google-api-client 0.9.26 → 0.9.28

data/generated/google/apis/genomics_v1/service.rb

@@ -46,14 +46,14 @@ module Google
           super('https://genomics.googleapis.com/', '')
         end
         
-        # Searches for reference sets which match the given criteria.
-        # For the definitions of references and other genomics resources, see
+        # Gets a list of variants matching the criteria.
+        # For the definitions of variants and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
         # Implements
-        # [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/
-        # v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
-        # @param [Google::Apis::GenomicsV1::SearchReferenceSetsRequest] search_reference_sets_request_object
+        # [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.
+        # 1/src/main/resources/avro/variantmethods.avdl#L126).
+        # @param [Google::Apis::GenomicsV1::SearchVariantsRequest] search_variants_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -63,34 +63,39 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::SearchReferenceSetsResponse]
+        # @return [Google::Apis::GenomicsV1::SearchVariantsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Gets a reference set.
-        # For the definitions of references and other genomics resources, see
+        # Updates a variant.
+        # For the definitions of variants and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Implements
-        # [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.
-        # 1/src/main/resources/avro/referencemethods.avdl#L83).
-        # @param [String] reference_set_id
-        #   The ID of the reference set.
+        # This method supports patch semantics. Returns the modified variant without
+        # its calls.
+        # @param [String] variant_id
+        #   The ID of the variant to be updated.
+        # @param [Google::Apis::GenomicsV1::Variant] variant_object
+        # @param [String] update_mask
+        #   An optional mask specifying which fields to update. At this time, mutable
+        #   fields are names and
+        #   info. Acceptable values are "names" and
+        #   "info". If unspecified, all mutable fields will be updated.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -100,39 +105,33 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::ReferenceSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::ReferenceSet]
+        # @return [Google::Apis::GenomicsV1::Variant]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Creates read group sets by asynchronously importing the provided
-        # information.
-        # For the definitions of read group sets and other genomics resources, see
+        # Gets a variant by ID.
+        # For the definitions of variants and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # The caller must have WRITE permissions to the dataset.
-        # ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
-        # - Tags will be converted to strings - tag types are not preserved
-        # - Comments (`@CO`) in the input file header will not be preserved
-        # - Original header order of references (`@SQ`) will not be preserved
-        # - Any reverse stranded unmapped reads will be reverse complemented, and
-        # their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
-        # - Unmapped reads will be stripped of positional information (reference name
-        # and position)
-        # @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_request_object
+        # @param [String] variant_id
+        #   The ID of the variant.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -142,32 +141,40 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Operation]
+        # @return [Google::Apis::GenomicsV1::Variant]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Deletes a read group set.
-        # For the definitions of read group sets and other genomics resources, see
+        # Creates variant data by asynchronously importing the provided information.
+        # For the definitions of variant sets and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] read_group_set_id
-        #   The ID of the read group set to be deleted. The caller must have WRITE
-        #   permissions to the dataset associated with this read group set.
+        # The variants for import will be merged with any existing variant that
+        # matches its reference sequence, start, end, reference bases, and
+        # alternative bases. If no such variant exists, a new one will be created.
+        # When variants are merged, the call information from the new variant
+        # is added to the existing variant, and Variant info fields are merged
+        # as specified in
+        # infoMergeConfig.
+        # As a special case, for single-sample VCF files, QUAL and FILTER fields will
+        # be moved to the call level; these are sometimes interpreted in a
+        # call-specific context.
+        # Imported VCF headers are appended to the metadata already in a variant set.
+        # @param [Google::Apis::GenomicsV1::ImportVariantsRequest] import_variants_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -177,36 +184,108 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Empty]
+        # @return [Google::Apis::GenomicsV1::Operation]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # 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
+        # Merges the given variants with existing variants.
+        # For the definitions of variants and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Note that currently there may be some differences between exported BAM
-        # files and the original BAM file at the time of import. See
-        # ImportReadGroupSets
-        # for caveats.
-        # @param [String] read_group_set_id
-        #   Required. The ID of the read group set to export. The caller must have
-        #   READ access to this read group set.
-        # @param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_request_object
+        # Each variant will be
+        # merged with an existing variant that matches its reference sequence,
+        # start, end, reference bases, and alternative bases. If no such variant
+        # exists, a new one will be created.
+        # When variants are merged, the call information from the new variant
+        # is added to the existing variant. Variant info fields are merged as
+        # specified in the
+        # infoMergeConfig
+        # field of the MergeVariantsRequest.
+        # Please exercise caution when using this method!  It is easy to introduce
+        # mistakes in existing variants and difficult to back out of them.  For
+        # example,
+        # suppose you were trying to merge a new variant with an existing one and
+        # both
+        # variants contain calls that belong to callsets with the same callset ID.
+        # // Existing variant - irrelevant fields trimmed for clarity
+        # `
+        # "variantSetId": "10473108253681171589",
+        # "referenceName": "1",
+        # "start": "10582",
+        # "referenceBases": "G",
+        # "alternateBases": [
+        # "A"
+        # ],
+        # "calls": [
+        # `
+        # "callSetId": "10473108253681171589-0",
+        # "callSetName": "CALLSET0",
+        # "genotype": [
+        # 0,
+        # 1
+        # ],
+        # `
+        # ]
+        # `
+        # // New variant with conflicting call information
+        # `
+        # "variantSetId": "10473108253681171589",
+        # "referenceName": "1",
+        # "start": "10582",
+        # "referenceBases": "G",
+        # "alternateBases": [
+        # "A"
+        # ],
+        # "calls": [
+        # `
+        # "callSetId": "10473108253681171589-0",
+        # "callSetName": "CALLSET0",
+        # "genotype": [
+        # 1,
+        # 1
+        # ],
+        # `
+        # ]
+        # `
+        # The resulting merged variant would overwrite the existing calls with those
+        # from the new variant:
+        # `
+        # "variantSetId": "10473108253681171589",
+        # "referenceName": "1",
+        # "start": "10582",
+        # "referenceBases": "G",
+        # "alternateBases": [
+        # "A"
+        # ],
+        # "calls": [
+        # `
+        # "callSetId": "10473108253681171589-0",
+        # "callSetName": "CALLSET0",
+        # "genotype": [
+        # 1,
+        # 1
+        # ],
+        # `
+        # ]
+        # `
+        # This may be the desired outcome, but it is up to the user to determine if
+        # if that is indeed the case.
+        # @param [Google::Apis::GenomicsV1::MergeVariantsRequest] merge_variants_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -216,34 +295,31 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Operation]
+        # @return [Google::Apis::GenomicsV1::Empty]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Searches for read group sets matching the criteria.
-        # For the definitions of read group sets and other genomics resources, see
+        # Deletes a variant.
+        # For the definitions of variants and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Implements
-        # [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/
-        # v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
-        # @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_request_object
+        # @param [String] variant_id
+        #   The ID of the variant to be deleted.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -253,40 +329,29 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse]
+        # @return [Google::Apis::GenomicsV1::Empty]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Updates a read group set.
-        # For the definitions of read group sets and other genomics resources, see
+        # Creates a new variant.
+        # For the definitions of variants and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # This method supports patch semantics.
-        # @param [String] read_group_set_id
-        #   The ID of the read group set to be updated. The caller must have WRITE
-        #   permissions to the dataset associated with this read group set.
-        # @param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object
-        # @param [String] update_mask
-        #   An optional mask specifying which fields to update. Supported fields:
-        #   * name.
-        #   * referenceSetId.
-        #   Leaving `updateMask` unset is equivalent to specifying all mutable
-        #   fields.
+        # @param [Google::Apis::GenomicsV1::Variant] variant_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -296,33 +361,29 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::ReadGroupSet]
+        # @return [Google::Apis::GenomicsV1::Variant]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Gets a read group set by ID.
-        # For the definitions of read group sets and other genomics resources, see
-        # [Fundamentals of Google
-        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] read_group_set_id
-        #   The ID of the read group set.
+        # Deletes an annotation set. Caller must have WRITE permission
+        # for the associated annotation set.
+        # @param [String] annotation_set_id
+        #   The ID of the annotation set to be deleted.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -332,62 +393,30 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::ReadGroupSet]
+        # @return [Google::Apis::GenomicsV1::Empty]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Coverage is defined as the number of reads which are aligned to a given
-        # base in the reference sequence. Coverage buckets are available at several
-        # precomputed bucket widths, enabling retrieval of various coverage 'zoom
-        # levels'. The caller must have READ permissions for the target read group
-        # set.
-        # @param [String] read_group_set_id
-        #   Required. The ID of the read group set over which coverage is requested.
-        # @param [String] end_
-        #   The end position of the range on the reference, 0-based exclusive. If
-        #   specified, `referenceName` must also be specified. If unset or 0, defaults
-        #   to the length of the reference.
-        # @param [String] page_token
-        #   The continuation token, which is used to page through large result sets.
-        #   To get the next page of results, set this parameter to the value of
-        #   `nextPageToken` from the previous response.
-        # @param [Fixnum] page_size
-        #   The maximum number of results to return in a single page. If unspecified,
-        #   defaults to 1024. The maximum value is 2048.
-        # @param [String] start
-        #   The start position of the range on the reference, 0-based inclusive. If
-        #   specified, `referenceName` must also be specified. Defaults to 0.
-        # @param [String] target_bucket_width
-        #   The desired width of each reported coverage bucket in base pairs. This
-        #   will be rounded down to the nearest precomputed bucket width; the value
-        #   of which is returned as `bucketWidth` in the response. Defaults
-        #   to infinity (each bucket spans an entire reference sequence) or the length
-        #   of the target range, if specified. The smallest precomputed
-        #   `bucketWidth` is currently 2048 base pairs; this is subject to
-        #   change.
-        # @param [String] reference_name
-        #   The name of the reference to query, within the reference set associated
-        #   with this query. Optional.
+        # Searches for annotation sets that match the given criteria. Annotation sets
+        # are returned in an unspecified order. This order is consistent, such that
+        # two queries for the same content (regardless of page size) yield annotation
+        # sets in the same order across their respective streams of paginated
+        # responses. Caller must have READ permission for the queried datasets.
+        # @param [Google::Apis::GenomicsV1::SearchAnnotationSetsRequest] search_annotation_sets_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -397,51 +426,29 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse]
+        # @return [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        def list_coverage_buckets(read_group_set_id, end_: nil, page_token: nil, page_size: nil, start: nil, target_bucket_width: nil, reference_name: 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['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['referenceName'] = reference_name unless reference_name.nil?
+        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
         
-        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Reads search operates over a genomic coordinate space of reference sequence
-        # & position defined over the reference sequences to which the requested
-        # read group sets are aligned.
-        # If a target positional range is specified, search returns all reads whose
-        # alignment to the reference genome overlap the range. A query which
-        # specifies only read group set IDs yields all reads in those read group
-        # sets, including unmapped reads.
-        # All reads returned (including reads on subsequent pages) are ordered by
-        # genomic coordinate (by reference sequence, then position). Reads with
-        # equivalent genomic coordinates are returned in an unspecified order. This
-        # order is consistent, such that two queries for the same content (regardless
-        # of page size) yield reads in the same order across their respective streams
-        # of paginated responses.
-        # Implements
-        # [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/
-        # src/main/resources/avro/readmethods.avdl#L85).
-        # @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_request_object
+        # Gets an annotation set. Caller must have READ permission for
+        # the associated dataset.
+        # @param [String] annotation_set_id
+        #   The ID of the annotation set to be retrieved.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -451,31 +458,36 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::SearchReadsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::SearchReadsResponse]
+        # @return [Google::Apis::GenomicsV1::AnnotationSet]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Deletes a call set.
-        # For the definitions of call sets and other genomics resources, see
-        # [Fundamentals of Google
-        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] call_set_id
-        #   The ID of the call set to be deleted.
+        # Updates an annotation set. The update must respect all mutability
+        # restrictions and other invariants described on the annotation set resource.
+        # Caller must have WRITE permission for the associated dataset.
+        # @param [String] annotation_set_id
+        #   The ID of the annotation set to be updated.
+        # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object
+        # @param [String] update_mask
+        #   An optional mask specifying which fields to update. Mutable fields are
+        #   name,
+        #   source_uri, and
+        #   info. If unspecified, all
+        #   mutable fields will be updated.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -485,32 +497,35 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Empty]
+        # @return [Google::Apis::GenomicsV1::AnnotationSet]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Gets a list of call sets matching the criteria.
-        # For the definitions of call sets and other genomics resources, see
-        # [Fundamentals of Google
-        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Implements
-        # [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.
-        # 1/src/main/resources/avro/variantmethods.avdl#L178).
-        # @param [Google::Apis::GenomicsV1::SearchCallSetsRequest] search_call_sets_request_object
+        # Creates a new annotation set. Caller must have WRITE permission for the
+        # associated dataset.
+        # The following fields are required:
+        # * datasetId
+        # * referenceSetId
+        # All other fields may be optionally specified, unless documented as being
+        # server-generated (for example, the `id` field).
+        # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -520,38 +535,33 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::SearchCallSetsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::SearchCallSetsResponse]
+        # @return [Google::Apis::GenomicsV1::AnnotationSet]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Updates a call set.
-        # For the definitions of call sets and other genomics resources, see
+        # Searches for references which match the given criteria.
+        # For the definitions of references and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # This method supports patch semantics.
-        # @param [String] call_set_id
-        #   The ID of the call set to be updated.
-        # @param [Google::Apis::GenomicsV1::CallSet] call_set_object
-        # @param [String] update_mask
-        #   An optional mask specifying which fields to update. At this time, the only
-        #   mutable field is name. The only
-        #   acceptable value is "name". If unspecified, all mutable fields will be
-        #   updated.
+        # Implements
+        # [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.
+        # 5.1/src/main/resources/avro/referencemethods.avdl#L146).
+        # @param [Google::Apis::GenomicsV1::SearchReferencesRequest] search_references_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -561,33 +571,34 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::SearchReferencesResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::CallSet]
+        # @return [Google::Apis::GenomicsV1::SearchReferencesResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Gets a call set by ID.
-        # For the definitions of call sets and other genomics resources, see
+        # Gets a reference.
+        # For the definitions of references and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] call_set_id
-        #   The ID of the call set.
+        # Implements
+        # [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/
+        # src/main/resources/avro/referencemethods.avdl#L158).
+        # @param [String] reference_id
+        #   The ID of the reference.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -597,29 +608,46 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Reference] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::CallSet]
+        # @return [Google::Apis::GenomicsV1::Reference]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Creates a new call set.
-        # For the definitions of call sets and other genomics resources, see
+        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [Google::Apis::GenomicsV1::CallSet] call_set_object
+        # Implements
+        # [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.
+        # 5.1/src/main/resources/avro/referencemethods.avdl#L221).
+        # @param [String] reference_id
+        #   The ID of the reference.
+        # @param [String] start_position
+        #   The start position (0-based) of this query. Defaults to 0.
+        # @param [String] end_position
+        #   The end position (0-based, exclusive) of this query. Defaults to the length
+        #   of this reference.
+        # @param [String] page_token
+        #   The continuation token, which is used to page through large result sets.
+        #   To get the next page of results, set this parameter to the value of
+        #   `nextPageToken` from the previous response.
+        # @param [Fixnum] page_size
+        #   The maximum number of bases to return in a single page. If unspecified,
+        #   defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base
+        #   pairs).
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -629,29 +657,41 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::ListBasesResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::CallSet]
+        # @return [Google::Apis::GenomicsV1::ListBasesResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        def list_reference_bases(reference_id, start_position: nil, end_position: nil, page_token: nil, page_size: 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['start'] = start_position unless start_position.nil?
+          command.query['end'] = end_position unless end_position.nil?
+          command.query['pageToken'] = page_token unless page_token.nil?
+          command.query['pageSize'] = page_size unless page_size.nil?
           command.query['quotaUser'] = quota_user unless quota_user.nil?
           command.query['fields'] = fields unless fields.nil?
           execute_or_queue_command(command, &block)
         end
         
-        # Deletes an annotation set. Caller must have WRITE permission
-        # for the associated annotation set.
-        # @param [String] annotation_set_id
-        #   The ID of the annotation set to be deleted.
+        # Updates a dataset.
+        # For the definitions of datasets and other genomics resources, see
+        # [Fundamentals of Google
+        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # This method supports patch semantics.
+        # @param [String] dataset_id
+        #   The ID of the dataset to be updated.
+        # @param [Google::Apis::GenomicsV1::Dataset] dataset_object
+        # @param [String] update_mask
+        #   An optional mask specifying which fields to update. At this time, the only
+        #   mutable field is name. The only
+        #   acceptable value is "name". If unspecified, all mutable fields will be
+        #   updated.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -661,30 +701,33 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Empty]
+        # @return [Google::Apis::GenomicsV1::Dataset]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Searches for annotation sets that match the given criteria. Annotation sets
-        # are returned in an unspecified order. This order is consistent, such that
-        # two queries for the same content (regardless of page size) yield annotation
-        # sets in the same order across their respective streams of paginated
-        # responses. Caller must have READ permission for the queried datasets.
-        # @param [Google::Apis::GenomicsV1::SearchAnnotationSetsRequest] search_annotation_sets_request_object
+        # Gets a dataset by ID.
+        # For the definitions of datasets and other genomics resources, see
+        # [Fundamentals of Google
+        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # @param [String] dataset_id
+        #   The ID of the dataset.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -694,29 +737,32 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse]
+        # @return [Google::Apis::GenomicsV1::Dataset]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Gets an annotation set. Caller must have READ permission for
-        # the associated dataset.
-        # @param [String] annotation_set_id
-        #   The ID of the annotation set to be retrieved.
+        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # This operation is only possible for a week after the deletion occurred.
+        # @param [String] dataset_id
+        #   The ID of the dataset to be undeleted.
+        # @param [Google::Apis::GenomicsV1::UndeleteDatasetRequest] undelete_dataset_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -726,36 +772,36 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::AnnotationSet]
+        # @return [Google::Apis::GenomicsV1::Dataset]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Updates an annotation set. The update must respect all mutability
-        # restrictions and other invariants described on the annotation set resource.
-        # Caller must have WRITE permission for the associated dataset.
-        # @param [String] annotation_set_id
-        #   The ID of the annotation set to be updated.
-        # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object
-        # @param [String] update_mask
-        #   An optional mask specifying which fields to update. Mutable fields are
-        #   name,
-        #   source_uri, and
-        #   info. If unspecified, all
-        #   mutable fields will be updated.
+        # Returns permissions that a caller has on the specified resource.
+        # See <a href="/iam/docs/managing-policies#testing_permissions">Testing
+        # Permissions</a> for more information.
+        # For the definitions of datasets and other genomics resources, see
+        # [Fundamentals of Google
+        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # @param [String] resource
+        #   REQUIRED: The resource for which policy is being specified. Format is
+        #   `datasets/<dataset ID>`.
+        # @param [Google::Apis::GenomicsV1::TestIamPermissionsRequest] test_iam_permissions_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -765,35 +811,37 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::TestIamPermissionsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::AnnotationSet]
+        # @return [Google::Apis::GenomicsV1::TestIamPermissionsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Creates a new annotation set. Caller must have WRITE permission for the
-        # associated dataset.
-        # The following fields are required:
-        # * datasetId
-        # * referenceSetId
-        # All other fields may be optionally specified, unless documented as being
-        # server-generated (for example, the `id` field).
-        # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object
+        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # @param [String] dataset_id
+        #   The ID of the dataset to be deleted.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -803,66 +851,37 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::AnnotationSet]
+        # @return [Google::Apis::GenomicsV1::Empty]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Creates a new variant.
-        # For the definitions of variants and other genomics resources, see
+        # Lists datasets within a project.
+        # For the definitions of datasets and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [Google::Apis::GenomicsV1::Variant] variant_object
-        # @param [String] quota_user
-        #   Available to use for quota purposes for server-side applications. Can be any
-        #   arbitrary string assigned to a user, but should not exceed 40 characters.
-        # @param [String] fields
-        #   Selector specifying which fields to include in a partial response.
-        # @param [Google::Apis::RequestOptions] options
-        #   Request-specific options
-        #
-        # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
-        # @yieldparam err [StandardError] error object if request failed
-        #
-        # @return [Google::Apis::GenomicsV1::Variant]
-        #
-        # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
-        # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
-        # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
-        
-        # Gets a list of variants matching the criteria.
-        # For the definitions of variants and other genomics resources, see
-        # [Fundamentals of Google
-        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Implements
-        # [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.
-        # 1/src/main/resources/avro/variantmethods.avdl#L126).
-        # @param [Google::Apis::GenomicsV1::SearchVariantsRequest] search_variants_request_object
+        # @param [String] page_token
+        #   The continuation token, which is used to page through large result sets.
+        #   To get the next page of results, set this parameter to the value of
+        #   `nextPageToken` from the previous response.
+        # @param [Fixnum] page_size
+        #   The maximum number of results to return in a single page. If unspecified,
+        #   defaults to 50. The maximum value is 1024.
+        # @param [String] project_id
+        #   Required. The Google Cloud project ID to list datasets for.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -872,39 +891,37 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::ListDatasetsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::SearchVariantsResponse]
+        # @return [Google::Apis::GenomicsV1::ListDatasetsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        def list_datasets(page_token: nil, page_size: nil, project_id: 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['pageToken'] = page_token unless page_token.nil?
+          command.query['pageSize'] = page_size unless page_size.nil?
+          command.query['projectId'] = project_id unless project_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
         
-        # Updates a variant.
-        # For the definitions of variants and other genomics resources, see
+        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # This method supports patch semantics. Returns the modified variant without
-        # its calls.
-        # @param [String] variant_id
-        #   The ID of the variant to be updated.
-        # @param [Google::Apis::GenomicsV1::Variant] variant_object
-        # @param [String] update_mask
-        #   An optional mask specifying which fields to update. At this time, mutable
-        #   fields are names and
-        #   info. Acceptable values are "names" and
-        #   "info". If unspecified, all mutable fields will be updated.
+        # See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
+        # Policy</a> for more information.
+        # @param [String] resource
+        #   REQUIRED: The resource for which policy is being specified. Format is
+        #   `datasets/<dataset ID>`.
+        # @param [Google::Apis::GenomicsV1::SetIamPolicyRequest] set_iam_policy_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -914,33 +931,31 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Variant]
+        # @return [Google::Apis::GenomicsV1::Policy]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Gets a variant by ID.
-        # For the definitions of variants and other genomics resources, see
+        # Creates a new dataset.
+        # For the definitions of datasets and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] variant_id
-        #   The ID of the variant.
+        # @param [Google::Apis::GenomicsV1::Dataset] dataset_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -950,30 +965,36 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Variant]
+        # @return [Google::Apis::GenomicsV1::Dataset]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Deletes a variant.
-        # For the definitions of variants and other genomics resources, see
+        # Gets the access control policy for the dataset. This is empty if the
+        # policy or resource does not exist.
+        # See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
+        # Policy</a> for more information.
+        # For the definitions of datasets and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] variant_id
-        #   The ID of the variant to be deleted.
+        # @param [String] resource
+        #   REQUIRED: The resource for which policy is being specified. Format is
+        #   `datasets/<dataset ID>`.
+        # @param [Google::Apis::GenomicsV1::GetIamPolicyRequest] get_iam_policy_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -983,40 +1004,30 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Empty]
+        # @return [Google::Apis::GenomicsV1::Policy]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Creates variant data by asynchronously importing the provided information.
-        # For the definitions of variant sets and other genomics resources, see
-        # [Fundamentals of Google
-        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # The variants for import will be merged with any existing variant that
-        # matches its reference sequence, start, end, reference bases, and
-        # alternative bases. If no such variant exists, a new one will be created.
-        # When variants are merged, the call information from the new variant
-        # is added to the existing variant, and Variant info fields are merged
-        # as specified in
-        # infoMergeConfig.
-        # As a special case, for single-sample VCF files, QUAL and FILTER fields will
-        # be moved to the call level; these are sometimes interpreted in a
-        # call-specific context.
-        # Imported VCF headers are appended to the metadata already in a variant set.
-        # @param [Google::Apis::GenomicsV1::ImportVariantsRequest] import_variants_request_object
+        # Deletes an annotation. Caller must have WRITE permission for
+        # the associated annotation set.
+        # @param [String] annotation_id
+        #   The ID of the annotation to be deleted.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1026,108 +1037,41 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Operation]
+        # @return [Google::Apis::GenomicsV1::Empty]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Merges the given variants with existing variants.
-        # For the definitions of variants and other genomics resources, see
-        # [Fundamentals of Google
-        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Each variant will be
-        # merged with an existing variant that matches its reference sequence,
-        # start, end, reference bases, and alternative bases. If no such variant
-        # exists, a new one will be created.
-        # When variants are merged, the call information from the new variant
-        # is added to the existing variant. Variant info fields are merged as
-        # specified in the
-        # infoMergeConfig
-        # field of the MergeVariantsRequest.
-        # Please exercise caution when using this method!  It is easy to introduce
-        # mistakes in existing variants and difficult to back out of them.  For
-        # example,
-        # suppose you were trying to merge a new variant with an existing one and
-        # both
-        # variants contain calls that belong to callsets with the same callset ID.
-        # // Existing variant - irrelevant fields trimmed for clarity
-        # `
-        # "variantSetId": "10473108253681171589",
-        # "referenceName": "1",
-        # "start": "10582",
-        # "referenceBases": "G",
-        # "alternateBases": [
-        # "A"
-        # ],
-        # "calls": [
-        # `
-        # "callSetId": "10473108253681171589-0",
-        # "callSetName": "CALLSET0",
-        # "genotype": [
-        # 0,
-        # 1
-        # ],
-        # `
-        # ]
-        # `
-        # // New variant with conflicting call information
-        # `
-        # "variantSetId": "10473108253681171589",
-        # "referenceName": "1",
-        # "start": "10582",
-        # "referenceBases": "G",
-        # "alternateBases": [
-        # "A"
-        # ],
-        # "calls": [
-        # `
-        # "callSetId": "10473108253681171589-0",
-        # "callSetName": "CALLSET0",
-        # "genotype": [
-        # 1,
-        # 1
-        # ],
-        # `
-        # ]
-        # `
-        # The resulting merged variant would overwrite the existing calls with those
-        # from the new variant:
-        # `
-        # "variantSetId": "10473108253681171589",
-        # "referenceName": "1",
-        # "start": "10582",
-        # "referenceBases": "G",
-        # "alternateBases": [
-        # "A"
-        # ],
-        # "calls": [
-        # `
-        # "callSetId": "10473108253681171589-0",
-        # "callSetName": "CALLSET0",
-        # "genotype": [
-        # 1,
-        # 1
-        # ],
-        # `
-        # ]
-        # `
-        # This may be the desired outcome, but it is up to the user to determine if
-        # if that is indeed the case.
-        # @param [Google::Apis::GenomicsV1::MergeVariantsRequest] merge_variants_request_object
+        # Creates a new annotation. Caller must have WRITE permission
+        # for the associated annotation set.
+        # The following fields are required:
+        # * annotationSetId
+        # * referenceName or
+        # referenceId
+        # ### Transcripts
+        # For annotations of type TRANSCRIPT, the following fields of
+        # transcript must be provided:
+        # * exons.start
+        # * exons.end
+        # All other fields may be optionally specified, unless documented as being
+        # server-generated (for example, the `id` field). The annotated
+        # range must be no longer than 100Mbp (mega base pairs). See the
+        # Annotation resource
+        # for additional restrictions on each field.
+        # @param [Google::Apis::GenomicsV1::Annotation] annotation_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1137,33 +1081,38 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Empty]
+        # @return [Google::Apis::GenomicsV1::Annotation]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Searches for references which match the given criteria.
-        # For the definitions of references and other genomics resources, see
-        # [Fundamentals of Google
-        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Implements
-        # [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.
-        # 5.1/src/main/resources/avro/referencemethods.avdl#L146).
-        # @param [Google::Apis::GenomicsV1::SearchReferencesRequest] search_references_request_object
+        # Creates one or more new annotations atomically. All annotations must
+        # belong to the same annotation set. Caller must have WRITE
+        # permission for this annotation set. For optimal performance, batch
+        # positionally adjacent annotations together.
+        # If the request has a systemic issue, such as an attempt to write to
+        # an inaccessible annotation set, the entire RPC will fail accordingly. For
+        # lesser data issues, when possible an error will be isolated to the
+        # corresponding batch entry in the response; the remaining well formed
+        # annotations will be created normally.
+        # For details on the requirements for each individual annotation resource,
+        # see
+        # CreateAnnotation.
+        # @param [Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest] batch_create_annotations_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1173,34 +1122,33 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::SearchReferencesResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::SearchReferencesResponse]
+        # @return [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Gets a reference.
-        # For the definitions of references and other genomics resources, see
-        # [Fundamentals of Google
-        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Implements
-        # [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/
-        # src/main/resources/avro/referencemethods.avdl#L158).
-        # @param [String] reference_id
-        #   The ID of the reference.
+        # Searches for annotations that match the given criteria. Results are
+        # ordered by genomic coordinate (by reference sequence, then position).
+        # Annotations with equivalent genomic coordinates are returned in an
+        # unspecified order. This order is consistent, such that two queries for the
+        # same content (regardless of page size) yield annotations in the same order
+        # across their respective streams of paginated responses. Caller must have
+        # READ permission for the queried annotation sets.
+        # @param [Google::Apis::GenomicsV1::SearchAnnotationsRequest] search_annotations_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1210,46 +1158,29 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Reference] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Reference]
+        # @return [Google::Apis::GenomicsV1::SearchAnnotationsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Implements
-        # [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.
-        # 5.1/src/main/resources/avro/referencemethods.avdl#L221).
-        # @param [String] reference_id
-        #   The ID of the reference.
-        # @param [String] start_position
-        #   The start position (0-based) of this query. Defaults to 0.
-        # @param [String] end_position
-        #   The end position (0-based, exclusive) of this query. Defaults to the length
-        #   of this reference.
-        # @param [String] page_token
-        #   The continuation token, which is used to page through large result sets.
-        #   To get the next page of results, set this parameter to the value of
-        #   `nextPageToken` from the previous response.
-        # @param [Fixnum] page_size
-        #   The maximum number of bases to return in a single page. If unspecified,
-        #   defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base
-        #   pairs).
+        # Gets an annotation. Caller must have READ permission
+        # for the associated annotation set.
+        # @param [String] annotation_id
+        #   The ID of the annotation to be retrieved.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1259,39 +1190,36 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::ListBasesResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::ListBasesResponse]
+        # @return [Google::Apis::GenomicsV1::Annotation]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        def list_reference_bases(reference_id, start_position: nil, end_position: nil, page_token: nil, page_size: 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['start'] = start_position unless start_position.nil?
-          command.query['end'] = end_position unless end_position.nil?
-          command.query['pageToken'] = page_token unless page_token.nil?
-          command.query['pageSize'] = page_size unless page_size.nil?
+        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
         
-        # Gets the access control policy for the dataset. This is empty if the
-        # policy or resource does not exist.
-        # See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
-        # Policy</a> for more information.
-        # For the definitions of datasets and other genomics resources, see
-        # [Fundamentals of Google
-        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] resource
-        #   REQUIRED: The resource for which policy is being specified. Format is
-        #   `datasets/<dataset ID>`.
-        # @param [Google::Apis::GenomicsV1::GetIamPolicyRequest] get_iam_policy_request_object
+        # Updates an annotation. Caller must have
+        # WRITE permission for the associated dataset.
+        # @param [String] annotation_id
+        #   The ID of the annotation to be updated.
+        # @param [Google::Apis::GenomicsV1::Annotation] annotation_object
+        # @param [String] update_mask
+        #   An optional mask specifying which fields to update. Mutable fields are
+        #   name,
+        #   variant,
+        #   transcript, and
+        #   info. If unspecified, all mutable
+        #   fields will be updated.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1301,39 +1229,35 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Policy]
+        # @return [Google::Apis::GenomicsV1::Annotation]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Updates a dataset.
-        # For the definitions of datasets and other genomics resources, see
+        # Exports variant set data to an external destination.
+        # For the definitions of variant sets and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # This method supports patch semantics.
-        # @param [String] dataset_id
-        #   The ID of the dataset to be updated.
-        # @param [Google::Apis::GenomicsV1::Dataset] dataset_object
-        # @param [String] update_mask
-        #   An optional mask specifying which fields to update. At this time, the only
-        #   mutable field is name. The only
-        #   acceptable value is "name". If unspecified, all mutable fields will be
-        #   updated.
+        # @param [String] variant_set_id
+        #   Required. The ID of the variant set that contains variant data which
+        #   should be exported. The caller must have READ access to this variant set.
+        # @param [Google::Apis::GenomicsV1::ExportVariantSetRequest] export_variant_set_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1343,33 +1267,34 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Dataset]
+        # @return [Google::Apis::GenomicsV1::Operation]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Gets a dataset by ID.
-        # For the definitions of datasets and other genomics resources, see
+        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] dataset_id
-        #   The ID of the dataset.
+        # Implements
+        # [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.
+        # 5.1/src/main/resources/avro/variantmethods.avdl#L49).
+        # @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1379,32 +1304,72 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantSetsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Dataset]
+        # @return [Google::Apis::GenomicsV1::SearchVariantSetsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
+        
+        # Gets a variant set by ID.
+        # For the definitions of variant sets and other genomics resources, see
+        # [Fundamentals of Google
+        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # @param [String] variant_set_id
+        #   Required. The ID of the variant set.
+        # @param [String] quota_user
+        #   Available to use for quota purposes for server-side applications. Can be any
+        #   arbitrary string assigned to a user, but should not exceed 40 characters.
+        # @param [String] fields
+        #   Selector specifying which fields to include in a partial response.
+        # @param [Google::Apis::RequestOptions] options
+        #   Request-specific options
+        #
+        # @yield [result, err] Result & error if block supplied
+        # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
+        # @yieldparam err [StandardError] error object if request failed
+        #
+        # @return [Google::Apis::GenomicsV1::VariantSet]
+        #
+        # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
+        # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
+        # @raise [Google::Apis::AuthorizationError] Authorization is required
+        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
         
-        # Undeletes a dataset by restoring a dataset which was deleted via this API.
-        # For the definitions of datasets and other genomics resources, see
+        # Updates a variant set using patch semantics.
+        # For the definitions of variant sets and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # This operation is only possible for a week after the deletion occurred.
-        # @param [String] dataset_id
-        #   The ID of the dataset to be undeleted.
-        # @param [Google::Apis::GenomicsV1::UndeleteDatasetRequest] undelete_dataset_request_object
+        # @param [String] variant_set_id
+        #   The ID of the variant to be updated (must already exist).
+        # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
+        # @param [String] update_mask
+        #   An optional mask specifying which fields to update. Supported fields:
+        #   * metadata.
+        #   * name.
+        #   * description.
+        #   Leaving `updateMask` unset is equivalent to specifying all mutable
+        #   fields.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1414,36 +1379,34 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Dataset]
+        # @return [Google::Apis::GenomicsV1::VariantSet]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Returns permissions that a caller has on the specified resource.
-        # See <a href="/iam/docs/managing-policies#testing_permissions">Testing
-        # Permissions</a> for more information.
-        # For the definitions of datasets and other genomics resources, see
+        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] resource
-        #   REQUIRED: The resource for which policy is being specified. Format is
-        #   `datasets/<dataset ID>`.
-        # @param [Google::Apis::GenomicsV1::TestIamPermissionsRequest] test_iam_permissions_request_object
+        # @param [String] variant_set_id
+        #   The ID of the variant set to be deleted.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1453,37 +1416,32 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::TestIamPermissionsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::TestIamPermissionsResponse]
+        # @return [Google::Apis::GenomicsV1::Empty]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # 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
+        # Creates a new variant set.
+        # For the definitions of variant sets and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] dataset_id
-        #   The ID of the dataset to be deleted.
+        # The provided variant set must have a valid `datasetId` set - all other
+        # fields are optional. Note that the `id` field will be ignored, as this is
+        # assigned by the server.
+        # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1493,37 +1451,32 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Empty]
+        # @return [Google::Apis::GenomicsV1::VariantSet]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Lists datasets within a project.
-        # For the definitions of datasets and other genomics resources, see
-        # [Fundamentals of Google
-        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] page_token
-        #   The continuation token, which is used to page through large result sets.
-        #   To get the next page of results, set this parameter to the value of
-        #   `nextPageToken` from the previous response.
-        # @param [Fixnum] page_size
-        #   The maximum number of results to return in a single page. If unspecified,
-        #   defaults to 50. The maximum value is 1024.
-        # @param [String] project_id
-        #   Required. The Google Cloud project ID to list datasets for.
+        # Starts asynchronous cancellation on a long-running operation. The server makes
+        # a best effort to cancel the operation, but success is not guaranteed. Clients
+        # may use Operations.GetOperation or Operations.ListOperations to check whether
+        # the cancellation succeeded or the operation completed despite cancellation.
+        # @param [String] name
+        #   The name of the operation resource to be cancelled.
+        # @param [Google::Apis::GenomicsV1::CancelOperationRequest] cancel_operation_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1533,37 +1486,51 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::ListDatasetsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::ListDatasetsResponse]
+        # @return [Google::Apis::GenomicsV1::Empty]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        def list_datasets(page_token: nil, page_size: nil, project_id: 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['pageToken'] = page_token unless page_token.nil?
-          command.query['pageSize'] = page_size unless page_size.nil?
-          command.query['projectId'] = project_id unless project_id.nil?
+        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
         
-        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
-        # Policy</a> for more information.
-        # @param [String] resource
-        #   REQUIRED: The resource for which policy is being specified. Format is
-        #   `datasets/<dataset ID>`.
-        # @param [Google::Apis::GenomicsV1::SetIamPolicyRequest] set_iam_policy_request_object
+        # Lists operations that match the specified filter in the request.
+        # @param [String] name
+        #   The name of the operation collection.
+        # @param [Fixnum] page_size
+        #   The maximum number of results to return. If unspecified, defaults to
+        #   256. The maximum value is 2048.
+        # @param [String] filter
+        #   A string for filtering Operations.
+        #   The following filter fields are supported&#58;
+        #   * projectId&#58; Required. Corresponds to
+        #   OperationMetadata.projectId.
+        #   * createTime&#58; The time this job was created, in seconds from the
+        #   [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`
+        #   operators.
+        #   * status&#58; Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only
+        #   one status may be specified.
+        #   * labels.key where key is a label key.
+        #   Examples&#58;
+        #   * `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`
+        # @param [String] page_token
+        #   The standard list page token.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1573,31 +1540,32 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::ListOperationsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Policy]
+        # @return [Google::Apis::GenomicsV1::ListOperationsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Creates a new dataset.
-        # For the definitions of datasets and other genomics resources, see
-        # [Fundamentals of Google
-        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [Google::Apis::GenomicsV1::Dataset] dataset_object
+        # Gets the latest state of a long-running operation.  Clients can use this
+        # method to poll the operation result at intervals as recommended by the API
+        # service.
+        # @param [String] name
+        #   The name of the operation resource.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1607,32 +1575,32 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Dataset]
+        # @return [Google::Apis::GenomicsV1::Operation]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # 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
+        # Searches for reference sets which match the given criteria.
+        # For the definitions of references and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] variant_set_id
-        #   The ID of the variant set to be deleted.
+        # Implements
+        # [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/
+        # v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
+        # @param [Google::Apis::GenomicsV1::SearchReferenceSetsRequest] search_reference_sets_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1642,32 +1610,34 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Empty]
+        # @return [Google::Apis::GenomicsV1::SearchReferenceSetsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Creates a new variant set.
-        # For the definitions of variant sets and other genomics resources, see
+        # Gets a reference set.
+        # For the definitions of references and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # The provided variant set must have a valid `datasetId` set - all other
-        # fields are optional. Note that the `id` field will be ignored, as this is
-        # assigned by the server.
-        # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
+        # Implements
+        # [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.
+        # 1/src/main/resources/avro/referencemethods.avdl#L83).
+        # @param [String] reference_set_id
+        #   The ID of the reference set.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1677,33 +1647,31 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::ReferenceSet] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::VariantSet]
+        # @return [Google::Apis::GenomicsV1::ReferenceSet]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Exports variant set data to an external destination.
-        # For the definitions of variant sets and other genomics resources, see
+        # Deletes a read group set.
+        # For the definitions of read group sets and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] variant_set_id
-        #   Required. The ID of the variant set that contains variant data which
-        #   should be exported. The caller must have READ access to this variant set.
-        # @param [Google::Apis::GenomicsV1::ExportVariantSetRequest] export_variant_set_request_object
+        # @param [String] read_group_set_id
+        #   The ID of the read group set to be deleted. The caller must have WRITE
+        #   permissions to the dataset associated with this read group set.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1713,34 +1681,39 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Operation]
+        # @return [Google::Apis::GenomicsV1::Empty]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Returns a list of all variant sets matching search criteria.
-        # For the definitions of variant sets and other genomics resources, see
+        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # Implements
-        # [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.
-        # 5.1/src/main/resources/avro/variantmethods.avdl#L49).
-        # @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_request_object
+        # The caller must have WRITE permissions to the dataset.
+        # ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
+        # - Tags will be converted to strings - tag types are not preserved
+        # - Comments (`@CO`) in the input file header will not be preserved
+        # - Original header order of references (`@SQ`) will not be preserved
+        # - Any reverse stranded unmapped reads will be reverse complemented, and
+        # their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
+        # - Unmapped reads will be stripped of positional information (reference name
+        # and position)
+        # @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1750,31 +1723,37 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantSetsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::SearchVariantSetsResponse]
+        # @return [Google::Apis::GenomicsV1::Operation]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Gets a variant set by ID.
-        # For the definitions of variant sets and other genomics resources, see
+        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] variant_set_id
-        #   Required. The ID of the variant set.
+        # 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.
+        # @param [String] read_group_set_id
+        #   Required. The ID of the read group set to export. The caller must have
+        #   READ access to this read group set.
+        # @param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1784,38 +1763,34 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::VariantSet]
+        # @return [Google::Apis::GenomicsV1::Operation]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Updates a variant set using patch semantics.
-        # For the definitions of variant sets and other genomics resources, see
+        # Searches for read group sets matching the criteria.
+        # For the definitions of read group sets and other genomics resources, see
         # [Fundamentals of Google
         # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
-        # @param [String] variant_set_id
-        #   The ID of the variant to be updated (must already exist).
-        # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
-        # @param [String] update_mask
-        #   An optional mask specifying which fields to update. Supported fields:
-        #   * metadata.
-        #   * name.
-        #   * description.
-        #   Leaving `updateMask` unset is equivalent to specifying all mutable
-        #   fields.
+        # Implements
+        # [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/
+        # v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
+        # @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1825,40 +1800,31 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::VariantSet]
+        # @return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Creates one or more new annotations atomically. All annotations must
-        # belong to the same annotation set. Caller must have WRITE
-        # permission for this annotation set. For optimal performance, batch
-        # positionally adjacent annotations together.
-        # If the request has a systemic issue, such as an attempt to write to
-        # an inaccessible annotation set, the entire RPC will fail accordingly. For
-        # lesser data issues, when possible an error will be isolated to the
-        # corresponding batch entry in the response; the remaining well formed
-        # annotations will be created normally.
-        # For details on the requirements for each individual annotation resource,
-        # see
-        # CreateAnnotation.
-        # @param [Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest] batch_create_annotations_request_object
+        # Gets a read group set by ID.
+        # For the definitions of read group sets and other genomics resources, see
+        # [Fundamentals of Google
+        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # @param [String] read_group_set_id
+        #   The ID of the read group set.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1868,33 +1834,39 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse]
+        # @return [Google::Apis::GenomicsV1::ReadGroupSet]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Searches for annotations that match the given criteria. Results are
-        # ordered by genomic coordinate (by reference sequence, then position).
-        # Annotations with equivalent genomic coordinates are returned in an
-        # unspecified order. This order is consistent, such that two queries for the
-        # same content (regardless of page size) yield annotations in the same order
-        # across their respective streams of paginated responses. Caller must have
-        # READ permission for the queried annotation sets.
-        # @param [Google::Apis::GenomicsV1::SearchAnnotationsRequest] search_annotations_request_object
+        # Updates a read group set.
+        # For the definitions of read group sets and other genomics resources, see
+        # [Fundamentals of Google
+        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # This method supports patch semantics.
+        # @param [String] read_group_set_id
+        #   The ID of the read group set to be updated. The caller must have WRITE
+        #   permissions to the dataset associated with this read group set.
+        # @param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object
+        # @param [String] update_mask
+        #   An optional mask specifying which fields to update. Supported fields:
+        #   * name.
+        #   * referenceSetId.
+        #   Leaving `updateMask` unset is equivalent to specifying all mutable
+        #   fields.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1904,29 +1876,65 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::SearchAnnotationsResponse]
+        # @return [Google::Apis::GenomicsV1::ReadGroupSet]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Gets an annotation. Caller must have READ permission
-        # for the associated annotation set.
-        # @param [String] annotation_id
-        #   The ID of the annotation to be retrieved.
+        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # Coverage is defined as the number of reads which are aligned to a given
+        # base in the reference sequence. Coverage buckets are available at several
+        # precomputed bucket widths, enabling retrieval of various coverage 'zoom
+        # levels'. The caller must have READ permissions for the target read group
+        # set.
+        # @param [String] read_group_set_id
+        #   Required. The ID of the read group set over which coverage is requested.
+        # @param [String] end_
+        #   The end position of the range on the reference, 0-based exclusive. If
+        #   specified, `referenceName` must also be specified. If unset or 0, defaults
+        #   to the length of the reference.
+        # @param [String] page_token
+        #   The continuation token, which is used to page through large result sets.
+        #   To get the next page of results, set this parameter to the value of
+        #   `nextPageToken` from the previous response.
+        # @param [Fixnum] page_size
+        #   The maximum number of results to return in a single page. If unspecified,
+        #   defaults to 1024. The maximum value is 2048.
+        # @param [String] start
+        #   The start position of the range on the reference, 0-based inclusive. If
+        #   specified, `referenceName` must also be specified. Defaults to 0.
+        # @param [String] target_bucket_width
+        #   The desired width of each reported coverage bucket in base pairs. This
+        #   will be rounded down to the nearest precomputed bucket width; the value
+        #   of which is returned as `bucketWidth` in the response. Defaults
+        #   to infinity (each bucket spans an entire reference sequence) or the length
+        #   of the target range, if specified. The smallest precomputed
+        #   `bucketWidth` is currently 2048 base pairs; this is subject to
+        #   change.
+        # @param [String] reference_name
+        #   The name of the reference to query, within the reference set associated
+        #   with this query. Optional.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1936,36 +1944,51 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Annotation]
+        # @return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        def list_coverage_buckets(read_group_set_id, end_: nil, page_token: nil, page_size: nil, start: nil, target_bucket_width: nil, reference_name: 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['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['referenceName'] = reference_name unless reference_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
         
-        # Updates an annotation. Caller must have
-        # WRITE permission for the associated dataset.
-        # @param [String] annotation_id
-        #   The ID of the annotation to be updated.
-        # @param [Google::Apis::GenomicsV1::Annotation] annotation_object
-        # @param [String] update_mask
-        #   An optional mask specifying which fields to update. Mutable fields are
-        #   name,
-        #   variant,
-        #   transcript, and
-        #   info. If unspecified, all mutable
-        #   fields will be updated.
+        # 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # Reads search operates over a genomic coordinate space of reference sequence
+        # & position defined over the reference sequences to which the requested
+        # read group sets are aligned.
+        # If a target positional range is specified, search returns all reads whose
+        # alignment to the reference genome overlap the range. A query which
+        # specifies only read group set IDs yields all reads in those read group
+        # sets, including unmapped reads.
+        # All reads returned (including reads on subsequent pages) are ordered by
+        # genomic coordinate (by reference sequence, then position). Reads with
+        # equivalent genomic coordinates are returned in an unspecified order. This
+        # order is consistent, such that two queries for the same content (regardless
+        # of page size) yield reads in the same order across their respective streams
+        # of paginated responses.
+        # Implements
+        # [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/
+        # src/main/resources/avro/readmethods.avdl#L85).
+        # @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -1975,31 +1998,33 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::SearchReadsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Annotation]
+        # @return [Google::Apis::GenomicsV1::SearchReadsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Deletes an annotation. Caller must have WRITE permission for
-        # the associated annotation set.
-        # @param [String] annotation_id
-        #   The ID of the annotation to be deleted.
+        # Gets a list of call sets matching the criteria.
+        # For the definitions of call sets and other genomics resources, see
+        # [Fundamentals of Google
+        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # Implements
+        # [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.
+        # 1/src/main/resources/avro/variantmethods.avdl#L178).
+        # @param [Google::Apis::GenomicsV1::SearchCallSetsRequest] search_call_sets_request_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -2009,41 +2034,38 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::SearchCallSetsResponse] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Empty]
+        # @return [Google::Apis::GenomicsV1::SearchCallSetsResponse]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Creates a new annotation. Caller must have WRITE permission
-        # for the associated annotation set.
-        # The following fields are required:
-        # * annotationSetId
-        # * referenceName or
-        # referenceId
-        # ### Transcripts
-        # For annotations of type TRANSCRIPT, the following fields of
-        # transcript must be provided:
-        # * exons.start
-        # * exons.end
-        # All other fields may be optionally specified, unless documented as being
-        # server-generated (for example, the `id` field). The annotated
-        # range must be no longer than 100Mbp (mega base pairs). See the
-        # Annotation resource
-        # for additional restrictions on each field.
-        # @param [Google::Apis::GenomicsV1::Annotation] annotation_object
+        # Updates a call set.
+        # For the definitions of call sets and other genomics resources, see
+        # [Fundamentals of Google
+        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # This method supports patch semantics.
+        # @param [String] call_set_id
+        #   The ID of the call set to be updated.
+        # @param [Google::Apis::GenomicsV1::CallSet] call_set_object
+        # @param [String] update_mask
+        #   An optional mask specifying which fields to update. At this time, the only
+        #   mutable field is name. The only
+        #   acceptable value is "name". If unspecified, all mutable fields will be
+        #   updated.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -2053,32 +2075,33 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Annotation]
+        # @return [Google::Apis::GenomicsV1::CallSet]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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
+        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
         
-        # Starts asynchronous cancellation on a long-running operation. The server makes
-        # a best effort to cancel the operation, but success is not guaranteed. Clients
-        # may use Operations.GetOperation or Operations.ListOperations to check whether
-        # the cancellation succeeded or the operation completed despite cancellation.
-        # @param [String] name
-        #   The name of the operation resource to be cancelled.
-        # @param [Google::Apis::GenomicsV1::CancelOperationRequest] cancel_operation_request_object
+        # Gets a call set by ID.
+        # For the definitions of call sets and other genomics resources, see
+        # [Fundamentals of Google
+        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # @param [String] call_set_id
+        #   The ID of the call set.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -2088,51 +2111,29 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Empty]
+        # @return [Google::Apis::GenomicsV1::CallSet]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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
         
-        # Lists operations that match the specified filter in the request.
-        # @param [String] name
-        #   The name of the operation collection.
-        # @param [String] page_token
-        #   The standard list page token.
-        # @param [Fixnum] page_size
-        #   The maximum number of results to return. If unspecified, defaults to
-        #   256. The maximum value is 2048.
-        # @param [String] filter
-        #   A string for filtering Operations.
-        #   The following filter fields are supported&#58;
-        #   * projectId&#58; Required. Corresponds to
-        #   OperationMetadata.projectId.
-        #   * createTime&#58; The time this job was created, in seconds from the
-        #   [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`
-        #   operators.
-        #   * status&#58; Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only
-        #   one status may be specified.
-        #   * labels.key where key is a label key.
-        #   Examples&#58;
-        #   * `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`
+        # Creates a new call set.
+        # For the definitions of call sets and other genomics resources, see
+        # [Fundamentals of Google
+        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # @param [Google::Apis::GenomicsV1::CallSet] call_set_object
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -2142,32 +2143,31 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::ListOperationsResponse] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::ListOperationsResponse]
+        # @return [Google::Apis::GenomicsV1::CallSet]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        def list_operations(name, page_token: nil, page_size: nil, filter: 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['pageToken'] = page_token unless page_token.nil?
-          command.query['pageSize'] = page_size unless page_size.nil?
-          command.query['filter'] = filter unless filter.nil?
+        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
         
-        # Gets the latest state of a long-running operation.  Clients can use this
-        # method to poll the operation result at intervals as recommended by the API
-        # service.
-        # @param [String] name
-        #   The name of the operation resource.
+        # Deletes a call set.
+        # For the definitions of call sets and other genomics resources, see
+        # [Fundamentals of Google
+        # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+        # @param [String] call_set_id
+        #   The ID of the call set to be deleted.
         # @param [String] quota_user
         #   Available to use for quota purposes for server-side applications. Can be any
         #   arbitrary string assigned to a user, but should not exceed 40 characters.
@@ -2177,19 +2177,19 @@ module Google
         #   Request-specific options
         #
         # @yield [result, err] Result & error if block supplied
-        # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
+        # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
         # @yieldparam err [StandardError] error object if request failed
         #
-        # @return [Google::Apis::GenomicsV1::Operation]
+        # @return [Google::Apis::GenomicsV1::Empty]
         #
         # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
         # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
         # @raise [Google::Apis::AuthorizationError] Authorization is required
-        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?
+        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)