name and position)
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# File 'generated/google/apis/genomics_v1/service.rb', line 1190 def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/readgroupsets:import', ) command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation command.request_object = import_read_group_sets_request_object command.response_representation = Google::Apis::GenomicsV1::Operation::Representation command.response_class = Google::Apis::GenomicsV1::Operation command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Operation
Creates variant data by asynchronously importing the provided information. The variants for import will be merged with any existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant, and Variant info fields are merged as specified in infoMergeConfig. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1692 def import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variants:import', ) command.request_representation = Google::Apis::GenomicsV1::ImportVariantsRequest::Representation command.request_object = import_variants_request_object command.response_representation = Google::Apis::GenomicsV1::Operation::Representation command.response_class = Google::Apis::GenomicsV1::Operation command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#list_coverage_buckets(read_group_set_id, end_: nil, page_size: nil, page_token: nil, reference_name: nil, start: nil, target_bucket_width: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListCoverageBucketsResponse
Lists fixed width coverage buckets for a read group set, each of which correspond to a range of a reference sequence. Each bucket summarizes coverage information across its corresponding genomic range. Coverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several precomputed bucket widths, enabling retrieval of various coverage 'zoom levels'. The caller must have READ permissions for the target read group set.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1328 def list_coverage_buckets(read_group_set_id, end_: nil, page_size: nil, page_token: nil, reference_name: nil, start: nil, target_bucket_width: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', ) command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['end'] = end_ unless end_.nil? command.query['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['referenceName'] = reference_name unless reference_name.nil? command.query['start'] = start unless start.nil? command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#list_datasets(page_size: nil, page_token: nil, project_id: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListDatasetsResponse
Lists datasets within a project.
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# File 'generated/google/apis/genomics_v1/service.rb', line 772 def list_datasets(page_size: nil, page_token: nil, project_id: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/datasets', ) command.response_representation = Google::Apis::GenomicsV1::ListDatasetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::ListDatasetsResponse command.query['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['projectId'] = project_id unless project_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#list_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListOperationsResponse
Lists operations that match the specified filter in the request.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1049 def list_operations(name, filter: nil, page_size: nil, page_token: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/{+name}', ) command.response_representation = Google::Apis::GenomicsV1::ListOperationsResponse::Representation command.response_class = Google::Apis::GenomicsV1::ListOperationsResponse command.params['name'] = name unless name.nil? command.query['filter'] = filter unless filter.nil? command.query['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#list_reference_bases(reference_id, end_position: nil, page_size: nil, page_token: nil, start_position: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ListBasesResponse
Lists the bases in a reference, optionally restricted to a range. Implements GlobalAllianceApi.getReferenceBases.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1492 def list_reference_bases(reference_id, end_position: nil, page_size: nil, page_token: nil, start_position: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:get, 'v1/references/{referenceId}/bases', ) command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation command.response_class = Google::Apis::GenomicsV1::ListBasesResponse command.params['referenceId'] = reference_id unless reference_id.nil? command.query['end'] = end_position unless end_position.nil? command.query['pageSize'] = page_size unless page_size.nil? command.query['pageToken'] = page_token unless page_token.nil? command.query['start'] = start_position unless start_position.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Empty
Merges the given variants with existing variants.
Each variant will be
merged with an existing variant that matches its reference sequence,
start, end, reference bases, and alternative bases. If no such variant
exists, a new one will be created.
When variants are merged, the call information from the new variant
is added to the existing variant. Variant info fields are merged as
specified in the
infoMergeConfig
field of the MergeVariantsRequest.
Please exercise caution when using this method! It is easy to introduce
mistakes in existing variants and difficult to back out of them. For
example,
suppose you were trying to merge a new variant with an existing one and
both
variants contain calls that belong to callsets with the same callset ID.
// Existing variant - irrelevant fields trimmed for clarity
"variantSetId": "10473108253681171589",
"referenceName": "1",
"start": "10582",
"referenceBases": "G",
"alternateBases": [
"A"
],
"calls": [
"callSetId": "10473108253681171589-0",
"callSetName": "CALLSET0",
"genotype": [
0,
1
],
]
// New variant with conflicting call information
"variantSetId": "10473108253681171589",
"referenceName": "1",
"start": "10582",
"referenceBases": "G",
"alternateBases": [
"A"
],
"calls": [
"callSetId": "10473108253681171589-0",
"callSetName": "CALLSET0",
"genotype": [
1,
1
],
]
The resulting merged variant would overwrite the existing calls with those
from the new variant:
"variantSetId": "10473108253681171589",
"referenceName": "1",
"start": "10582",
"referenceBases": "G",
"alternateBases": [
"A"
],
"calls": [
"callSetId": "10473108253681171589-0",
"callSetName": "CALLSET0",
"genotype": [
1,
1
],
]
This may be the desired outcome, but it is up to the user to determine if
if that is indeed the case.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1800 def merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variants:merge', ) command.request_representation = Google::Apis::GenomicsV1::MergeVariantsRequest::Representation command.request_object = merge_variants_request_object command.response_representation = Google::Apis::GenomicsV1::Empty::Representation command.response_class = Google::Apis::GenomicsV1::Empty command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::CallSet
Updates a call set. This method supports patch semantics.
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# File 'generated/google/apis/genomics_v1/service.rb', line 567 def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:patch, 'v1/callsets/{callSetId}', ) command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation command.request_object = call_set_object command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation command.response_class = Google::Apis::GenomicsV1::CallSet command.params['callSetId'] = call_set_id unless call_set_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset
Updates a dataset. This method supports patch semantics.
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# File 'generated/google/apis/genomics_v1/service.rb', line 811 def patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:patch, 'v1/datasets/{datasetId}', ) command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation command.request_object = dataset_object command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation command.response_class = Google::Apis::GenomicsV1::Dataset command.params['datasetId'] = dataset_id unless dataset_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::ReadGroupSet
Updates a read group set. This method supports patch semantics.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1230 def patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:patch, 'v1/readgroupsets/{readGroupSetId}', ) command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation command.request_object = read_group_set_object command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation command.response_class = Google::Apis::GenomicsV1::ReadGroupSet command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Variant
Updates a variant. This method supports patch semantics. Returns the modified variant without its calls.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1839 def patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:patch, 'v1/variants/{variantId}', ) command.request_representation = Google::Apis::GenomicsV1::Variant::Representation command.request_object = variant_object command.response_representation = Google::Apis::GenomicsV1::Variant::Representation command.response_class = Google::Apis::GenomicsV1::Variant command.params['variantId'] = variant_id unless variant_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::VariantSet
Updates a variant set using patch semantics.
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# File 'generated/google/apis/genomics_v1/service.rb', line 2041 def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:patch, 'v1/variantsets/{variantSetId}', ) command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation command.request_object = variant_set_object command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation command.response_class = Google::Apis::GenomicsV1::VariantSet command.params['variantSetId'] = variant_set_id unless variant_set_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchAnnotationsResponse
Searches for annotations that match the given criteria. Results are ordered by genomic coordinate (by reference sequence, then position). Annotations with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotations in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried annotation sets.
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# File 'generated/google/apis/genomics_v1/service.rb', line 223 def search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/annotations/search', ) command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationsRequest::Representation command.request_object = search_annotations_request_object command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchAnnotationsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchAnnotationSetsResponse
Searches for annotation sets that match the given criteria. Annotation sets are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotation sets in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried datasets.
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# File 'generated/google/apis/genomics_v1/service.rb', line 397 def search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/annotationsets/search', ) command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsRequest::Representation command.request_object = search_annotation_sets_request_object command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchCallSetsResponse
Gets a list of call sets matching the criteria. Implements GlobalAllianceApi.searchCallSets.
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# File 'generated/google/apis/genomics_v1/service.rb', line 602 def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/callsets/search', ) command.request_representation = Google::Apis::GenomicsV1::SearchCallSetsRequest::Representation command.request_object = search_call_sets_request_object command.response_representation = Google::Apis::GenomicsV1::SearchCallSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchCallSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReadGroupSetsResponse
Searches for read group sets matching the criteria. Implements GlobalAllianceApi.searchReadGroupSets.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1265 def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/readgroupsets/search', ) command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation command.request_object = search_read_group_sets_request_object command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReadsResponse
Gets a list of reads for one or more read group sets. Reads search operates over a genomic coordinate space of reference sequence & position defined over the reference sequences to which the requested read group sets are aligned. If a target positional range is specified, search returns all reads whose alignment to the reference genome overlap the range. A query which specifies only read group set IDs yields all reads in those read group sets, including unmapped reads. All reads returned (including reads on subsequent pages) are ordered by genomic coordinate (by reference sequence, then position). Reads with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield reads in the same order across their respective streams of paginated responses. Implements GlobalAllianceApi.searchReads.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1379 def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/reads/search', ) command.request_representation = Google::Apis::GenomicsV1::SearchReadsRequest::Representation command.request_object = search_reads_request_object command.response_representation = Google::Apis::GenomicsV1::SearchReadsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchReadsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReferenceSetsResponse
Searches for reference sets which match the given criteria. Implements GlobalAllianceApi.searchReferenceSets
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# File 'generated/google/apis/genomics_v1/service.rb', line 1561 def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/referencesets/search', ) command.request_representation = Google::Apis::GenomicsV1::SearchReferenceSetsRequest::Representation command.request_object = search_reference_sets_request_object command.response_representation = Google::Apis::GenomicsV1::SearchReferenceSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchReferenceSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchReferencesResponse
Searches for references which match the given criteria. Implements GlobalAllianceApi.searchReferences.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1445 def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/references/search', ) command.request_representation = Google::Apis::GenomicsV1::SearchReferencesRequest::Representation command.request_object = search_references_request_object command.response_representation = Google::Apis::GenomicsV1::SearchReferencesResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchReferencesResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchVariantSetsResponse
Returns a list of all variant sets matching search criteria. Implements GlobalAllianceApi.searchVariantSets.
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# File 'generated/google/apis/genomics_v1/service.rb', line 2076 def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variantsets/search', ) command.request_representation = Google::Apis::GenomicsV1::SearchVariantSetsRequest::Representation command.request_object = search_variant_sets_request_object command.response_representation = Google::Apis::GenomicsV1::SearchVariantSetsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchVariantSetsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::SearchVariantsResponse
Gets a list of variants matching the criteria. Implements GlobalAllianceApi.searchVariants.
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# File 'generated/google/apis/genomics_v1/service.rb', line 1874 def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/variants/search', ) command.request_representation = Google::Apis::GenomicsV1::SearchVariantsRequest::Representation command.request_object = search_variants_request_object command.response_representation = Google::Apis::GenomicsV1::SearchVariantsResponse::Representation command.response_class = Google::Apis::GenomicsV1::SearchVariantsResponse command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Policy
Sets the access control policy on the specified dataset. Replaces any existing policy. See Setting a Policy for more information.
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# File 'generated/google/apis/genomics_v1/service.rb', line 849 def set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/{+resource}:setIamPolicy', ) command.request_representation = Google::Apis::GenomicsV1::SetIamPolicyRequest::Representation command.request_object = set_iam_policy_request_object command.response_representation = Google::Apis::GenomicsV1::Policy::Representation command.response_class = Google::Apis::GenomicsV1::Policy command.params['resource'] = resource unless resource.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::TestIamPermissionsResponse
Returns permissions that a caller has on the specified resource. See Testing Permissions for more information.
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# File 'generated/google/apis/genomics_v1/service.rb', line 885 def (resource, = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/{+resource}:testIamPermissions', ) command.request_representation = Google::Apis::GenomicsV1::TestIamPermissionsRequest::Representation command.request_object = command.response_representation = Google::Apis::GenomicsV1::TestIamPermissionsResponse::Representation command.response_class = Google::Apis::GenomicsV1::TestIamPermissionsResponse command.params['resource'] = resource unless resource.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Dataset
Undeletes a dataset by restoring a dataset which was deleted via this API. This operation is only possible for a week after the deletion occurred.
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# File 'generated/google/apis/genomics_v1/service.rb', line 919 def undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:post, 'v1/datasets/{datasetId}:undelete', ) command.request_representation = Google::Apis::GenomicsV1::UndeleteDatasetRequest::Representation command.request_object = undelete_dataset_request_object command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation command.response_class = Google::Apis::GenomicsV1::Dataset command.params['datasetId'] = dataset_id unless dataset_id.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#update_annotation(annotation_id, annotation_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::Annotation
Updates an annotation. Caller must have WRITE permission for the associated dataset.
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# File 'generated/google/apis/genomics_v1/service.rb', line 263 def update_annotation(annotation_id, annotation_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:put, 'v1/annotations/{annotationId}', ) command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation command.request_object = annotation_object command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation command.response_class = Google::Apis::GenomicsV1::Annotation command.params['annotationId'] = annotation_id unless annotation_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |
#update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil) {|result, err| ... } ⇒ Google::Apis::GenomicsV1::AnnotationSet
Updates an annotation set. The update must respect all mutability restrictions and other invariants described on the annotation set resource. Caller must have WRITE permission for the associated dataset.
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# File 'generated/google/apis/genomics_v1/service.rb', line 437 def update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block) command = make_simple_command(:put, 'v1/annotationsets/{annotationSetId}', ) command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation command.request_object = annotation_set_object command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation command.response_class = Google::Apis::GenomicsV1::AnnotationSet command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil? command.query['updateMask'] = update_mask unless update_mask.nil? command.query['fields'] = fields unless fields.nil? command.query['quotaUser'] = quota_user unless quota_user.nil? execute_or_queue_command(command, &block) end |