2208 lines
132 KiB
Ruby
2208 lines
132 KiB
Ruby
# Copyright 2015 Google Inc.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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require 'google/apis/core/base_service'
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require 'google/apis/core/json_representation'
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require 'google/apis/core/hashable'
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require 'google/apis/errors'
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module Google
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module Apis
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module GenomicsV1
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# Genomics API
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#
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# Upload, process, query, and search Genomics data in the cloud.
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#
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# @example
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# require 'google/apis/genomics_v1'
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#
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# Genomics = Google::Apis::GenomicsV1 # Alias the module
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# service = Genomics::GenomicsService.new
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#
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# @see https://cloud.google.com/genomics
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class GenomicsService < Google::Apis::Core::BaseService
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# @return [String]
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# API key. Your API key identifies your project and provides you with API access,
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# quota, and reports. Required unless you provide an OAuth 2.0 token.
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attr_accessor :key
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# @return [String]
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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attr_accessor :quota_user
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def initialize
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super('https://genomics.googleapis.com/', '')
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end
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# Deletes a read group set.
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# For the definitions of read group sets and other genomics resources, see
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# [Fundamentals of Google
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# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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# @param [String] read_group_set_id
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# The ID of the read group set to be deleted. The caller must have WRITE
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# permissions to the dataset associated with this read group set.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::Empty]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def delete_read_group_set(read_group_set_id, quota_user: nil, fields: nil, options: nil, &block)
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command = make_simple_command(:delete, 'v1/readgroupsets/{readGroupSetId}', options)
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command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
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command.response_class = Google::Apis::GenomicsV1::Empty
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command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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command.query['fields'] = fields unless fields.nil?
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execute_or_queue_command(command, &block)
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end
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# Creates read group sets by asynchronously importing the provided
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# information.
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# For the definitions of read group sets and other genomics resources, see
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# [Fundamentals of Google
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# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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# The caller must have WRITE permissions to the dataset.
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# ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
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# - Tags will be converted to strings - tag types are not preserved
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# - Comments (`@CO`) in the input file header will not be preserved
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# - Original header order of references (`@SQ`) will not be preserved
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# - Any reverse stranded unmapped reads will be reverse complemented, and
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# their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
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# - Unmapped reads will be stripped of positional information (reference name
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# and position)
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# @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_request_object
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::Operation]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def import_read_group_sets(import_read_group_sets_request_object = nil, quota_user: nil, fields: nil, options: nil, &block)
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command = make_simple_command(:post, 'v1/readgroupsets:import', options)
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command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation
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command.request_object = import_read_group_sets_request_object
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command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
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command.response_class = Google::Apis::GenomicsV1::Operation
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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command.query['fields'] = fields unless fields.nil?
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execute_or_queue_command(command, &block)
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end
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# Exports a read group set to a BAM file in Google Cloud Storage.
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# For the definitions of read group sets and other genomics resources, see
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# [Fundamentals of Google
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# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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# Note that currently there may be some differences between exported BAM
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# files and the original BAM file at the time of import. See
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# ImportReadGroupSets
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# for caveats.
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# @param [String] read_group_set_id
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# Required. The ID of the read group set to export. The caller must have
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# READ access to this read group set.
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# @param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_request_object
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::Operation]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, quota_user: nil, fields: nil, options: nil, &block)
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command = make_simple_command(:post, 'v1/readgroupsets/{readGroupSetId}:export', options)
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command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation
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command.request_object = export_read_group_set_request_object
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command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
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command.response_class = Google::Apis::GenomicsV1::Operation
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command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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command.query['fields'] = fields unless fields.nil?
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execute_or_queue_command(command, &block)
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end
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# Searches for read group sets matching the criteria.
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# For the definitions of read group sets and other genomics resources, see
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# [Fundamentals of Google
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# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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# Implements
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# [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/
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# v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
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# @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_request_object
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def search_read_group_sets(search_read_group_sets_request_object = nil, quota_user: nil, fields: nil, options: nil, &block)
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command = make_simple_command(:post, 'v1/readgroupsets/search', options)
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command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation
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command.request_object = search_read_group_sets_request_object
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command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation
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command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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command.query['fields'] = fields unless fields.nil?
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execute_or_queue_command(command, &block)
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end
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# Updates a read group set.
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# For the definitions of read group sets and other genomics resources, see
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# [Fundamentals of Google
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# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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# This method supports patch semantics.
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# @param [String] read_group_set_id
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# The ID of the read group set to be updated. The caller must have WRITE
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# permissions to the dataset associated with this read group set.
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# @param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object
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# @param [String] update_mask
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# An optional mask specifying which fields to update. Supported fields:
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# * name.
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# * referenceSetId.
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# Leaving `updateMask` unset is equivalent to specifying all mutable
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# fields.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::ReadGroupSet]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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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)
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command = make_simple_command(:patch, 'v1/readgroupsets/{readGroupSetId}', options)
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command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
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command.request_object = read_group_set_object
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command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
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command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
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command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
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command.query['updateMask'] = update_mask unless update_mask.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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command.query['fields'] = fields unless fields.nil?
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execute_or_queue_command(command, &block)
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end
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# Gets a read group set by ID.
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# For the definitions of read group sets and other genomics resources, see
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# [Fundamentals of Google
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# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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# @param [String] read_group_set_id
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# The ID of the read group set.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::ReadGroupSet]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def get_read_group_set(read_group_set_id, quota_user: nil, fields: nil, options: nil, &block)
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command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}', options)
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command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
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command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
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command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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command.query['fields'] = fields unless fields.nil?
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execute_or_queue_command(command, &block)
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end
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# Lists fixed width coverage buckets for a read group set, each of which
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# correspond to a range of a reference sequence. Each bucket summarizes
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# coverage information across its corresponding genomic range.
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# For the definitions of read group sets and other genomics resources, see
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# [Fundamentals of Google
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# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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# Coverage is defined as the number of reads which are aligned to a given
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# base in the reference sequence. Coverage buckets are available at several
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# precomputed bucket widths, enabling retrieval of various coverage 'zoom
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# levels'. The caller must have READ permissions for the target read group
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# set.
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# @param [String] read_group_set_id
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# Required. The ID of the read group set over which coverage is requested.
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# @param [String] reference_name
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# The name of the reference to query, within the reference set associated
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# with this query. Optional.
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# @param [String] end_
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# The end position of the range on the reference, 0-based exclusive. If
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# specified, `referenceName` must also be specified. If unset or 0, defaults
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# to the length of the reference.
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# @param [String] page_token
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# The continuation token, which is used to page through large result sets.
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# To get the next page of results, set this parameter to the value of
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# `nextPageToken` from the previous response.
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# @param [Fixnum] page_size
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# The maximum number of results to return in a single page. If unspecified,
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# defaults to 1024. The maximum value is 2048.
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# @param [String] start
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# The start position of the range on the reference, 0-based inclusive. If
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# specified, `referenceName` must also be specified. Defaults to 0.
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# @param [String] target_bucket_width
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# The desired width of each reported coverage bucket in base pairs. This
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# will be rounded down to the nearest precomputed bucket width; the value
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# of which is returned as `bucketWidth` in the response. Defaults
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# to infinity (each bucket spans an entire reference sequence) or the length
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# of the target range, if specified. The smallest precomputed
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# `bucketWidth` is currently 2048 base pairs; this is subject to
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# change.
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [String] fields
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# Selector specifying which fields to include in a partial response.
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# @param [Google::Apis::RequestOptions] options
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# Request-specific options
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#
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# @yield [result, err] Result & error if block supplied
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# @yieldparam result [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] parsed result object
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# @yieldparam err [StandardError] error object if request failed
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#
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# @return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse]
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#
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# @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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# @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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# @raise [Google::Apis::AuthorizationError] Authorization is required
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def list_coverage_buckets(read_group_set_id, reference_name: nil, end_: nil, page_token: nil, page_size: nil, start: nil, target_bucket_width: nil, quota_user: nil, fields: nil, options: nil, &block)
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command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', options)
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command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation
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command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse
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command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
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command.query['referenceName'] = reference_name unless reference_name.nil?
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command.query['end'] = end_ unless end_.nil?
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command.query['pageToken'] = page_token unless page_token.nil?
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command.query['pageSize'] = page_size unless page_size.nil?
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command.query['start'] = start unless start.nil?
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command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil?
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command.query['quotaUser'] = quota_user unless quota_user.nil?
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command.query['fields'] = fields unless fields.nil?
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execute_or_queue_command(command, &block)
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end
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# Gets a list of reads for one or more read group sets.
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# For the definitions of read group sets and other genomics resources, see
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# [Fundamentals of Google
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# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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# Reads search operates over a genomic coordinate space of reference sequence
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# & position defined over the reference sequences to which the requested
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# read group sets are aligned.
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# If a target positional range is specified, search returns all reads whose
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# alignment to the reference genome overlap the range. A query which
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# specifies only read group set IDs yields all reads in those read group
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# sets, including unmapped reads.
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# All reads returned (including reads on subsequent pages) are ordered by
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# genomic coordinate (by reference sequence, then position). Reads with
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# equivalent genomic coordinates are returned in an unspecified order. This
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# order is consistent, such that two queries for the same content (regardless
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# of page size) yield reads in the same order across their respective streams
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# of paginated responses.
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# Implements
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# [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/
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# src/main/resources/avro/readmethods.avdl#L85).
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# @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_request_object
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# @param [String] quota_user
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# Available to use for quota purposes for server-side applications. Can be any
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# arbitrary string assigned to a user, but should not exceed 40 characters.
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# @param [String] fields
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# 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::SearchReadsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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 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.
|
|
# @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::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 delete_call_set(call_set_id, quota_user: nil, fields: nil, options: nil, &block)
|
|
command = make_simple_command(:delete, 'v1/callsets/{callSetId}', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::Empty
|
|
command.params['callSetId'] = call_set_id unless call_set_id.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# 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.
|
|
# @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::SearchCallSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::CallSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::CallSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::CallSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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_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
|
|
|
|
# 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.
|
|
# @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::AnnotationSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::SearchAnnotationSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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 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.
|
|
# @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::AnnotationSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::AnnotationSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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)
|
|
# @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.
|
|
# @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::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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
|
|
# @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::Operation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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
|
|
# @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::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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)
|
|
# @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] 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::SearchVariantsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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_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 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)
|
|
# @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.
|
|
# @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 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
|
|
|
|
# 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)
|
|
# 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.
|
|
# @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 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
|
|
|
|
# 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
|
|
# @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::SearchReferencesResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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 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.
|
|
# @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::Reference] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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_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
|
|
|
|
# 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] 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] start_position
|
|
# The start position (0-based) of this query. Defaults to 0.
|
|
# @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::ListBasesResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 list_reference_bases(reference_id, end_position: nil, page_token: nil, page_size: nil, start_position: nil, quota_user: nil, fields: nil, options: nil, &block)
|
|
command = make_simple_command(:get, 'v1/references/{referenceId}/bases', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::ListBasesResponse
|
|
command.params['referenceId'] = reference_id unless reference_id.nil?
|
|
command.query['end'] = end_position unless end_position.nil?
|
|
command.query['pageToken'] = page_token unless page_token.nil?
|
|
command.query['pageSize'] = page_size unless page_size.nil?
|
|
command.query['start'] = start_position unless start_position.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# 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
|
|
# @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::Policy] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::Dataset] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::Dataset] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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_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
|
|
|
|
# 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.
|
|
# @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::Dataset] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::TestIamPermissionsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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 [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] page_token
|
|
# The continuation token, which is used to page through large result sets.
|
|
# To get the next page of results, set this parameter to the value of
|
|
# `nextPageToken` from the previous response.
|
|
# @param [String] 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::ListDatasetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 list_datasets(page_size: nil, project_id: nil, page_token: nil, quota_user: nil, fields: nil, options: nil, &block)
|
|
command = make_simple_command(:get, 'v1/datasets', options)
|
|
command.response_representation = Google::Apis::GenomicsV1::ListDatasetsResponse::Representation
|
|
command.response_class = Google::Apis::GenomicsV1::ListDatasetsResponse
|
|
command.query['pageSize'] = page_size unless page_size.nil?
|
|
command.query['projectId'] = project_id unless project_id.nil?
|
|
command.query['pageToken'] = page_token unless page_token.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
command.query['fields'] = fields unless fields.nil?
|
|
execute_or_queue_command(command, &block)
|
|
end
|
|
|
|
# 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
|
|
# @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::Dataset] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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
|
|
# @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::Policy] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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] 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.
|
|
# @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::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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)
|
|
# 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.
|
|
# @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 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
|
|
|
|
# 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)
|
|
# @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.
|
|
# @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::Operation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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)
|
|
# 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.
|
|
# @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::SearchVariantSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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)
|
|
# @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.
|
|
# @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 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
|
|
|
|
# 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
|
|
|
|
# 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.
|
|
# @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::Annotation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::BatchCreateAnnotationsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::SearchAnnotationsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::Annotation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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_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
|
|
|
|
# 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.
|
|
# @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::Annotation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::Empty] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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:
|
|
# * projectId: Required. Corresponds to
|
|
# OperationMetadata.projectId.
|
|
# * createTime: The time this job was created, in seconds from the
|
|
# [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`
|
|
# operators.
|
|
# * status: Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only
|
|
# one status may be specified.
|
|
# * labels.key where key is a label key.
|
|
# Examples:
|
|
# * `projectId = my-project AND createTime >= 1432140000`
|
|
# * `projectId = my-project AND createTime >= 1432140000 AND createTime <=
|
|
# 1432150000 AND status = RUNNING`
|
|
# * `projectId = my-project AND labels.color = *`
|
|
# * `projectId = my-project AND labels.color = red`
|
|
# @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.
|
|
# @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::ListOperationsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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.
|
|
# @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::Operation] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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_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
|
|
|
|
# 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)
|
|
# 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.
|
|
# @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::SearchReferenceSetsResponse] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
# 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)
|
|
# 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.
|
|
# @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::ReferenceSet] parsed result object
|
|
# @yieldparam err [StandardError] error object if request failed
|
|
#
|
|
# @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 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
|
|
|
|
protected
|
|
|
|
def apply_command_defaults(command)
|
|
command.query['key'] = key unless key.nil?
|
|
command.query['quotaUser'] = quota_user unless quota_user.nil?
|
|
end
|
|
end
|
|
end
|
|
end
|
|
end
|