3754 lines
152 KiB
Ruby
3754 lines
152 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 'date'
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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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# An annotation describes a region of reference genome. The value of an
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# annotation may be one of several canonical types, supplemented by arbitrary
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# info tags. An annotation is not inherently associated with a specific
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# sample or individual (though a client could choose to use annotations in
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# this way). Example canonical annotation types are `GENE` and
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# `VARIANT`.
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class Annotation
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include Google::Apis::Core::Hashable
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# The annotation set to which this annotation belongs.
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# Corresponds to the JSON property `annotationSetId`
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# @return [String]
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attr_accessor :annotation_set_id
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# The end position of the range on the reference, 0-based exclusive.
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# Corresponds to the JSON property `end`
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# @return [Fixnum]
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attr_accessor :end
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# The server-generated annotation ID, unique across all annotations.
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# Corresponds to the JSON property `id`
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# @return [String]
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attr_accessor :id
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# A map of additional read alignment information. This must be of the form
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# map<string, string[]> (string key mapping to a list of string values).
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# Corresponds to the JSON property `info`
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# @return [Hash<String,Array<Object>>]
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attr_accessor :info
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# The display name of this annotation.
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# Corresponds to the JSON property `name`
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# @return [String]
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attr_accessor :name
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# The ID of the Google Genomics reference associated with this range.
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# Corresponds to the JSON property `referenceId`
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# @return [String]
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attr_accessor :reference_id
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# The display name corresponding to the reference specified by
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# `referenceId`, for example `chr1`, `1`, or `chrX`.
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# Corresponds to the JSON property `referenceName`
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# @return [String]
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attr_accessor :reference_name
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# Whether this range refers to the reverse strand, as opposed to the forward
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# strand. Note that regardless of this field, the start/end position of the
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# range always refer to the forward strand.
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# Corresponds to the JSON property `reverseStrand`
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# @return [Boolean]
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attr_accessor :reverse_strand
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alias_method :reverse_strand?, :reverse_strand
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# The start position of the range on the reference, 0-based inclusive.
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# Corresponds to the JSON property `start`
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# @return [Fixnum]
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attr_accessor :start
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# A transcript represents the assertion that a particular region of the
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# reference genome may be transcribed as RNA.
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# Corresponds to the JSON property `transcript`
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# @return [Google::Apis::GenomicsV1::Transcript]
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attr_accessor :transcript
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# The data type for this annotation. Must match the containing annotation
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# set's type.
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# Corresponds to the JSON property `type`
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# @return [String]
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attr_accessor :type
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# A variant annotation, which describes the effect of a variant on the
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# genome, the coding sequence, and/or higher level consequences at the
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# organism level e.g. pathogenicity. This field is only set for annotations
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# of type `VARIANT`.
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# Corresponds to the JSON property `variant`
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# @return [Google::Apis::GenomicsV1::VariantAnnotation]
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attr_accessor :variant
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@annotation_set_id = args[:annotation_set_id] if args.key?(:annotation_set_id)
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@end = args[:end] if args.key?(:end)
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@id = args[:id] if args.key?(:id)
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@info = args[:info] if args.key?(:info)
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@name = args[:name] if args.key?(:name)
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@reference_id = args[:reference_id] if args.key?(:reference_id)
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@reference_name = args[:reference_name] if args.key?(:reference_name)
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@reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
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@start = args[:start] if args.key?(:start)
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@transcript = args[:transcript] if args.key?(:transcript)
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@type = args[:type] if args.key?(:type)
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@variant = args[:variant] if args.key?(:variant)
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end
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end
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# An annotation set is a logical grouping of annotations that share consistent
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# type information and provenance. Examples of annotation sets include 'all
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# genes from refseq', and 'all variant annotations from ClinVar'.
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class AnnotationSet
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include Google::Apis::Core::Hashable
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# The dataset to which this annotation set belongs.
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# Corresponds to the JSON property `datasetId`
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# @return [String]
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attr_accessor :dataset_id
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# The server-generated annotation set ID, unique across all annotation sets.
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# Corresponds to the JSON property `id`
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# @return [String]
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attr_accessor :id
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# A map of additional read alignment information. This must be of the form
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# map<string, string[]> (string key mapping to a list of string values).
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# Corresponds to the JSON property `info`
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# @return [Hash<String,Array<Object>>]
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attr_accessor :info
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# The display name for this annotation set.
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# Corresponds to the JSON property `name`
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# @return [String]
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attr_accessor :name
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# The ID of the reference set that defines the coordinate space for this
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# set's annotations.
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# Corresponds to the JSON property `referenceSetId`
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# @return [String]
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attr_accessor :reference_set_id
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# The source URI describing the file from which this annotation set was
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# generated, if any.
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# Corresponds to the JSON property `sourceUri`
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# @return [String]
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attr_accessor :source_uri
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# The type of annotations contained within this set.
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# Corresponds to the JSON property `type`
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# @return [String]
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attr_accessor :type
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
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@id = args[:id] if args.key?(:id)
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@info = args[:info] if args.key?(:info)
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@name = args[:name] if args.key?(:name)
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@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
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@source_uri = args[:source_uri] if args.key?(:source_uri)
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@type = args[:type] if args.key?(:type)
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end
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end
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#
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class BatchCreateAnnotationsRequest
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include Google::Apis::Core::Hashable
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# The annotations to be created. At most 4096 can be specified in a single
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# request.
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# Corresponds to the JSON property `annotations`
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# @return [Array<Google::Apis::GenomicsV1::Annotation>]
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attr_accessor :annotations
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# A unique request ID which enables the server to detect duplicated requests.
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# If provided, duplicated requests will result in the same response; if not
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# provided, duplicated requests may result in duplicated data. For a given
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# annotation set, callers should not reuse `request_id`s when writing
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# different batches of annotations - behavior in this case is undefined.
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# A common approach is to use a UUID. For batch jobs where worker crashes are
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# a possibility, consider using some unique variant of a worker or run ID.
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# Corresponds to the JSON property `requestId`
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# @return [String]
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attr_accessor :request_id
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@annotations = args[:annotations] if args.key?(:annotations)
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@request_id = args[:request_id] if args.key?(:request_id)
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end
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end
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#
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class BatchCreateAnnotationsResponse
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include Google::Apis::Core::Hashable
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# The resulting per-annotation entries, ordered consistently with the
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# original request.
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# Corresponds to the JSON property `entries`
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# @return [Array<Google::Apis::GenomicsV1::Entry>]
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attr_accessor :entries
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@entries = args[:entries] if args.key?(:entries)
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end
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end
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# Associates `members` with a `role`.
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class Binding
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include Google::Apis::Core::Hashable
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# Specifies the identities requesting access for a Cloud Platform resource.
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# `members` can have the following values:
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# * `allUsers`: A special identifier that represents anyone who is
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# on the internet; with or without a Google account.
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# * `allAuthenticatedUsers`: A special identifier that represents anyone
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# who is authenticated with a Google account or a service account.
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# * `user:`emailid``: An email address that represents a specific Google
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# account. For example, `alice@gmail.com` .
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# * `serviceAccount:`emailid``: An email address that represents a service
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# account. For example, `my-other-app@appspot.gserviceaccount.com`.
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# * `group:`emailid``: An email address that represents a Google group.
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# For example, `admins@example.com`.
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# * `domain:`domain``: A Google Apps domain name that represents all the
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# users of that domain. For example, `google.com` or `example.com`.
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# Corresponds to the JSON property `members`
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# @return [Array<String>]
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attr_accessor :members
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# Role that is assigned to `members`.
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# For example, `roles/viewer`, `roles/editor`, or `roles/owner`.
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# Required
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# Corresponds to the JSON property `role`
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# @return [String]
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attr_accessor :role
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@members = args[:members] if args.key?(:members)
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@role = args[:role] if args.key?(:role)
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end
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end
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# A call set is a collection of variant calls, typically for one sample. It
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# belongs to a variant set.
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class CallSet
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include Google::Apis::Core::Hashable
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# The date this call set was created in milliseconds from the epoch.
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# Corresponds to the JSON property `created`
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# @return [Fixnum]
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attr_accessor :created
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# The server-generated call set ID, unique across all call sets.
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# Corresponds to the JSON property `id`
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# @return [String]
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attr_accessor :id
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# A map of additional call set information. This must be of the form
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# map<string, string[]> (string key mapping to a list of string values).
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# Corresponds to the JSON property `info`
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# @return [Hash<String,Array<Object>>]
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attr_accessor :info
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# The call set name.
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# Corresponds to the JSON property `name`
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# @return [String]
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attr_accessor :name
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# The sample ID this call set corresponds to.
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# Corresponds to the JSON property `sampleId`
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# @return [String]
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attr_accessor :sample_id
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# The IDs of the variant sets this call set belongs to. This field must
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# have exactly length one, as a call set belongs to a single variant set.
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# This field is repeated for compatibility with the
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# [GA4GH 0.5.1
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# API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/
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# variants.avdl#L76).
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# Corresponds to the JSON property `variantSetIds`
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# @return [Array<String>]
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attr_accessor :variant_set_ids
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@created = args[:created] if args.key?(:created)
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@id = args[:id] if args.key?(:id)
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@info = args[:info] if args.key?(:info)
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@name = args[:name] if args.key?(:name)
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@sample_id = args[:sample_id] if args.key?(:sample_id)
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@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
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end
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end
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# The request message for Operations.CancelOperation.
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class CancelOperationRequest
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include Google::Apis::Core::Hashable
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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end
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end
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# A single CIGAR operation.
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class CigarUnit
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include Google::Apis::Core::Hashable
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#
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# Corresponds to the JSON property `operation`
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# @return [String]
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attr_accessor :operation
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# The number of genomic bases that the operation runs for. Required.
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# Corresponds to the JSON property `operationLength`
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# @return [Fixnum]
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attr_accessor :operation_length
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# `referenceSequence` is only used at mismatches
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# (`SEQUENCE_MISMATCH`) and deletions (`DELETE`).
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# Filling this field replaces SAM's MD tag. If the relevant information is
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# not available, this field is unset.
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# Corresponds to the JSON property `referenceSequence`
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# @return [String]
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attr_accessor :reference_sequence
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@operation = args[:operation] if args.key?(:operation)
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@operation_length = args[:operation_length] if args.key?(:operation_length)
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@reference_sequence = args[:reference_sequence] if args.key?(:reference_sequence)
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end
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end
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#
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class ClinicalCondition
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include Google::Apis::Core::Hashable
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# The MedGen concept id associated with this gene.
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# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
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# Corresponds to the JSON property `conceptId`
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# @return [String]
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attr_accessor :concept_id
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# The set of external IDs for this condition.
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# Corresponds to the JSON property `externalIds`
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# @return [Array<Google::Apis::GenomicsV1::ExternalId>]
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attr_accessor :external_ids
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# A set of names for the condition.
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# Corresponds to the JSON property `names`
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# @return [Array<String>]
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attr_accessor :names
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# The OMIM id for this condition.
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# Search for these IDs at http://omim.org/
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# Corresponds to the JSON property `omimId`
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# @return [String]
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attr_accessor :omim_id
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@concept_id = args[:concept_id] if args.key?(:concept_id)
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@external_ids = args[:external_ids] if args.key?(:external_ids)
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@names = args[:names] if args.key?(:names)
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@omim_id = args[:omim_id] if args.key?(:omim_id)
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end
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end
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#
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class CodingSequence
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include Google::Apis::Core::Hashable
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# The end of the coding sequence on this annotation's reference sequence,
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# 0-based exclusive. Note that this position is relative to the reference
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# start, and *not* the containing annotation start.
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# Corresponds to the JSON property `end`
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# @return [Fixnum]
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attr_accessor :end
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# The start of the coding sequence on this annotation's reference sequence,
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# 0-based inclusive. Note that this position is relative to the reference
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# start, and *not* the containing annotation start.
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# Corresponds to the JSON property `start`
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# @return [Fixnum]
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attr_accessor :start
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@end = args[:end] if args.key?(:end)
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@start = args[:start] if args.key?(:start)
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end
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end
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# Describes a Compute Engine resource that is being managed by a running
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# pipeline.
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class ComputeEngine
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include Google::Apis::Core::Hashable
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# The names of the disks that were created for this pipeline.
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# Corresponds to the JSON property `diskNames`
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# @return [Array<String>]
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attr_accessor :disk_names
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# The instance on which the operation is running.
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# Corresponds to the JSON property `instanceName`
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# @return [String]
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attr_accessor :instance_name
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# The machine type of the instance.
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# Corresponds to the JSON property `machineType`
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# @return [String]
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attr_accessor :machine_type
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# The availability zone in which the instance resides.
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# Corresponds to the JSON property `zone`
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# @return [String]
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attr_accessor :zone
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@disk_names = args[:disk_names] if args.key?(:disk_names)
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@instance_name = args[:instance_name] if args.key?(:instance_name)
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@machine_type = args[:machine_type] if args.key?(:machine_type)
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@zone = args[:zone] if args.key?(:zone)
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end
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end
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# This event is generated when a container starts.
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class ContainerStartedEvent
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include Google::Apis::Core::Hashable
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# The numeric ID of the action that started this container.
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# Corresponds to the JSON property `actionId`
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# @return [Fixnum]
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attr_accessor :action_id
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# The public IP address that can be used to connect to the container. This
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# field is only populated when at least one port mapping is present. If the
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# instance was created with a private address this field will be empty even
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# if port mappings exist.
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# Corresponds to the JSON property `ipAddress`
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# @return [String]
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attr_accessor :ip_address
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# The container to host port mappings installed for this container. This
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# set will contain any ports exposed using the PUBLISH_EXPOSED_PORTS flag as
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# well as any specified in the Action definition.
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# Corresponds to the JSON property `portMappings`
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# @return [Hash<String,Fixnum>]
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attr_accessor :port_mappings
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@action_id = args[:action_id] if args.key?(:action_id)
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@ip_address = args[:ip_address] if args.key?(:ip_address)
|
|
@port_mappings = args[:port_mappings] if args.key?(:port_mappings)
|
|
end
|
|
end
|
|
|
|
# This event is generated when a container exits.
|
|
class ContainerStoppedEvent
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The numeric ID of the action that started this container.
|
|
# Corresponds to the JSON property `actionId`
|
|
# @return [Fixnum]
|
|
attr_accessor :action_id
|
|
|
|
# The exit status of the container.
|
|
# Corresponds to the JSON property `exitStatus`
|
|
# @return [Fixnum]
|
|
attr_accessor :exit_status
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@action_id = args[:action_id] if args.key?(:action_id)
|
|
@exit_status = args[:exit_status] if args.key?(:exit_status)
|
|
end
|
|
end
|
|
|
|
# A bucket over which read coverage has been precomputed. A bucket corresponds
|
|
# to a specific range of the reference sequence.
|
|
class CoverageBucket
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The average number of reads which are aligned to each individual
|
|
# reference base in this bucket.
|
|
# Corresponds to the JSON property `meanCoverage`
|
|
# @return [Float]
|
|
attr_accessor :mean_coverage
|
|
|
|
# A 0-based half-open genomic coordinate range for search requests.
|
|
# Corresponds to the JSON property `range`
|
|
# @return [Google::Apis::GenomicsV1::Range]
|
|
attr_accessor :range
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@mean_coverage = args[:mean_coverage] if args.key?(:mean_coverage)
|
|
@range = args[:range] if args.key?(:range)
|
|
end
|
|
end
|
|
|
|
# A Dataset is a collection of genomic data.
|
|
class Dataset
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The time this dataset was created, in seconds from the epoch.
|
|
# Corresponds to the JSON property `createTime`
|
|
# @return [String]
|
|
attr_accessor :create_time
|
|
|
|
# The server-generated dataset ID, unique across all datasets.
|
|
# Corresponds to the JSON property `id`
|
|
# @return [String]
|
|
attr_accessor :id
|
|
|
|
# The dataset name.
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
# The Google Cloud project ID that this dataset belongs to.
|
|
# Corresponds to the JSON property `projectId`
|
|
# @return [String]
|
|
attr_accessor :project_id
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@create_time = args[:create_time] if args.key?(:create_time)
|
|
@id = args[:id] if args.key?(:id)
|
|
@name = args[:name] if args.key?(:name)
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
end
|
|
end
|
|
|
|
# This event is generated whenever a resource limitation or transient error
|
|
# delays execution of a pipeline that was otherwise ready to run.
|
|
class DelayedEvent
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# A textual description of the cause of the delay. The string may change
|
|
# without notice since it is often generated by another service (such as
|
|
# Compute Engine).
|
|
# Corresponds to the JSON property `cause`
|
|
# @return [String]
|
|
attr_accessor :cause
|
|
|
|
# If the delay was caused by a resource shortage, this field lists the
|
|
# Compute Engine metrics that are preventing this operation from running
|
|
# (for example, CPUS or INSTANCES). If the particular metric is not known,
|
|
# a single UNKNOWN metric will be present.
|
|
# Corresponds to the JSON property `metrics`
|
|
# @return [Array<String>]
|
|
attr_accessor :metrics
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@cause = args[:cause] if args.key?(:cause)
|
|
@metrics = args[:metrics] if args.key?(:metrics)
|
|
end
|
|
end
|
|
|
|
# A generic empty message that you can re-use to avoid defining duplicated
|
|
# empty messages in your APIs. A typical example is to use it as the request
|
|
# or the response type of an API method. For instance:
|
|
# service Foo `
|
|
# rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty);
|
|
# `
|
|
# The JSON representation for `Empty` is empty JSON object ````.
|
|
class Empty
|
|
include Google::Apis::Core::Hashable
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
end
|
|
end
|
|
|
|
#
|
|
class Entry
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# An annotation describes a region of reference genome. The value of an
|
|
# annotation may be one of several canonical types, supplemented by arbitrary
|
|
# info tags. An annotation is not inherently associated with a specific
|
|
# sample or individual (though a client could choose to use annotations in
|
|
# this way). Example canonical annotation types are `GENE` and
|
|
# `VARIANT`.
|
|
# Corresponds to the JSON property `annotation`
|
|
# @return [Google::Apis::GenomicsV1::Annotation]
|
|
attr_accessor :annotation
|
|
|
|
# The `Status` type defines a logical error model that is suitable for different
|
|
# programming environments, including REST APIs and RPC APIs. It is used by
|
|
# [gRPC](https://github.com/grpc). The error model is designed to be:
|
|
# - Simple to use and understand for most users
|
|
# - Flexible enough to meet unexpected needs
|
|
# # Overview
|
|
# The `Status` message contains three pieces of data: error code, error message,
|
|
# and error details. The error code should be an enum value of
|
|
# google.rpc.Code, but it may accept additional error codes if needed. The
|
|
# error message should be a developer-facing English message that helps
|
|
# developers *understand* and *resolve* the error. If a localized user-facing
|
|
# error message is needed, put the localized message in the error details or
|
|
# localize it in the client. The optional error details may contain arbitrary
|
|
# information about the error. There is a predefined set of error detail types
|
|
# in the package `google.rpc` that can be used for common error conditions.
|
|
# # Language mapping
|
|
# The `Status` message is the logical representation of the error model, but it
|
|
# is not necessarily the actual wire format. When the `Status` message is
|
|
# exposed in different client libraries and different wire protocols, it can be
|
|
# mapped differently. For example, it will likely be mapped to some exceptions
|
|
# in Java, but more likely mapped to some error codes in C.
|
|
# # Other uses
|
|
# The error model and the `Status` message can be used in a variety of
|
|
# environments, either with or without APIs, to provide a
|
|
# consistent developer experience across different environments.
|
|
# Example uses of this error model include:
|
|
# - Partial errors. If a service needs to return partial errors to the client,
|
|
# it may embed the `Status` in the normal response to indicate the partial
|
|
# errors.
|
|
# - Workflow errors. A typical workflow has multiple steps. Each step may
|
|
# have a `Status` message for error reporting.
|
|
# - Batch operations. If a client uses batch request and batch response, the
|
|
# `Status` message should be used directly inside batch response, one for
|
|
# each error sub-response.
|
|
# - Asynchronous operations. If an API call embeds asynchronous operation
|
|
# results in its response, the status of those operations should be
|
|
# represented directly using the `Status` message.
|
|
# - Logging. If some API errors are stored in logs, the message `Status` could
|
|
# be used directly after any stripping needed for security/privacy reasons.
|
|
# Corresponds to the JSON property `status`
|
|
# @return [Google::Apis::GenomicsV1::Status]
|
|
attr_accessor :status
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@annotation = args[:annotation] if args.key?(:annotation)
|
|
@status = args[:status] if args.key?(:status)
|
|
end
|
|
end
|
|
|
|
# Event carries information about events that occur during pipeline execution.
|
|
class Event
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# A human readable description of the event. Note that these strings may
|
|
# change at any time without notice. Any application logic must use the
|
|
# information in the details field.
|
|
# Corresponds to the JSON property `description`
|
|
# @return [String]
|
|
attr_accessor :description
|
|
|
|
# Machine readable details about the event.
|
|
# Corresponds to the JSON property `details`
|
|
# @return [Hash<String,Object>]
|
|
attr_accessor :details
|
|
|
|
# The time that the event occurred.
|
|
# Corresponds to the JSON property `timestamp`
|
|
# @return [String]
|
|
attr_accessor :timestamp
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@description = args[:description] if args.key?(:description)
|
|
@details = args[:details] if args.key?(:details)
|
|
@timestamp = args[:timestamp] if args.key?(:timestamp)
|
|
end
|
|
end
|
|
|
|
#
|
|
class Exon
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The end position of the exon on this annotation's reference sequence,
|
|
# 0-based exclusive. Note that this is relative to the reference start, and
|
|
# *not* the containing annotation start.
|
|
# Corresponds to the JSON property `end`
|
|
# @return [Fixnum]
|
|
attr_accessor :end
|
|
|
|
# The frame of this exon. Contains a value of 0, 1, or 2, which indicates
|
|
# the offset of the first coding base of the exon within the reading frame
|
|
# of the coding DNA sequence, if any. This field is dependent on the
|
|
# strandedness of this annotation (see
|
|
# Annotation.reverse_strand).
|
|
# For forward stranded annotations, this offset is relative to the
|
|
# exon.start. For reverse
|
|
# strand annotations, this offset is relative to the
|
|
# exon.end `- 1`.
|
|
# Unset if this exon does not intersect the coding sequence. Upon creation
|
|
# of a transcript, the frame must be populated for all or none of the
|
|
# coding exons.
|
|
# Corresponds to the JSON property `frame`
|
|
# @return [Fixnum]
|
|
attr_accessor :frame
|
|
|
|
# The start position of the exon on this annotation's reference sequence,
|
|
# 0-based inclusive. Note that this is relative to the reference start, and
|
|
# **not** the containing annotation start.
|
|
# Corresponds to the JSON property `start`
|
|
# @return [Fixnum]
|
|
attr_accessor :start
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@end = args[:end] if args.key?(:end)
|
|
@frame = args[:frame] if args.key?(:frame)
|
|
@start = args[:start] if args.key?(:start)
|
|
end
|
|
end
|
|
|
|
#
|
|
class Experiment
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The instrument model used as part of this experiment. This maps to
|
|
# sequencing technology in the SAM spec.
|
|
# Corresponds to the JSON property `instrumentModel`
|
|
# @return [String]
|
|
attr_accessor :instrument_model
|
|
|
|
# A client-supplied library identifier; a library is a collection of DNA
|
|
# fragments which have been prepared for sequencing from a sample. This
|
|
# field is important for quality control as error or bias can be introduced
|
|
# during sample preparation.
|
|
# Corresponds to the JSON property `libraryId`
|
|
# @return [String]
|
|
attr_accessor :library_id
|
|
|
|
# The platform unit used as part of this experiment, for example
|
|
# flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
|
|
# @RG PU field in the SAM spec.
|
|
# Corresponds to the JSON property `platformUnit`
|
|
# @return [String]
|
|
attr_accessor :platform_unit
|
|
|
|
# The sequencing center used as part of this experiment.
|
|
# Corresponds to the JSON property `sequencingCenter`
|
|
# @return [String]
|
|
attr_accessor :sequencing_center
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@instrument_model = args[:instrument_model] if args.key?(:instrument_model)
|
|
@library_id = args[:library_id] if args.key?(:library_id)
|
|
@platform_unit = args[:platform_unit] if args.key?(:platform_unit)
|
|
@sequencing_center = args[:sequencing_center] if args.key?(:sequencing_center)
|
|
end
|
|
end
|
|
|
|
# The read group set export request.
|
|
class ExportReadGroupSetRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Required. A Google Cloud Storage URI for the exported BAM file.
|
|
# The currently authenticated user must have write access to the new file.
|
|
# An error will be returned if the URI already contains data.
|
|
# Corresponds to the JSON property `exportUri`
|
|
# @return [String]
|
|
attr_accessor :export_uri
|
|
|
|
# Required. The Google Cloud project ID that owns this
|
|
# export. The caller must have WRITE access to this project.
|
|
# Corresponds to the JSON property `projectId`
|
|
# @return [String]
|
|
attr_accessor :project_id
|
|
|
|
# The reference names to export. If this is not specified, all reference
|
|
# sequences, including unmapped reads, are exported.
|
|
# Use `*` to export only unmapped reads.
|
|
# Corresponds to the JSON property `referenceNames`
|
|
# @return [Array<String>]
|
|
attr_accessor :reference_names
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@export_uri = args[:export_uri] if args.key?(:export_uri)
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
@reference_names = args[:reference_names] if args.key?(:reference_names)
|
|
end
|
|
end
|
|
|
|
# The variant data export request.
|
|
class ExportVariantSetRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Required. The BigQuery dataset to export data to. This dataset must already
|
|
# exist. Note that this is distinct from the Genomics concept of "dataset".
|
|
# Corresponds to the JSON property `bigqueryDataset`
|
|
# @return [String]
|
|
attr_accessor :bigquery_dataset
|
|
|
|
# Required. The BigQuery table to export data to.
|
|
# If the table doesn't exist, it will be created. If it already exists, it
|
|
# will be overwritten.
|
|
# Corresponds to the JSON property `bigqueryTable`
|
|
# @return [String]
|
|
attr_accessor :bigquery_table
|
|
|
|
# If provided, only variant call information from the specified call sets
|
|
# will be exported. By default all variant calls are exported.
|
|
# Corresponds to the JSON property `callSetIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :call_set_ids
|
|
|
|
# The format for the exported data.
|
|
# Corresponds to the JSON property `format`
|
|
# @return [String]
|
|
attr_accessor :format
|
|
|
|
# Required. The Google Cloud project ID that owns the destination
|
|
# BigQuery dataset. The caller must have WRITE access to this project. This
|
|
# project will also own the resulting export job.
|
|
# Corresponds to the JSON property `projectId`
|
|
# @return [String]
|
|
attr_accessor :project_id
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@bigquery_dataset = args[:bigquery_dataset] if args.key?(:bigquery_dataset)
|
|
@bigquery_table = args[:bigquery_table] if args.key?(:bigquery_table)
|
|
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
|
@format = args[:format] if args.key?(:format)
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
end
|
|
end
|
|
|
|
#
|
|
class ExternalId
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The id used by the source of this data.
|
|
# Corresponds to the JSON property `id`
|
|
# @return [String]
|
|
attr_accessor :id
|
|
|
|
# The name of the source of this data.
|
|
# Corresponds to the JSON property `sourceName`
|
|
# @return [String]
|
|
attr_accessor :source_name
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@id = args[:id] if args.key?(:id)
|
|
@source_name = args[:source_name] if args.key?(:source_name)
|
|
end
|
|
end
|
|
|
|
# This event is generated when the execution of a pipeline has failed. Note
|
|
# that other events may continue to occur after this event.
|
|
class FailedEvent
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The human readable description of the cause of the failure.
|
|
# Corresponds to the JSON property `cause`
|
|
# @return [String]
|
|
attr_accessor :cause
|
|
|
|
# The Google standard error code that best describes this failure.
|
|
# Corresponds to the JSON property `code`
|
|
# @return [String]
|
|
attr_accessor :code
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@cause = args[:cause] if args.key?(:cause)
|
|
@code = args[:code] if args.key?(:code)
|
|
end
|
|
end
|
|
|
|
# Request message for `GetIamPolicy` method.
|
|
class GetIamPolicyRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
end
|
|
end
|
|
|
|
# The read group set import request.
|
|
class ImportReadGroupSetsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Required. The ID of the dataset these read group sets will belong to. The
|
|
# caller must have WRITE permissions to this dataset.
|
|
# Corresponds to the JSON property `datasetId`
|
|
# @return [String]
|
|
attr_accessor :dataset_id
|
|
|
|
# The partition strategy describes how read groups are partitioned into read
|
|
# group sets.
|
|
# Corresponds to the JSON property `partitionStrategy`
|
|
# @return [String]
|
|
attr_accessor :partition_strategy
|
|
|
|
# The reference set to which the imported read group sets are aligned to, if
|
|
# any. The reference names of this reference set must be a superset of those
|
|
# found in the imported file headers. If no reference set id is provided, a
|
|
# best effort is made to associate with a matching reference set.
|
|
# Corresponds to the JSON property `referenceSetId`
|
|
# @return [String]
|
|
attr_accessor :reference_set_id
|
|
|
|
# A list of URIs pointing at [BAM
|
|
# files](https://samtools.github.io/hts-specs/SAMv1.pdf)
|
|
# in Google Cloud Storage.
|
|
# Those URIs can include wildcards (*), but do not add or remove
|
|
# matching files before import has completed.
|
|
# Note that Google Cloud Storage object listing is only eventually
|
|
# consistent: files added may be not be immediately visible to
|
|
# everyone. Thus, if using a wildcard it is preferable not to start
|
|
# the import immediately after the files are created.
|
|
# Corresponds to the JSON property `sourceUris`
|
|
# @return [Array<String>]
|
|
attr_accessor :source_uris
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
@partition_strategy = args[:partition_strategy] if args.key?(:partition_strategy)
|
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
@source_uris = args[:source_uris] if args.key?(:source_uris)
|
|
end
|
|
end
|
|
|
|
# The read group set import response.
|
|
class ImportReadGroupSetsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# IDs of the read group sets that were created.
|
|
# Corresponds to the JSON property `readGroupSetIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :read_group_set_ids
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids)
|
|
end
|
|
end
|
|
|
|
# The variant data import request.
|
|
class ImportVariantsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The format of the variant data being imported. If unspecified, defaults to
|
|
# to `VCF`.
|
|
# Corresponds to the JSON property `format`
|
|
# @return [String]
|
|
attr_accessor :format
|
|
|
|
# A mapping between info field keys and the InfoMergeOperations to
|
|
# be performed on them. This is plumbed down to the MergeVariantRequests
|
|
# generated by the resulting import job.
|
|
# Corresponds to the JSON property `infoMergeConfig`
|
|
# @return [Hash<String,String>]
|
|
attr_accessor :info_merge_config
|
|
|
|
# Convert reference names to the canonical representation.
|
|
# hg19 haploytypes (those reference names containing "_hap")
|
|
# are not modified in any way.
|
|
# All other reference names are modified according to the following rules:
|
|
# The reference name is capitalized.
|
|
# The "chr" prefix is dropped for all autosomes and sex chromsomes.
|
|
# For example "chr17" becomes "17" and "chrX" becomes "X".
|
|
# All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
|
|
# Corresponds to the JSON property `normalizeReferenceNames`
|
|
# @return [Boolean]
|
|
attr_accessor :normalize_reference_names
|
|
alias_method :normalize_reference_names?, :normalize_reference_names
|
|
|
|
# A list of URIs referencing variant files in Google Cloud Storage. URIs can
|
|
# include wildcards [as described
|
|
# here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames).
|
|
# Note that recursive wildcards ('**') are not supported.
|
|
# Corresponds to the JSON property `sourceUris`
|
|
# @return [Array<String>]
|
|
attr_accessor :source_uris
|
|
|
|
# Required. The variant set to which variant data should be imported.
|
|
# Corresponds to the JSON property `variantSetId`
|
|
# @return [String]
|
|
attr_accessor :variant_set_id
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@format = args[:format] if args.key?(:format)
|
|
@info_merge_config = args[:info_merge_config] if args.key?(:info_merge_config)
|
|
@normalize_reference_names = args[:normalize_reference_names] if args.key?(:normalize_reference_names)
|
|
@source_uris = args[:source_uris] if args.key?(:source_uris)
|
|
@variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
|
|
end
|
|
end
|
|
|
|
# The variant data import response.
|
|
class ImportVariantsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# IDs of the call sets created during the import.
|
|
# Corresponds to the JSON property `callSetIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :call_set_ids
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
|
end
|
|
end
|
|
|
|
# A linear alignment can be represented by one CIGAR string. Describes the
|
|
# mapped position and local alignment of the read to the reference.
|
|
class LinearAlignment
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Represents the local alignment of this sequence (alignment matches, indels,
|
|
# etc) against the reference.
|
|
# Corresponds to the JSON property `cigar`
|
|
# @return [Array<Google::Apis::GenomicsV1::CigarUnit>]
|
|
attr_accessor :cigar
|
|
|
|
# The mapping quality of this alignment. Represents how likely
|
|
# the read maps to this position as opposed to other locations.
|
|
# Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
|
|
# the nearest integer.
|
|
# Corresponds to the JSON property `mappingQuality`
|
|
# @return [Fixnum]
|
|
attr_accessor :mapping_quality
|
|
|
|
# An abstraction for referring to a genomic position, in relation to some
|
|
# already known reference. For now, represents a genomic position as a
|
|
# reference name, a base number on that reference (0-based), and a
|
|
# determination of forward or reverse strand.
|
|
# Corresponds to the JSON property `position`
|
|
# @return [Google::Apis::GenomicsV1::Position]
|
|
attr_accessor :position
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@cigar = args[:cigar] if args.key?(:cigar)
|
|
@mapping_quality = args[:mapping_quality] if args.key?(:mapping_quality)
|
|
@position = args[:position] if args.key?(:position)
|
|
end
|
|
end
|
|
|
|
#
|
|
class ListBasesResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
# The offset position (0-based) of the given `sequence` from the
|
|
# start of this `Reference`. This value will differ for each page
|
|
# in a paginated request.
|
|
# Corresponds to the JSON property `offset`
|
|
# @return [Fixnum]
|
|
attr_accessor :offset
|
|
|
|
# A substring of the bases that make up this reference.
|
|
# Corresponds to the JSON property `sequence`
|
|
# @return [String]
|
|
attr_accessor :sequence
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
@offset = args[:offset] if args.key?(:offset)
|
|
@sequence = args[:sequence] if args.key?(:sequence)
|
|
end
|
|
end
|
|
|
|
#
|
|
class ListCoverageBucketsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The length of each coverage bucket in base pairs. Note that buckets at the
|
|
# end of a reference sequence may be shorter. This value is omitted if the
|
|
# bucket width is infinity (the default behaviour, with no range or
|
|
# `targetBucketWidth`).
|
|
# Corresponds to the JSON property `bucketWidth`
|
|
# @return [Fixnum]
|
|
attr_accessor :bucket_width
|
|
|
|
# The coverage buckets. The list of buckets is sparse; a bucket with 0
|
|
# overlapping reads is not returned. A bucket never crosses more than one
|
|
# reference sequence. Each bucket has width `bucketWidth`, unless
|
|
# its end is the end of the reference sequence.
|
|
# Corresponds to the JSON property `coverageBuckets`
|
|
# @return [Array<Google::Apis::GenomicsV1::CoverageBucket>]
|
|
attr_accessor :coverage_buckets
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@bucket_width = args[:bucket_width] if args.key?(:bucket_width)
|
|
@coverage_buckets = args[:coverage_buckets] if args.key?(:coverage_buckets)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
end
|
|
end
|
|
|
|
# The dataset list response.
|
|
class ListDatasetsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The list of matching Datasets.
|
|
# Corresponds to the JSON property `datasets`
|
|
# @return [Array<Google::Apis::GenomicsV1::Dataset>]
|
|
attr_accessor :datasets
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@datasets = args[:datasets] if args.key?(:datasets)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
end
|
|
end
|
|
|
|
# The response message for Operations.ListOperations.
|
|
class ListOperationsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The standard List next-page token.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
# A list of operations that matches the specified filter in the request.
|
|
# Corresponds to the JSON property `operations`
|
|
# @return [Array<Google::Apis::GenomicsV1::Operation>]
|
|
attr_accessor :operations
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
@operations = args[:operations] if args.key?(:operations)
|
|
end
|
|
end
|
|
|
|
#
|
|
class MergeVariantsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# A mapping between info field keys and the InfoMergeOperations to
|
|
# be performed on them.
|
|
# Corresponds to the JSON property `infoMergeConfig`
|
|
# @return [Hash<String,String>]
|
|
attr_accessor :info_merge_config
|
|
|
|
# The destination variant set.
|
|
# Corresponds to the JSON property `variantSetId`
|
|
# @return [String]
|
|
attr_accessor :variant_set_id
|
|
|
|
# The variants to be merged with existing variants.
|
|
# Corresponds to the JSON property `variants`
|
|
# @return [Array<Google::Apis::GenomicsV1::Variant>]
|
|
attr_accessor :variants
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@info_merge_config = args[:info_merge_config] if args.key?(:info_merge_config)
|
|
@variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
|
|
@variants = args[:variants] if args.key?(:variants)
|
|
end
|
|
end
|
|
|
|
# This resource represents a long-running operation that is the result of a
|
|
# network API call.
|
|
class Operation
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# If the value is `false`, it means the operation is still in progress.
|
|
# If `true`, the operation is completed, and either `error` or `response` is
|
|
# available.
|
|
# Corresponds to the JSON property `done`
|
|
# @return [Boolean]
|
|
attr_accessor :done
|
|
alias_method :done?, :done
|
|
|
|
# The `Status` type defines a logical error model that is suitable for different
|
|
# programming environments, including REST APIs and RPC APIs. It is used by
|
|
# [gRPC](https://github.com/grpc). The error model is designed to be:
|
|
# - Simple to use and understand for most users
|
|
# - Flexible enough to meet unexpected needs
|
|
# # Overview
|
|
# The `Status` message contains three pieces of data: error code, error message,
|
|
# and error details. The error code should be an enum value of
|
|
# google.rpc.Code, but it may accept additional error codes if needed. The
|
|
# error message should be a developer-facing English message that helps
|
|
# developers *understand* and *resolve* the error. If a localized user-facing
|
|
# error message is needed, put the localized message in the error details or
|
|
# localize it in the client. The optional error details may contain arbitrary
|
|
# information about the error. There is a predefined set of error detail types
|
|
# in the package `google.rpc` that can be used for common error conditions.
|
|
# # Language mapping
|
|
# The `Status` message is the logical representation of the error model, but it
|
|
# is not necessarily the actual wire format. When the `Status` message is
|
|
# exposed in different client libraries and different wire protocols, it can be
|
|
# mapped differently. For example, it will likely be mapped to some exceptions
|
|
# in Java, but more likely mapped to some error codes in C.
|
|
# # Other uses
|
|
# The error model and the `Status` message can be used in a variety of
|
|
# environments, either with or without APIs, to provide a
|
|
# consistent developer experience across different environments.
|
|
# Example uses of this error model include:
|
|
# - Partial errors. If a service needs to return partial errors to the client,
|
|
# it may embed the `Status` in the normal response to indicate the partial
|
|
# errors.
|
|
# - Workflow errors. A typical workflow has multiple steps. Each step may
|
|
# have a `Status` message for error reporting.
|
|
# - Batch operations. If a client uses batch request and batch response, the
|
|
# `Status` message should be used directly inside batch response, one for
|
|
# each error sub-response.
|
|
# - Asynchronous operations. If an API call embeds asynchronous operation
|
|
# results in its response, the status of those operations should be
|
|
# represented directly using the `Status` message.
|
|
# - Logging. If some API errors are stored in logs, the message `Status` could
|
|
# be used directly after any stripping needed for security/privacy reasons.
|
|
# Corresponds to the JSON property `error`
|
|
# @return [Google::Apis::GenomicsV1::Status]
|
|
attr_accessor :error
|
|
|
|
# An OperationMetadata or Metadata object. This will always be returned with the
|
|
# Operation.
|
|
# Corresponds to the JSON property `metadata`
|
|
# @return [Hash<String,Object>]
|
|
attr_accessor :metadata
|
|
|
|
# The server-assigned name, which is only unique within the same service that
|
|
# originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-
|
|
# qzoWAgEw`
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
# If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If
|
|
# importing Variants, an ImportVariantsResponse is returned. For pipelines and
|
|
# exports, an Empty response is returned.
|
|
# Corresponds to the JSON property `response`
|
|
# @return [Hash<String,Object>]
|
|
attr_accessor :response
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@done = args[:done] if args.key?(:done)
|
|
@error = args[:error] if args.key?(:error)
|
|
@metadata = args[:metadata] if args.key?(:metadata)
|
|
@name = args[:name] if args.key?(:name)
|
|
@response = args[:response] if args.key?(:response)
|
|
end
|
|
end
|
|
|
|
# An event that occurred during an Operation.
|
|
class OperationEvent
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Required description of event.
|
|
# Corresponds to the JSON property `description`
|
|
# @return [String]
|
|
attr_accessor :description
|
|
|
|
# Optional time of when event finished. An event can have a start time and no
|
|
# finish time. If an event has a finish time, there must be a start time.
|
|
# Corresponds to the JSON property `endTime`
|
|
# @return [String]
|
|
attr_accessor :end_time
|
|
|
|
# Optional time of when event started.
|
|
# Corresponds to the JSON property `startTime`
|
|
# @return [String]
|
|
attr_accessor :start_time
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@description = args[:description] if args.key?(:description)
|
|
@end_time = args[:end_time] if args.key?(:end_time)
|
|
@start_time = args[:start_time] if args.key?(:start_time)
|
|
end
|
|
end
|
|
|
|
# Metadata describing an Operation.
|
|
class OperationMetadata
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# This field is deprecated. Use `labels` instead. Optionally provided by the
|
|
# caller when submitting the request that creates the operation.
|
|
# Corresponds to the JSON property `clientId`
|
|
# @return [String]
|
|
attr_accessor :client_id
|
|
|
|
# The time at which the job was submitted to the Genomics service.
|
|
# Corresponds to the JSON property `createTime`
|
|
# @return [String]
|
|
attr_accessor :create_time
|
|
|
|
# The time at which the job stopped running.
|
|
# Corresponds to the JSON property `endTime`
|
|
# @return [String]
|
|
attr_accessor :end_time
|
|
|
|
# Optional event messages that were generated during the job's execution.
|
|
# This also contains any warnings that were generated during import
|
|
# or export.
|
|
# Corresponds to the JSON property `events`
|
|
# @return [Array<Google::Apis::GenomicsV1::OperationEvent>]
|
|
attr_accessor :events
|
|
|
|
# Optionally provided by the caller when submitting the request that creates
|
|
# the operation.
|
|
# Corresponds to the JSON property `labels`
|
|
# @return [Hash<String,String>]
|
|
attr_accessor :labels
|
|
|
|
# The Google Cloud Project in which the job is scoped.
|
|
# Corresponds to the JSON property `projectId`
|
|
# @return [String]
|
|
attr_accessor :project_id
|
|
|
|
# The original request that started the operation. Note that this will be in
|
|
# current version of the API. If the operation was started with v1beta2 API
|
|
# and a GetOperation is performed on v1 API, a v1 request will be returned.
|
|
# Corresponds to the JSON property `request`
|
|
# @return [Hash<String,Object>]
|
|
attr_accessor :request
|
|
|
|
# Runtime metadata on this Operation.
|
|
# Corresponds to the JSON property `runtimeMetadata`
|
|
# @return [Hash<String,Object>]
|
|
attr_accessor :runtime_metadata
|
|
|
|
# The time at which the job began to run.
|
|
# Corresponds to the JSON property `startTime`
|
|
# @return [String]
|
|
attr_accessor :start_time
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@client_id = args[:client_id] if args.key?(:client_id)
|
|
@create_time = args[:create_time] if args.key?(:create_time)
|
|
@end_time = args[:end_time] if args.key?(:end_time)
|
|
@events = args[:events] if args.key?(:events)
|
|
@labels = args[:labels] if args.key?(:labels)
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
@request = args[:request] if args.key?(:request)
|
|
@runtime_metadata = args[:runtime_metadata] if args.key?(:runtime_metadata)
|
|
@start_time = args[:start_time] if args.key?(:start_time)
|
|
end
|
|
end
|
|
|
|
# Defines an Identity and Access Management (IAM) policy. It is used to
|
|
# specify access control policies for Cloud Platform resources.
|
|
# A `Policy` consists of a list of `bindings`. A `binding` binds a list of
|
|
# `members` to a `role`, where the members can be user accounts, Google groups,
|
|
# Google domains, and service accounts. A `role` is a named list of permissions
|
|
# defined by IAM.
|
|
# **JSON Example**
|
|
# `
|
|
# "bindings": [
|
|
# `
|
|
# "role": "roles/owner",
|
|
# "members": [
|
|
# "user:mike@example.com",
|
|
# "group:admins@example.com",
|
|
# "domain:google.com",
|
|
# "serviceAccount:my-other-app@appspot.gserviceaccount.com"
|
|
# ]
|
|
# `,
|
|
# `
|
|
# "role": "roles/viewer",
|
|
# "members": ["user:sean@example.com"]
|
|
# `
|
|
# ]
|
|
# `
|
|
# **YAML Example**
|
|
# bindings:
|
|
# - members:
|
|
# - user:mike@example.com
|
|
# - group:admins@example.com
|
|
# - domain:google.com
|
|
# - serviceAccount:my-other-app@appspot.gserviceaccount.com
|
|
# role: roles/owner
|
|
# - members:
|
|
# - user:sean@example.com
|
|
# role: roles/viewer
|
|
# For a description of IAM and its features, see the
|
|
# [IAM developer's guide](https://cloud.google.com/iam/docs).
|
|
class Policy
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Associates a list of `members` to a `role`.
|
|
# `bindings` with no members will result in an error.
|
|
# Corresponds to the JSON property `bindings`
|
|
# @return [Array<Google::Apis::GenomicsV1::Binding>]
|
|
attr_accessor :bindings
|
|
|
|
# `etag` is used for optimistic concurrency control as a way to help
|
|
# prevent simultaneous updates of a policy from overwriting each other.
|
|
# It is strongly suggested that systems make use of the `etag` in the
|
|
# read-modify-write cycle to perform policy updates in order to avoid race
|
|
# conditions: An `etag` is returned in the response to `getIamPolicy`, and
|
|
# systems are expected to put that etag in the request to `setIamPolicy` to
|
|
# ensure that their change will be applied to the same version of the policy.
|
|
# If no `etag` is provided in the call to `setIamPolicy`, then the existing
|
|
# policy is overwritten blindly.
|
|
# Corresponds to the JSON property `etag`
|
|
# NOTE: Values are automatically base64 encoded/decoded in the client library.
|
|
# @return [String]
|
|
attr_accessor :etag
|
|
|
|
# Deprecated.
|
|
# Corresponds to the JSON property `version`
|
|
# @return [Fixnum]
|
|
attr_accessor :version
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@bindings = args[:bindings] if args.key?(:bindings)
|
|
@etag = args[:etag] if args.key?(:etag)
|
|
@version = args[:version] if args.key?(:version)
|
|
end
|
|
end
|
|
|
|
# An abstraction for referring to a genomic position, in relation to some
|
|
# already known reference. For now, represents a genomic position as a
|
|
# reference name, a base number on that reference (0-based), and a
|
|
# determination of forward or reverse strand.
|
|
class Position
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The 0-based offset from the start of the forward strand for that reference.
|
|
# Corresponds to the JSON property `position`
|
|
# @return [Fixnum]
|
|
attr_accessor :position
|
|
|
|
# The name of the reference in whatever reference set is being used.
|
|
# Corresponds to the JSON property `referenceName`
|
|
# @return [String]
|
|
attr_accessor :reference_name
|
|
|
|
# Whether this position is on the reverse strand, as opposed to the forward
|
|
# strand.
|
|
# Corresponds to the JSON property `reverseStrand`
|
|
# @return [Boolean]
|
|
attr_accessor :reverse_strand
|
|
alias_method :reverse_strand?, :reverse_strand
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@position = args[:position] if args.key?(:position)
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
@reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
|
|
end
|
|
end
|
|
|
|
#
|
|
class Program
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The command line used to run this program.
|
|
# Corresponds to the JSON property `commandLine`
|
|
# @return [String]
|
|
attr_accessor :command_line
|
|
|
|
# The user specified locally unique ID of the program. Used along with
|
|
# `prevProgramId` to define an ordering between programs.
|
|
# Corresponds to the JSON property `id`
|
|
# @return [String]
|
|
attr_accessor :id
|
|
|
|
# The display name of the program. This is typically the colloquial name of
|
|
# the tool used, for example 'bwa' or 'picard'.
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
# The ID of the program run before this one.
|
|
# Corresponds to the JSON property `prevProgramId`
|
|
# @return [String]
|
|
attr_accessor :prev_program_id
|
|
|
|
# The version of the program run.
|
|
# Corresponds to the JSON property `version`
|
|
# @return [String]
|
|
attr_accessor :version
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@command_line = args[:command_line] if args.key?(:command_line)
|
|
@id = args[:id] if args.key?(:id)
|
|
@name = args[:name] if args.key?(:name)
|
|
@prev_program_id = args[:prev_program_id] if args.key?(:prev_program_id)
|
|
@version = args[:version] if args.key?(:version)
|
|
end
|
|
end
|
|
|
|
# This event is generated when the worker starts pulling an image.
|
|
class PullStartedEvent
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The URI of the image that was pulled.
|
|
# Corresponds to the JSON property `imageUri`
|
|
# @return [String]
|
|
attr_accessor :image_uri
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@image_uri = args[:image_uri] if args.key?(:image_uri)
|
|
end
|
|
end
|
|
|
|
# This event is generated when the worker stops pulling an image.
|
|
class PullStoppedEvent
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The URI of the image that was pulled.
|
|
# Corresponds to the JSON property `imageUri`
|
|
# @return [String]
|
|
attr_accessor :image_uri
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@image_uri = args[:image_uri] if args.key?(:image_uri)
|
|
end
|
|
end
|
|
|
|
# A 0-based half-open genomic coordinate range for search requests.
|
|
class Range
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The end position of the range on the reference, 0-based exclusive.
|
|
# Corresponds to the JSON property `end`
|
|
# @return [Fixnum]
|
|
attr_accessor :end
|
|
|
|
# The reference sequence name, for example `chr1`,
|
|
# `1`, or `chrX`.
|
|
# Corresponds to the JSON property `referenceName`
|
|
# @return [String]
|
|
attr_accessor :reference_name
|
|
|
|
# The start position of the range on the reference, 0-based inclusive.
|
|
# Corresponds to the JSON property `start`
|
|
# @return [Fixnum]
|
|
attr_accessor :start
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@end = args[:end] if args.key?(:end)
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
@start = args[:start] if args.key?(:start)
|
|
end
|
|
end
|
|
|
|
# A read alignment describes a linear alignment of a string of DNA to a
|
|
# reference sequence, in addition to metadata
|
|
# about the fragment (the molecule of DNA sequenced) and the read (the bases
|
|
# which were read by the sequencer). A read is equivalent to a line in a SAM
|
|
# file. A read belongs to exactly one read group and exactly one
|
|
# read group set.
|
|
# ### Reverse-stranded reads
|
|
# Mapped reads (reads having a non-null `alignment`) can be aligned to either
|
|
# the forward or the reverse strand of their associated reference. Strandedness
|
|
# of a mapped read is encoded by `alignment.position.reverseStrand`.
|
|
# If we consider the reference to be a forward-stranded coordinate space of
|
|
# `[0, reference.length)` with `0` as the left-most position and
|
|
# `reference.length` as the right-most position, reads are always aligned left
|
|
# to right. That is, `alignment.position.position` always refers to the
|
|
# left-most reference coordinate and `alignment.cigar` describes the alignment
|
|
# of this read to the reference from left to right. All per-base fields such as
|
|
# `alignedSequence` and `alignedQuality` share this same left-to-right
|
|
# orientation; this is true of reads which are aligned to either strand. For
|
|
# reverse-stranded reads, this means that `alignedSequence` is the reverse
|
|
# complement of the bases that were originally reported by the sequencing
|
|
# machine.
|
|
# ### Generating a reference-aligned sequence string
|
|
# When interacting with mapped reads, it's often useful to produce a string
|
|
# representing the local alignment of the read to reference. The following
|
|
# pseudocode demonstrates one way of doing this:
|
|
# out = ""
|
|
# offset = 0
|
|
# for c in read.alignment.cigar `
|
|
# switch c.operation `
|
|
# case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH":
|
|
# out += read.alignedSequence[offset:offset+c.operationLength]
|
|
# offset += c.operationLength
|
|
# break
|
|
# case "CLIP_SOFT", "INSERT":
|
|
# offset += c.operationLength
|
|
# break
|
|
# case "PAD":
|
|
# out += repeat("*", c.operationLength)
|
|
# break
|
|
# case "DELETE":
|
|
# out += repeat("-", c.operationLength)
|
|
# break
|
|
# case "SKIP":
|
|
# out += repeat(" ", c.operationLength)
|
|
# break
|
|
# case "CLIP_HARD":
|
|
# break
|
|
# `
|
|
# `
|
|
# return out
|
|
# ### Converting to SAM's CIGAR string
|
|
# The following pseudocode generates a SAM CIGAR string from the
|
|
# `cigar` field. Note that this is a lossy conversion
|
|
# (`cigar.referenceSequence` is lost).
|
|
# cigarMap = `
|
|
# "ALIGNMENT_MATCH": "M",
|
|
# "INSERT": "I",
|
|
# "DELETE": "D",
|
|
# "SKIP": "N",
|
|
# "CLIP_SOFT": "S",
|
|
# "CLIP_HARD": "H",
|
|
# "PAD": "P",
|
|
# "SEQUENCE_MATCH": "=",
|
|
# "SEQUENCE_MISMATCH": "X",
|
|
# `
|
|
# cigarStr = ""
|
|
# for c in read.alignment.cigar `
|
|
# cigarStr += c.operationLength + cigarMap[c.operation]
|
|
# `
|
|
# return cigarStr
|
|
class Read
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The quality of the read sequence contained in this alignment record
|
|
# (equivalent to QUAL in SAM).
|
|
# `alignedSequence` and `alignedQuality` may be shorter than the full read
|
|
# sequence and quality. This will occur if the alignment is part of a
|
|
# chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
|
|
# for this read will begin/end with a hard clip operator that will indicate
|
|
# the length of the excised sequence.
|
|
# Corresponds to the JSON property `alignedQuality`
|
|
# @return [Array<Fixnum>]
|
|
attr_accessor :aligned_quality
|
|
|
|
# The bases of the read sequence contained in this alignment record,
|
|
# **without CIGAR operations applied** (equivalent to SEQ in SAM).
|
|
# `alignedSequence` and `alignedQuality` may be
|
|
# shorter than the full read sequence and quality. This will occur if the
|
|
# alignment is part of a chimeric alignment, or if the read was trimmed. When
|
|
# this occurs, the CIGAR for this read will begin/end with a hard clip
|
|
# operator that will indicate the length of the excised sequence.
|
|
# Corresponds to the JSON property `alignedSequence`
|
|
# @return [String]
|
|
attr_accessor :aligned_sequence
|
|
|
|
# A linear alignment can be represented by one CIGAR string. Describes the
|
|
# mapped position and local alignment of the read to the reference.
|
|
# Corresponds to the JSON property `alignment`
|
|
# @return [Google::Apis::GenomicsV1::LinearAlignment]
|
|
attr_accessor :alignment
|
|
|
|
# The fragment is a PCR or optical duplicate (SAM flag 0x400).
|
|
# Corresponds to the JSON property `duplicateFragment`
|
|
# @return [Boolean]
|
|
attr_accessor :duplicate_fragment
|
|
alias_method :duplicate_fragment?, :duplicate_fragment
|
|
|
|
# Whether this read did not pass filters, such as platform or vendor quality
|
|
# controls (SAM flag 0x200).
|
|
# Corresponds to the JSON property `failedVendorQualityChecks`
|
|
# @return [Boolean]
|
|
attr_accessor :failed_vendor_quality_checks
|
|
alias_method :failed_vendor_quality_checks?, :failed_vendor_quality_checks
|
|
|
|
# The observed length of the fragment, equivalent to TLEN in SAM.
|
|
# Corresponds to the JSON property `fragmentLength`
|
|
# @return [Fixnum]
|
|
attr_accessor :fragment_length
|
|
|
|
# The fragment name. Equivalent to QNAME (query template name) in SAM.
|
|
# Corresponds to the JSON property `fragmentName`
|
|
# @return [String]
|
|
attr_accessor :fragment_name
|
|
|
|
# The server-generated read ID, unique across all reads. This is different
|
|
# from the `fragmentName`.
|
|
# Corresponds to the JSON property `id`
|
|
# @return [String]
|
|
attr_accessor :id
|
|
|
|
# A map of additional read alignment information. This must be of the form
|
|
# map<string, string[]> (string key mapping to a list of string values).
|
|
# Corresponds to the JSON property `info`
|
|
# @return [Hash<String,Array<Object>>]
|
|
attr_accessor :info
|
|
|
|
# An abstraction for referring to a genomic position, in relation to some
|
|
# already known reference. For now, represents a genomic position as a
|
|
# reference name, a base number on that reference (0-based), and a
|
|
# determination of forward or reverse strand.
|
|
# Corresponds to the JSON property `nextMatePosition`
|
|
# @return [Google::Apis::GenomicsV1::Position]
|
|
attr_accessor :next_mate_position
|
|
|
|
# The number of reads in the fragment (extension to SAM flag 0x1).
|
|
# Corresponds to the JSON property `numberReads`
|
|
# @return [Fixnum]
|
|
attr_accessor :number_reads
|
|
|
|
# The orientation and the distance between reads from the fragment are
|
|
# consistent with the sequencing protocol (SAM flag 0x2).
|
|
# Corresponds to the JSON property `properPlacement`
|
|
# @return [Boolean]
|
|
attr_accessor :proper_placement
|
|
alias_method :proper_placement?, :proper_placement
|
|
|
|
# The ID of the read group this read belongs to. A read belongs to exactly
|
|
# one read group. This is a server-generated ID which is distinct from SAM's
|
|
# RG tag (for that value, see
|
|
# ReadGroup.name).
|
|
# Corresponds to the JSON property `readGroupId`
|
|
# @return [String]
|
|
attr_accessor :read_group_id
|
|
|
|
# The ID of the read group set this read belongs to. A read belongs to
|
|
# exactly one read group set.
|
|
# Corresponds to the JSON property `readGroupSetId`
|
|
# @return [String]
|
|
attr_accessor :read_group_set_id
|
|
|
|
# The read number in sequencing. 0-based and less than numberReads. This
|
|
# field replaces SAM flag 0x40 and 0x80.
|
|
# Corresponds to the JSON property `readNumber`
|
|
# @return [Fixnum]
|
|
attr_accessor :read_number
|
|
|
|
# Whether this alignment is secondary. Equivalent to SAM flag 0x100.
|
|
# A secondary alignment represents an alternative to the primary alignment
|
|
# for this read. Aligners may return secondary alignments if a read can map
|
|
# ambiguously to multiple coordinates in the genome. By convention, each read
|
|
# has one and only one alignment where both `secondaryAlignment`
|
|
# and `supplementaryAlignment` are false.
|
|
# Corresponds to the JSON property `secondaryAlignment`
|
|
# @return [Boolean]
|
|
attr_accessor :secondary_alignment
|
|
alias_method :secondary_alignment?, :secondary_alignment
|
|
|
|
# Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
|
|
# Supplementary alignments are used in the representation of a chimeric
|
|
# alignment. In a chimeric alignment, a read is split into multiple
|
|
# linear alignments that map to different reference contigs. The first
|
|
# linear alignment in the read will be designated as the representative
|
|
# alignment; the remaining linear alignments will be designated as
|
|
# supplementary alignments. These alignments may have different mapping
|
|
# quality scores. In each linear alignment in a chimeric alignment, the read
|
|
# will be hard clipped. The `alignedSequence` and
|
|
# `alignedQuality` fields in the alignment record will only
|
|
# represent the bases for its respective linear alignment.
|
|
# Corresponds to the JSON property `supplementaryAlignment`
|
|
# @return [Boolean]
|
|
attr_accessor :supplementary_alignment
|
|
alias_method :supplementary_alignment?, :supplementary_alignment
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@aligned_quality = args[:aligned_quality] if args.key?(:aligned_quality)
|
|
@aligned_sequence = args[:aligned_sequence] if args.key?(:aligned_sequence)
|
|
@alignment = args[:alignment] if args.key?(:alignment)
|
|
@duplicate_fragment = args[:duplicate_fragment] if args.key?(:duplicate_fragment)
|
|
@failed_vendor_quality_checks = args[:failed_vendor_quality_checks] if args.key?(:failed_vendor_quality_checks)
|
|
@fragment_length = args[:fragment_length] if args.key?(:fragment_length)
|
|
@fragment_name = args[:fragment_name] if args.key?(:fragment_name)
|
|
@id = args[:id] if args.key?(:id)
|
|
@info = args[:info] if args.key?(:info)
|
|
@next_mate_position = args[:next_mate_position] if args.key?(:next_mate_position)
|
|
@number_reads = args[:number_reads] if args.key?(:number_reads)
|
|
@proper_placement = args[:proper_placement] if args.key?(:proper_placement)
|
|
@read_group_id = args[:read_group_id] if args.key?(:read_group_id)
|
|
@read_group_set_id = args[:read_group_set_id] if args.key?(:read_group_set_id)
|
|
@read_number = args[:read_number] if args.key?(:read_number)
|
|
@secondary_alignment = args[:secondary_alignment] if args.key?(:secondary_alignment)
|
|
@supplementary_alignment = args[:supplementary_alignment] if args.key?(:supplementary_alignment)
|
|
end
|
|
end
|
|
|
|
# A read group is all the data that's processed the same way by the sequencer.
|
|
class ReadGroup
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The dataset to which this read group belongs.
|
|
# Corresponds to the JSON property `datasetId`
|
|
# @return [String]
|
|
attr_accessor :dataset_id
|
|
|
|
# A free-form text description of this read group.
|
|
# Corresponds to the JSON property `description`
|
|
# @return [String]
|
|
attr_accessor :description
|
|
|
|
# The experiment used to generate this read group.
|
|
# Corresponds to the JSON property `experiment`
|
|
# @return [Google::Apis::GenomicsV1::Experiment]
|
|
attr_accessor :experiment
|
|
|
|
# The server-generated read group ID, unique for all read groups.
|
|
# Note: This is different than the @RG ID field in the SAM spec. For that
|
|
# value, see name.
|
|
# Corresponds to the JSON property `id`
|
|
# @return [String]
|
|
attr_accessor :id
|
|
|
|
# A map of additional read group information. This must be of the form
|
|
# map<string, string[]> (string key mapping to a list of string values).
|
|
# Corresponds to the JSON property `info`
|
|
# @return [Hash<String,Array<Object>>]
|
|
attr_accessor :info
|
|
|
|
# The read group name. This corresponds to the @RG ID field in the SAM spec.
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
# The predicted insert size of this read group. The insert size is the length
|
|
# the sequenced DNA fragment from end-to-end, not including the adapters.
|
|
# Corresponds to the JSON property `predictedInsertSize`
|
|
# @return [Fixnum]
|
|
attr_accessor :predicted_insert_size
|
|
|
|
# The programs used to generate this read group. Programs are always
|
|
# identical for all read groups within a read group set. For this reason,
|
|
# only the first read group in a returned set will have this field
|
|
# populated.
|
|
# Corresponds to the JSON property `programs`
|
|
# @return [Array<Google::Apis::GenomicsV1::Program>]
|
|
attr_accessor :programs
|
|
|
|
# The reference set the reads in this read group are aligned to.
|
|
# Corresponds to the JSON property `referenceSetId`
|
|
# @return [String]
|
|
attr_accessor :reference_set_id
|
|
|
|
# A client-supplied sample identifier for the reads in this read group.
|
|
# Corresponds to the JSON property `sampleId`
|
|
# @return [String]
|
|
attr_accessor :sample_id
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
@description = args[:description] if args.key?(:description)
|
|
@experiment = args[:experiment] if args.key?(:experiment)
|
|
@id = args[:id] if args.key?(:id)
|
|
@info = args[:info] if args.key?(:info)
|
|
@name = args[:name] if args.key?(:name)
|
|
@predicted_insert_size = args[:predicted_insert_size] if args.key?(:predicted_insert_size)
|
|
@programs = args[:programs] if args.key?(:programs)
|
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
@sample_id = args[:sample_id] if args.key?(:sample_id)
|
|
end
|
|
end
|
|
|
|
# A read group set is a logical collection of read groups, which are
|
|
# collections of reads produced by a sequencer. A read group set typically
|
|
# models reads corresponding to one sample, sequenced one way, and aligned one
|
|
# way.
|
|
# * A read group set belongs to one dataset.
|
|
# * A read group belongs to one read group set.
|
|
# * A read belongs to one read group.
|
|
class ReadGroupSet
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The dataset to which this read group set belongs.
|
|
# Corresponds to the JSON property `datasetId`
|
|
# @return [String]
|
|
attr_accessor :dataset_id
|
|
|
|
# The filename of the original source file for this read group set, if any.
|
|
# Corresponds to the JSON property `filename`
|
|
# @return [String]
|
|
attr_accessor :filename
|
|
|
|
# The server-generated read group set ID, unique for all read group sets.
|
|
# Corresponds to the JSON property `id`
|
|
# @return [String]
|
|
attr_accessor :id
|
|
|
|
# A map of additional read group set information.
|
|
# Corresponds to the JSON property `info`
|
|
# @return [Hash<String,Array<Object>>]
|
|
attr_accessor :info
|
|
|
|
# The read group set name. By default this will be initialized to the sample
|
|
# name of the sequenced data contained in this set.
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
# The read groups in this set. There are typically 1-10 read groups in a read
|
|
# group set.
|
|
# Corresponds to the JSON property `readGroups`
|
|
# @return [Array<Google::Apis::GenomicsV1::ReadGroup>]
|
|
attr_accessor :read_groups
|
|
|
|
# The reference set to which the reads in this read group set are aligned.
|
|
# Corresponds to the JSON property `referenceSetId`
|
|
# @return [String]
|
|
attr_accessor :reference_set_id
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
@filename = args[:filename] if args.key?(:filename)
|
|
@id = args[:id] if args.key?(:id)
|
|
@info = args[:info] if args.key?(:info)
|
|
@name = args[:name] if args.key?(:name)
|
|
@read_groups = args[:read_groups] if args.key?(:read_groups)
|
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
end
|
|
end
|
|
|
|
# A reference is a canonical assembled DNA sequence, intended to act as a
|
|
# reference coordinate space for other genomic annotations. A single reference
|
|
# might represent the human chromosome 1 or mitochandrial DNA, for instance. A
|
|
# reference belongs to one or more reference sets.
|
|
class Reference
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The server-generated reference ID, unique across all references.
|
|
# Corresponds to the JSON property `id`
|
|
# @return [String]
|
|
attr_accessor :id
|
|
|
|
# The length of this reference's sequence.
|
|
# Corresponds to the JSON property `length`
|
|
# @return [Fixnum]
|
|
attr_accessor :length
|
|
|
|
# MD5 of the upper-case sequence excluding all whitespace characters (this
|
|
# is equivalent to SQ:M5 in SAM). This value is represented in lower case
|
|
# hexadecimal format.
|
|
# Corresponds to the JSON property `md5checksum`
|
|
# @return [String]
|
|
attr_accessor :md5checksum
|
|
|
|
# The name of this reference, for example `22`.
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
# ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
|
|
# Corresponds to the JSON property `ncbiTaxonId`
|
|
# @return [Fixnum]
|
|
attr_accessor :ncbi_taxon_id
|
|
|
|
# All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
|
# with a version number, for example `GCF_000001405.26`.
|
|
# Corresponds to the JSON property `sourceAccessions`
|
|
# @return [Array<String>]
|
|
attr_accessor :source_accessions
|
|
|
|
# The URI from which the sequence was obtained. Typically specifies a FASTA
|
|
# format file.
|
|
# Corresponds to the JSON property `sourceUri`
|
|
# @return [String]
|
|
attr_accessor :source_uri
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@id = args[:id] if args.key?(:id)
|
|
@length = args[:length] if args.key?(:length)
|
|
@md5checksum = args[:md5checksum] if args.key?(:md5checksum)
|
|
@name = args[:name] if args.key?(:name)
|
|
@ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
|
|
@source_accessions = args[:source_accessions] if args.key?(:source_accessions)
|
|
@source_uri = args[:source_uri] if args.key?(:source_uri)
|
|
end
|
|
end
|
|
|
|
# ReferenceBound records an upper bound for the starting coordinate of
|
|
# variants in a particular reference.
|
|
class ReferenceBound
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The name of the reference associated with this reference bound.
|
|
# Corresponds to the JSON property `referenceName`
|
|
# @return [String]
|
|
attr_accessor :reference_name
|
|
|
|
# An upper bound (inclusive) on the starting coordinate of any
|
|
# variant in the reference sequence.
|
|
# Corresponds to the JSON property `upperBound`
|
|
# @return [Fixnum]
|
|
attr_accessor :upper_bound
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
@upper_bound = args[:upper_bound] if args.key?(:upper_bound)
|
|
end
|
|
end
|
|
|
|
# A reference set is a set of references which typically comprise a reference
|
|
# assembly for a species, such as `GRCh38` which is representative
|
|
# of the human genome. A reference set defines a common coordinate space for
|
|
# comparing reference-aligned experimental data. A reference set contains 1 or
|
|
# more references.
|
|
class ReferenceSet
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Public id of this reference set, such as `GRCh37`.
|
|
# Corresponds to the JSON property `assemblyId`
|
|
# @return [String]
|
|
attr_accessor :assembly_id
|
|
|
|
# Free text description of this reference set.
|
|
# Corresponds to the JSON property `description`
|
|
# @return [String]
|
|
attr_accessor :description
|
|
|
|
# The server-generated reference set ID, unique across all reference sets.
|
|
# Corresponds to the JSON property `id`
|
|
# @return [String]
|
|
attr_accessor :id
|
|
|
|
# Order-independent MD5 checksum which identifies this reference set. The
|
|
# checksum is computed by sorting all lower case hexidecimal string
|
|
# `reference.md5checksum` (for all reference in this set) in
|
|
# ascending lexicographic order, concatenating, and taking the MD5 of that
|
|
# value. The resulting value is represented in lower case hexadecimal format.
|
|
# Corresponds to the JSON property `md5checksum`
|
|
# @return [String]
|
|
attr_accessor :md5checksum
|
|
|
|
# ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
|
|
# indicating the species which this reference set is intended to model. Note
|
|
# that contained references may specify a different `ncbiTaxonId`, as
|
|
# assemblies may contain reference sequences which do not belong to the
|
|
# modeled species, for example EBV in a human reference genome.
|
|
# Corresponds to the JSON property `ncbiTaxonId`
|
|
# @return [Fixnum]
|
|
attr_accessor :ncbi_taxon_id
|
|
|
|
# The IDs of the reference objects that are part of this set.
|
|
# `Reference.md5checksum` must be unique within this set.
|
|
# Corresponds to the JSON property `referenceIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :reference_ids
|
|
|
|
# All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
|
# with a version number, for example `NC_000001.11`.
|
|
# Corresponds to the JSON property `sourceAccessions`
|
|
# @return [Array<String>]
|
|
attr_accessor :source_accessions
|
|
|
|
# The URI from which the references were obtained.
|
|
# Corresponds to the JSON property `sourceUri`
|
|
# @return [String]
|
|
attr_accessor :source_uri
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@assembly_id = args[:assembly_id] if args.key?(:assembly_id)
|
|
@description = args[:description] if args.key?(:description)
|
|
@id = args[:id] if args.key?(:id)
|
|
@md5checksum = args[:md5checksum] if args.key?(:md5checksum)
|
|
@ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
|
|
@reference_ids = args[:reference_ids] if args.key?(:reference_ids)
|
|
@source_accessions = args[:source_accessions] if args.key?(:source_accessions)
|
|
@source_uri = args[:source_uri] if args.key?(:source_uri)
|
|
end
|
|
end
|
|
|
|
# Runtime metadata that will be populated in the
|
|
# runtimeMetadata
|
|
# field of the Operation associated with a RunPipeline execution.
|
|
class RuntimeMetadata
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Describes a Compute Engine resource that is being managed by a running
|
|
# pipeline.
|
|
# Corresponds to the JSON property `computeEngine`
|
|
# @return [Google::Apis::GenomicsV1::ComputeEngine]
|
|
attr_accessor :compute_engine
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@compute_engine = args[:compute_engine] if args.key?(:compute_engine)
|
|
end
|
|
end
|
|
|
|
#
|
|
class SearchAnnotationSetsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Required. The dataset IDs to search within. Caller must have `READ` access
|
|
# to these datasets.
|
|
# Corresponds to the JSON property `datasetIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :dataset_ids
|
|
|
|
# Only return annotations sets for which a substring of the name matches this
|
|
# string (case insensitive).
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
# defaults to 128. The maximum value is 1024.
|
|
# Corresponds to the JSON property `pageSize`
|
|
# @return [Fixnum]
|
|
attr_accessor :page_size
|
|
|
|
# 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.
|
|
# Corresponds to the JSON property `pageToken`
|
|
# @return [String]
|
|
attr_accessor :page_token
|
|
|
|
# If specified, only annotation sets associated with the given reference set
|
|
# are returned.
|
|
# Corresponds to the JSON property `referenceSetId`
|
|
# @return [String]
|
|
attr_accessor :reference_set_id
|
|
|
|
# If specified, only annotation sets that have any of these types are
|
|
# returned.
|
|
# Corresponds to the JSON property `types`
|
|
# @return [Array<String>]
|
|
attr_accessor :types
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
|
|
@name = args[:name] if args.key?(:name)
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
@types = args[:types] if args.key?(:types)
|
|
end
|
|
end
|
|
|
|
#
|
|
class SearchAnnotationSetsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The matching annotation sets.
|
|
# Corresponds to the JSON property `annotationSets`
|
|
# @return [Array<Google::Apis::GenomicsV1::AnnotationSet>]
|
|
attr_accessor :annotation_sets
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@annotation_sets = args[:annotation_sets] if args.key?(:annotation_sets)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
end
|
|
end
|
|
|
|
#
|
|
class SearchAnnotationsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Required. The annotation sets to search within. The caller must have
|
|
# `READ` access to these annotation sets.
|
|
# All queried annotation sets must have the same type.
|
|
# Corresponds to the JSON property `annotationSetIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :annotation_set_ids
|
|
|
|
# The end position of the range on the reference, 0-based exclusive. If
|
|
# referenceId or
|
|
# referenceName
|
|
# must be specified, Defaults to the length of the reference.
|
|
# Corresponds to the JSON property `end`
|
|
# @return [Fixnum]
|
|
attr_accessor :end
|
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
# defaults to 256. The maximum value is 2048.
|
|
# Corresponds to the JSON property `pageSize`
|
|
# @return [Fixnum]
|
|
attr_accessor :page_size
|
|
|
|
# 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.
|
|
# Corresponds to the JSON property `pageToken`
|
|
# @return [String]
|
|
attr_accessor :page_token
|
|
|
|
# The ID of the reference to query.
|
|
# Corresponds to the JSON property `referenceId`
|
|
# @return [String]
|
|
attr_accessor :reference_id
|
|
|
|
# The name of the reference to query, within the reference set associated
|
|
# with this query.
|
|
# Corresponds to the JSON property `referenceName`
|
|
# @return [String]
|
|
attr_accessor :reference_name
|
|
|
|
# The start position of the range on the reference, 0-based inclusive. If
|
|
# specified,
|
|
# referenceId or
|
|
# referenceName
|
|
# must be specified. Defaults to 0.
|
|
# Corresponds to the JSON property `start`
|
|
# @return [Fixnum]
|
|
attr_accessor :start
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@annotation_set_ids = args[:annotation_set_ids] if args.key?(:annotation_set_ids)
|
|
@end = args[:end] if args.key?(:end)
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
@reference_id = args[:reference_id] if args.key?(:reference_id)
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
@start = args[:start] if args.key?(:start)
|
|
end
|
|
end
|
|
|
|
#
|
|
class SearchAnnotationsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The matching annotations.
|
|
# Corresponds to the JSON property `annotations`
|
|
# @return [Array<Google::Apis::GenomicsV1::Annotation>]
|
|
attr_accessor :annotations
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@annotations = args[:annotations] if args.key?(:annotations)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
end
|
|
end
|
|
|
|
# The call set search request.
|
|
class SearchCallSetsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Only return call sets for which a substring of the name matches this
|
|
# string.
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
# defaults to 1024.
|
|
# Corresponds to the JSON property `pageSize`
|
|
# @return [Fixnum]
|
|
attr_accessor :page_size
|
|
|
|
# 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.
|
|
# Corresponds to the JSON property `pageToken`
|
|
# @return [String]
|
|
attr_accessor :page_token
|
|
|
|
# Restrict the query to call sets within the given variant sets. At least one
|
|
# ID must be provided.
|
|
# Corresponds to the JSON property `variantSetIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :variant_set_ids
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@name = args[:name] if args.key?(:name)
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
|
end
|
|
end
|
|
|
|
# The call set search response.
|
|
class SearchCallSetsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The list of matching call sets.
|
|
# Corresponds to the JSON property `callSets`
|
|
# @return [Array<Google::Apis::GenomicsV1::CallSet>]
|
|
attr_accessor :call_sets
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@call_sets = args[:call_sets] if args.key?(:call_sets)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
end
|
|
end
|
|
|
|
# The read group set search request.
|
|
class SearchReadGroupSetsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Restricts this query to read group sets within the given datasets. At least
|
|
# one ID must be provided.
|
|
# Corresponds to the JSON property `datasetIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :dataset_ids
|
|
|
|
# Only return read group sets for which a substring of the name matches this
|
|
# string.
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
# defaults to 256. The maximum value is 1024.
|
|
# Corresponds to the JSON property `pageSize`
|
|
# @return [Fixnum]
|
|
attr_accessor :page_size
|
|
|
|
# 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.
|
|
# Corresponds to the JSON property `pageToken`
|
|
# @return [String]
|
|
attr_accessor :page_token
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
|
|
@name = args[:name] if args.key?(:name)
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
end
|
|
end
|
|
|
|
# The read group set search response.
|
|
class SearchReadGroupSetsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
# The list of matching read group sets.
|
|
# Corresponds to the JSON property `readGroupSets`
|
|
# @return [Array<Google::Apis::GenomicsV1::ReadGroupSet>]
|
|
attr_accessor :read_group_sets
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
@read_group_sets = args[:read_group_sets] if args.key?(:read_group_sets)
|
|
end
|
|
end
|
|
|
|
# The read search request.
|
|
class SearchReadsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The end position of the range on the reference, 0-based exclusive. If
|
|
# specified, `referenceName` must also be specified.
|
|
# Corresponds to the JSON property `end`
|
|
# @return [Fixnum]
|
|
attr_accessor :end
|
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
# defaults to 256. The maximum value is 2048.
|
|
# Corresponds to the JSON property `pageSize`
|
|
# @return [Fixnum]
|
|
attr_accessor :page_size
|
|
|
|
# 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.
|
|
# Corresponds to the JSON property `pageToken`
|
|
# @return [String]
|
|
attr_accessor :page_token
|
|
|
|
# The IDs of the read groups within which to search for reads. All specified
|
|
# read groups must belong to the same read group sets. Must specify one of
|
|
# `readGroupSetIds` or `readGroupIds`.
|
|
# Corresponds to the JSON property `readGroupIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :read_group_ids
|
|
|
|
# The IDs of the read groups sets within which to search for reads. All
|
|
# specified read group sets must be aligned against a common set of reference
|
|
# sequences; this defines the genomic coordinates for the query. Must specify
|
|
# one of `readGroupSetIds` or `readGroupIds`.
|
|
# Corresponds to the JSON property `readGroupSetIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :read_group_set_ids
|
|
|
|
# The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to
|
|
# `*`, only unmapped reads are returned. If unspecified, all reads (mapped
|
|
# and unmapped) are returned.
|
|
# Corresponds to the JSON property `referenceName`
|
|
# @return [String]
|
|
attr_accessor :reference_name
|
|
|
|
# The start position of the range on the reference, 0-based inclusive. If
|
|
# specified, `referenceName` must also be specified.
|
|
# Corresponds to the JSON property `start`
|
|
# @return [Fixnum]
|
|
attr_accessor :start
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@end = args[:end] if args.key?(:end)
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
@read_group_ids = args[:read_group_ids] if args.key?(:read_group_ids)
|
|
@read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids)
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
@start = args[:start] if args.key?(:start)
|
|
end
|
|
end
|
|
|
|
# The read search response.
|
|
class SearchReadsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The list of matching alignments sorted by mapped genomic coordinate,
|
|
# if any, ascending in position within the same reference. Unmapped reads,
|
|
# which have no position, are returned contiguously and are sorted in
|
|
# ascending lexicographic order by fragment name.
|
|
# Corresponds to the JSON property `alignments`
|
|
# @return [Array<Google::Apis::GenomicsV1::Read>]
|
|
attr_accessor :alignments
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@alignments = args[:alignments] if args.key?(:alignments)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
end
|
|
end
|
|
|
|
#
|
|
class SearchReferenceSetsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# If present, return reference sets for which a prefix of any of
|
|
# sourceAccessions
|
|
# match any of these strings. Accession numbers typically have a main number
|
|
# and a version, for example `NC_000001.11`.
|
|
# Corresponds to the JSON property `accessions`
|
|
# @return [Array<String>]
|
|
attr_accessor :accessions
|
|
|
|
# If present, return reference sets for which a substring of their
|
|
# `assemblyId` matches this string (case insensitive).
|
|
# Corresponds to the JSON property `assemblyId`
|
|
# @return [String]
|
|
attr_accessor :assembly_id
|
|
|
|
# If present, return reference sets for which the
|
|
# md5checksum matches exactly.
|
|
# Corresponds to the JSON property `md5checksums`
|
|
# @return [Array<String>]
|
|
attr_accessor :md5checksums
|
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
# defaults to 1024. The maximum value is 4096.
|
|
# Corresponds to the JSON property `pageSize`
|
|
# @return [Fixnum]
|
|
attr_accessor :page_size
|
|
|
|
# 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.
|
|
# Corresponds to the JSON property `pageToken`
|
|
# @return [String]
|
|
attr_accessor :page_token
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@accessions = args[:accessions] if args.key?(:accessions)
|
|
@assembly_id = args[:assembly_id] if args.key?(:assembly_id)
|
|
@md5checksums = args[:md5checksums] if args.key?(:md5checksums)
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
end
|
|
end
|
|
|
|
#
|
|
class SearchReferenceSetsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
# The matching references sets.
|
|
# Corresponds to the JSON property `referenceSets`
|
|
# @return [Array<Google::Apis::GenomicsV1::ReferenceSet>]
|
|
attr_accessor :reference_sets
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
@reference_sets = args[:reference_sets] if args.key?(:reference_sets)
|
|
end
|
|
end
|
|
|
|
#
|
|
class SearchReferencesRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# If present, return references for which a prefix of any of
|
|
# sourceAccessions match
|
|
# any of these strings. Accession numbers typically have a main number and a
|
|
# version, for example `GCF_000001405.26`.
|
|
# Corresponds to the JSON property `accessions`
|
|
# @return [Array<String>]
|
|
attr_accessor :accessions
|
|
|
|
# If present, return references for which the
|
|
# md5checksum matches exactly.
|
|
# Corresponds to the JSON property `md5checksums`
|
|
# @return [Array<String>]
|
|
attr_accessor :md5checksums
|
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
# defaults to 1024. The maximum value is 4096.
|
|
# Corresponds to the JSON property `pageSize`
|
|
# @return [Fixnum]
|
|
attr_accessor :page_size
|
|
|
|
# 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.
|
|
# Corresponds to the JSON property `pageToken`
|
|
# @return [String]
|
|
attr_accessor :page_token
|
|
|
|
# If present, return only references which belong to this reference set.
|
|
# Corresponds to the JSON property `referenceSetId`
|
|
# @return [String]
|
|
attr_accessor :reference_set_id
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@accessions = args[:accessions] if args.key?(:accessions)
|
|
@md5checksums = args[:md5checksums] if args.key?(:md5checksums)
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
end
|
|
end
|
|
|
|
#
|
|
class SearchReferencesResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
# The matching references.
|
|
# Corresponds to the JSON property `references`
|
|
# @return [Array<Google::Apis::GenomicsV1::Reference>]
|
|
attr_accessor :references
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
@references = args[:references] if args.key?(:references)
|
|
end
|
|
end
|
|
|
|
# The search variant sets request.
|
|
class SearchVariantSetsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Exactly one dataset ID must be provided here. Only variant sets which
|
|
# belong to this dataset will be returned.
|
|
# Corresponds to the JSON property `datasetIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :dataset_ids
|
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
# defaults to 1024.
|
|
# Corresponds to the JSON property `pageSize`
|
|
# @return [Fixnum]
|
|
attr_accessor :page_size
|
|
|
|
# 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.
|
|
# Corresponds to the JSON property `pageToken`
|
|
# @return [String]
|
|
attr_accessor :page_token
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
end
|
|
end
|
|
|
|
# The search variant sets response.
|
|
class SearchVariantSetsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
# The variant sets belonging to the requested dataset.
|
|
# Corresponds to the JSON property `variantSets`
|
|
# @return [Array<Google::Apis::GenomicsV1::VariantSet>]
|
|
attr_accessor :variant_sets
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
@variant_sets = args[:variant_sets] if args.key?(:variant_sets)
|
|
end
|
|
end
|
|
|
|
# The variant search request.
|
|
class SearchVariantsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Only return variant calls which belong to call sets with these ids.
|
|
# Leaving this blank returns all variant calls. If a variant has no
|
|
# calls belonging to any of these call sets, it won't be returned at all.
|
|
# Corresponds to the JSON property `callSetIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :call_set_ids
|
|
|
|
# The end of the window, 0-based exclusive. If unspecified or 0, defaults to
|
|
# the length of the reference.
|
|
# Corresponds to the JSON property `end`
|
|
# @return [Fixnum]
|
|
attr_accessor :end
|
|
|
|
# The maximum number of calls to return in a single page. Note that this
|
|
# limit may be exceeded in the event that a matching variant contains more
|
|
# calls than the requested maximum. If unspecified, defaults to 5000. The
|
|
# maximum value is 10000.
|
|
# Corresponds to the JSON property `maxCalls`
|
|
# @return [Fixnum]
|
|
attr_accessor :max_calls
|
|
|
|
# The maximum number of variants to return in a single page. If unspecified,
|
|
# defaults to 5000. The maximum value is 10000.
|
|
# Corresponds to the JSON property `pageSize`
|
|
# @return [Fixnum]
|
|
attr_accessor :page_size
|
|
|
|
# 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.
|
|
# Corresponds to the JSON property `pageToken`
|
|
# @return [String]
|
|
attr_accessor :page_token
|
|
|
|
# Required. Only return variants in this reference sequence.
|
|
# Corresponds to the JSON property `referenceName`
|
|
# @return [String]
|
|
attr_accessor :reference_name
|
|
|
|
# The beginning of the window (0-based, inclusive) for which
|
|
# overlapping variants should be returned. If unspecified, defaults to 0.
|
|
# Corresponds to the JSON property `start`
|
|
# @return [Fixnum]
|
|
attr_accessor :start
|
|
|
|
# Only return variants which have exactly this name.
|
|
# Corresponds to the JSON property `variantName`
|
|
# @return [String]
|
|
attr_accessor :variant_name
|
|
|
|
# At most one variant set ID must be provided. Only variants from this
|
|
# variant set will be returned. If omitted, a call set id must be included in
|
|
# the request.
|
|
# Corresponds to the JSON property `variantSetIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :variant_set_ids
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
|
@end = args[:end] if args.key?(:end)
|
|
@max_calls = args[:max_calls] if args.key?(:max_calls)
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
@start = args[:start] if args.key?(:start)
|
|
@variant_name = args[:variant_name] if args.key?(:variant_name)
|
|
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
|
end
|
|
end
|
|
|
|
# The variant search response.
|
|
class SearchVariantsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The continuation token, which is used to page through large result sets.
|
|
# Provide this value in a subsequent request to return the next page of
|
|
# results. This field will be empty if there aren't any additional results.
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
# @return [String]
|
|
attr_accessor :next_page_token
|
|
|
|
# The list of matching Variants.
|
|
# Corresponds to the JSON property `variants`
|
|
# @return [Array<Google::Apis::GenomicsV1::Variant>]
|
|
attr_accessor :variants
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
@variants = args[:variants] if args.key?(:variants)
|
|
end
|
|
end
|
|
|
|
# Request message for `SetIamPolicy` method.
|
|
class SetIamPolicyRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# Defines an Identity and Access Management (IAM) policy. It is used to
|
|
# specify access control policies for Cloud Platform resources.
|
|
# A `Policy` consists of a list of `bindings`. A `binding` binds a list of
|
|
# `members` to a `role`, where the members can be user accounts, Google groups,
|
|
# Google domains, and service accounts. A `role` is a named list of permissions
|
|
# defined by IAM.
|
|
# **JSON Example**
|
|
# `
|
|
# "bindings": [
|
|
# `
|
|
# "role": "roles/owner",
|
|
# "members": [
|
|
# "user:mike@example.com",
|
|
# "group:admins@example.com",
|
|
# "domain:google.com",
|
|
# "serviceAccount:my-other-app@appspot.gserviceaccount.com"
|
|
# ]
|
|
# `,
|
|
# `
|
|
# "role": "roles/viewer",
|
|
# "members": ["user:sean@example.com"]
|
|
# `
|
|
# ]
|
|
# `
|
|
# **YAML Example**
|
|
# bindings:
|
|
# - members:
|
|
# - user:mike@example.com
|
|
# - group:admins@example.com
|
|
# - domain:google.com
|
|
# - serviceAccount:my-other-app@appspot.gserviceaccount.com
|
|
# role: roles/owner
|
|
# - members:
|
|
# - user:sean@example.com
|
|
# role: roles/viewer
|
|
# For a description of IAM and its features, see the
|
|
# [IAM developer's guide](https://cloud.google.com/iam/docs).
|
|
# Corresponds to the JSON property `policy`
|
|
# @return [Google::Apis::GenomicsV1::Policy]
|
|
attr_accessor :policy
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@policy = args[:policy] if args.key?(:policy)
|
|
end
|
|
end
|
|
|
|
# The `Status` type defines a logical error model that is suitable for different
|
|
# programming environments, including REST APIs and RPC APIs. It is used by
|
|
# [gRPC](https://github.com/grpc). The error model is designed to be:
|
|
# - Simple to use and understand for most users
|
|
# - Flexible enough to meet unexpected needs
|
|
# # Overview
|
|
# The `Status` message contains three pieces of data: error code, error message,
|
|
# and error details. The error code should be an enum value of
|
|
# google.rpc.Code, but it may accept additional error codes if needed. The
|
|
# error message should be a developer-facing English message that helps
|
|
# developers *understand* and *resolve* the error. If a localized user-facing
|
|
# error message is needed, put the localized message in the error details or
|
|
# localize it in the client. The optional error details may contain arbitrary
|
|
# information about the error. There is a predefined set of error detail types
|
|
# in the package `google.rpc` that can be used for common error conditions.
|
|
# # Language mapping
|
|
# The `Status` message is the logical representation of the error model, but it
|
|
# is not necessarily the actual wire format. When the `Status` message is
|
|
# exposed in different client libraries and different wire protocols, it can be
|
|
# mapped differently. For example, it will likely be mapped to some exceptions
|
|
# in Java, but more likely mapped to some error codes in C.
|
|
# # Other uses
|
|
# The error model and the `Status` message can be used in a variety of
|
|
# environments, either with or without APIs, to provide a
|
|
# consistent developer experience across different environments.
|
|
# Example uses of this error model include:
|
|
# - Partial errors. If a service needs to return partial errors to the client,
|
|
# it may embed the `Status` in the normal response to indicate the partial
|
|
# errors.
|
|
# - Workflow errors. A typical workflow has multiple steps. Each step may
|
|
# have a `Status` message for error reporting.
|
|
# - Batch operations. If a client uses batch request and batch response, the
|
|
# `Status` message should be used directly inside batch response, one for
|
|
# each error sub-response.
|
|
# - Asynchronous operations. If an API call embeds asynchronous operation
|
|
# results in its response, the status of those operations should be
|
|
# represented directly using the `Status` message.
|
|
# - Logging. If some API errors are stored in logs, the message `Status` could
|
|
# be used directly after any stripping needed for security/privacy reasons.
|
|
class Status
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The status code, which should be an enum value of google.rpc.Code.
|
|
# Corresponds to the JSON property `code`
|
|
# @return [Fixnum]
|
|
attr_accessor :code
|
|
|
|
# A list of messages that carry the error details. There is a common set of
|
|
# message types for APIs to use.
|
|
# Corresponds to the JSON property `details`
|
|
# @return [Array<Hash<String,Object>>]
|
|
attr_accessor :details
|
|
|
|
# A developer-facing error message, which should be in English. Any
|
|
# user-facing error message should be localized and sent in the
|
|
# google.rpc.Status.details field, or localized by the client.
|
|
# Corresponds to the JSON property `message`
|
|
# @return [String]
|
|
attr_accessor :message
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@code = args[:code] if args.key?(:code)
|
|
@details = args[:details] if args.key?(:details)
|
|
@message = args[:message] if args.key?(:message)
|
|
end
|
|
end
|
|
|
|
# Request message for `TestIamPermissions` method.
|
|
class TestIamPermissionsRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# REQUIRED: The set of permissions to check for the 'resource'.
|
|
# Permissions with wildcards (such as '*' or 'storage.*') are not allowed.
|
|
# Allowed permissions are:
|
|
# * `genomics.datasets.create`
|
|
# * `genomics.datasets.delete`
|
|
# * `genomics.datasets.get`
|
|
# * `genomics.datasets.list`
|
|
# * `genomics.datasets.update`
|
|
# * `genomics.datasets.getIamPolicy`
|
|
# * `genomics.datasets.setIamPolicy`
|
|
# Corresponds to the JSON property `permissions`
|
|
# @return [Array<String>]
|
|
attr_accessor :permissions
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@permissions = args[:permissions] if args.key?(:permissions)
|
|
end
|
|
end
|
|
|
|
# Response message for `TestIamPermissions` method.
|
|
class TestIamPermissionsResponse
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# A subset of `TestPermissionsRequest.permissions` that the caller is
|
|
# allowed.
|
|
# Corresponds to the JSON property `permissions`
|
|
# @return [Array<String>]
|
|
attr_accessor :permissions
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@permissions = args[:permissions] if args.key?(:permissions)
|
|
end
|
|
end
|
|
|
|
# A transcript represents the assertion that a particular region of the
|
|
# reference genome may be transcribed as RNA.
|
|
class Transcript
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The range of the coding sequence for this transcript, if any. To determine
|
|
# the exact ranges of coding sequence, intersect this range with those of the
|
|
# exons, if any. If there are any
|
|
# exons, the
|
|
# codingSequence must start
|
|
# and end within them.
|
|
# Note that in some cases, the reference genome will not exactly match the
|
|
# observed mRNA transcript e.g. due to variance in the source genome from
|
|
# reference. In these cases,
|
|
# exon.frame will not necessarily
|
|
# match the expected reference reading frame and coding exon reference bases
|
|
# cannot necessarily be concatenated to produce the original transcript mRNA.
|
|
# Corresponds to the JSON property `codingSequence`
|
|
# @return [Google::Apis::GenomicsV1::CodingSequence]
|
|
attr_accessor :coding_sequence
|
|
|
|
# The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose
|
|
# this transcript. This field should be unset for genomes where transcript
|
|
# splicing does not occur, for example prokaryotes.
|
|
# Introns are regions of the transcript that are not included in the
|
|
# spliced RNA product. Though not explicitly modeled here, intron ranges can
|
|
# be deduced; all regions of this transcript that are not exons are introns.
|
|
# Exonic sequences do not necessarily code for a translational product
|
|
# (amino acids). Only the regions of exons bounded by the
|
|
# codingSequence correspond
|
|
# to coding DNA sequence.
|
|
# Exons are ordered by start position and may not overlap.
|
|
# Corresponds to the JSON property `exons`
|
|
# @return [Array<Google::Apis::GenomicsV1::Exon>]
|
|
attr_accessor :exons
|
|
|
|
# The annotation ID of the gene from which this transcript is transcribed.
|
|
# Corresponds to the JSON property `geneId`
|
|
# @return [String]
|
|
attr_accessor :gene_id
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@coding_sequence = args[:coding_sequence] if args.key?(:coding_sequence)
|
|
@exons = args[:exons] if args.key?(:exons)
|
|
@gene_id = args[:gene_id] if args.key?(:gene_id)
|
|
end
|
|
end
|
|
|
|
#
|
|
class UndeleteDatasetRequest
|
|
include Google::Apis::Core::Hashable
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
end
|
|
end
|
|
|
|
# This event is generated when the execution of a container results in a
|
|
# non-zero exit status that was not otherwise ignored. Execution will
|
|
# continue, but only actions that are flagged as ALWAYS_RUN will be executed:
|
|
# other actions will be skipped.
|
|
class UnexpectedExitStatusEvent
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The numeric ID of the action that started the container.
|
|
# Corresponds to the JSON property `actionId`
|
|
# @return [Fixnum]
|
|
attr_accessor :action_id
|
|
|
|
# The exit status of the container.
|
|
# Corresponds to the JSON property `exitStatus`
|
|
# @return [Fixnum]
|
|
attr_accessor :exit_status
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@action_id = args[:action_id] if args.key?(:action_id)
|
|
@exit_status = args[:exit_status] if args.key?(:exit_status)
|
|
end
|
|
end
|
|
|
|
# A variant represents a change in DNA sequence relative to a reference
|
|
# sequence. For example, a variant could represent a SNP or an insertion.
|
|
# Variants belong to a variant set.
|
|
# Each of the calls on a variant represent a determination of genotype with
|
|
# respect to that variant. For example, a call might assign probability of 0.32
|
|
# to the occurrence of a SNP named rs1234 in a sample named NA12345. A call
|
|
# belongs to a call set, which contains related calls typically from one
|
|
# sample.
|
|
class Variant
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The bases that appear instead of the reference bases.
|
|
# Corresponds to the JSON property `alternateBases`
|
|
# @return [Array<String>]
|
|
attr_accessor :alternate_bases
|
|
|
|
# The variant calls for this particular variant. Each one represents the
|
|
# determination of genotype with respect to this variant.
|
|
# Corresponds to the JSON property `calls`
|
|
# @return [Array<Google::Apis::GenomicsV1::VariantCall>]
|
|
attr_accessor :calls
|
|
|
|
# The date this variant was created, in milliseconds from the epoch.
|
|
# Corresponds to the JSON property `created`
|
|
# @return [Fixnum]
|
|
attr_accessor :created
|
|
|
|
# The end position (0-based) of this variant. This corresponds to the first
|
|
# base after the last base in the reference allele. So, the length of
|
|
# the reference allele is (end - start). This is useful for variants
|
|
# that don't explicitly give alternate bases, for example large deletions.
|
|
# Corresponds to the JSON property `end`
|
|
# @return [Fixnum]
|
|
attr_accessor :end
|
|
|
|
# A list of filters (normally quality filters) this variant has failed.
|
|
# `PASS` indicates this variant has passed all filters.
|
|
# Corresponds to the JSON property `filter`
|
|
# @return [Array<String>]
|
|
attr_accessor :filter
|
|
|
|
# The server-generated variant ID, unique across all variants.
|
|
# Corresponds to the JSON property `id`
|
|
# @return [String]
|
|
attr_accessor :id
|
|
|
|
# A map of additional variant information. This must be of the form
|
|
# map<string, string[]> (string key mapping to a list of string values).
|
|
# Corresponds to the JSON property `info`
|
|
# @return [Hash<String,Array<Object>>]
|
|
attr_accessor :info
|
|
|
|
# Names for the variant, for example a RefSNP ID.
|
|
# Corresponds to the JSON property `names`
|
|
# @return [Array<String>]
|
|
attr_accessor :names
|
|
|
|
# A measure of how likely this variant is to be real.
|
|
# A higher value is better.
|
|
# Corresponds to the JSON property `quality`
|
|
# @return [Float]
|
|
attr_accessor :quality
|
|
|
|
# The reference bases for this variant. They start at the given
|
|
# position.
|
|
# Corresponds to the JSON property `referenceBases`
|
|
# @return [String]
|
|
attr_accessor :reference_bases
|
|
|
|
# The reference on which this variant occurs.
|
|
# (such as `chr20` or `X`)
|
|
# Corresponds to the JSON property `referenceName`
|
|
# @return [String]
|
|
attr_accessor :reference_name
|
|
|
|
# The position at which this variant occurs (0-based).
|
|
# This corresponds to the first base of the string of reference bases.
|
|
# Corresponds to the JSON property `start`
|
|
# @return [Fixnum]
|
|
attr_accessor :start
|
|
|
|
# The ID of the variant set this variant belongs to.
|
|
# Corresponds to the JSON property `variantSetId`
|
|
# @return [String]
|
|
attr_accessor :variant_set_id
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@alternate_bases = args[:alternate_bases] if args.key?(:alternate_bases)
|
|
@calls = args[:calls] if args.key?(:calls)
|
|
@created = args[:created] if args.key?(:created)
|
|
@end = args[:end] if args.key?(:end)
|
|
@filter = args[:filter] if args.key?(:filter)
|
|
@id = args[:id] if args.key?(:id)
|
|
@info = args[:info] if args.key?(:info)
|
|
@names = args[:names] if args.key?(:names)
|
|
@quality = args[:quality] if args.key?(:quality)
|
|
@reference_bases = args[:reference_bases] if args.key?(:reference_bases)
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
@start = args[:start] if args.key?(:start)
|
|
@variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
|
|
end
|
|
end
|
|
|
|
#
|
|
class VariantAnnotation
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The alternate allele for this variant. If multiple alternate alleles
|
|
# exist at this location, create a separate variant for each one, as they
|
|
# may represent distinct conditions.
|
|
# Corresponds to the JSON property `alternateBases`
|
|
# @return [String]
|
|
attr_accessor :alternate_bases
|
|
|
|
# Describes the clinical significance of a variant.
|
|
# It is adapted from the ClinVar controlled vocabulary for clinical
|
|
# significance described at:
|
|
# http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
|
|
# Corresponds to the JSON property `clinicalSignificance`
|
|
# @return [String]
|
|
attr_accessor :clinical_significance
|
|
|
|
# The set of conditions associated with this variant.
|
|
# A condition describes the way a variant influences human health.
|
|
# Corresponds to the JSON property `conditions`
|
|
# @return [Array<Google::Apis::GenomicsV1::ClinicalCondition>]
|
|
attr_accessor :conditions
|
|
|
|
# Effect of the variant on the coding sequence.
|
|
# Corresponds to the JSON property `effect`
|
|
# @return [String]
|
|
attr_accessor :effect
|
|
|
|
# Google annotation ID of the gene affected by this variant. This should
|
|
# be provided when the variant is created.
|
|
# Corresponds to the JSON property `geneId`
|
|
# @return [String]
|
|
attr_accessor :gene_id
|
|
|
|
# Google annotation IDs of the transcripts affected by this variant. These
|
|
# should be provided when the variant is created.
|
|
# Corresponds to the JSON property `transcriptIds`
|
|
# @return [Array<String>]
|
|
attr_accessor :transcript_ids
|
|
|
|
# Type has been adapted from ClinVar's list of variant types.
|
|
# Corresponds to the JSON property `type`
|
|
# @return [String]
|
|
attr_accessor :type
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@alternate_bases = args[:alternate_bases] if args.key?(:alternate_bases)
|
|
@clinical_significance = args[:clinical_significance] if args.key?(:clinical_significance)
|
|
@conditions = args[:conditions] if args.key?(:conditions)
|
|
@effect = args[:effect] if args.key?(:effect)
|
|
@gene_id = args[:gene_id] if args.key?(:gene_id)
|
|
@transcript_ids = args[:transcript_ids] if args.key?(:transcript_ids)
|
|
@type = args[:type] if args.key?(:type)
|
|
end
|
|
end
|
|
|
|
# A call represents the determination of genotype with respect to a particular
|
|
# variant. It may include associated information such as quality and phasing.
|
|
# For example, a call might assign a probability of 0.32 to the occurrence of
|
|
# a SNP named rs1234 in a call set with the name NA12345.
|
|
class VariantCall
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The ID of the call set this variant call belongs to.
|
|
# Corresponds to the JSON property `callSetId`
|
|
# @return [String]
|
|
attr_accessor :call_set_id
|
|
|
|
# The name of the call set this variant call belongs to.
|
|
# Corresponds to the JSON property `callSetName`
|
|
# @return [String]
|
|
attr_accessor :call_set_name
|
|
|
|
# The genotype of this variant call. Each value represents either the value
|
|
# of the `referenceBases` field or a 1-based index into
|
|
# `alternateBases`. If a variant had a `referenceBases`
|
|
# value of `T` and an `alternateBases`
|
|
# value of `["A", "C"]`, and the `genotype` was
|
|
# `[2, 1]`, that would mean the call
|
|
# represented the heterozygous value `CA` for this variant.
|
|
# If the `genotype` was instead `[0, 1]`, the
|
|
# represented value would be `TA`. Ordering of the
|
|
# genotype values is important if the `phaseset` is present.
|
|
# If a genotype is not called (that is, a `.` is present in the
|
|
# GT string) -1 is returned.
|
|
# Corresponds to the JSON property `genotype`
|
|
# @return [Array<Fixnum>]
|
|
attr_accessor :genotype
|
|
|
|
# The genotype likelihoods for this variant call. Each array entry
|
|
# represents how likely a specific genotype is for this call. The value
|
|
# ordering is defined by the GL tag in the VCF spec.
|
|
# If Phred-scaled genotype likelihood scores (PL) are available and
|
|
# log10(P) genotype likelihood scores (GL) are not, PL scores are converted
|
|
# to GL scores. If both are available, PL scores are stored in `info`.
|
|
# Corresponds to the JSON property `genotypeLikelihood`
|
|
# @return [Array<Float>]
|
|
attr_accessor :genotype_likelihood
|
|
|
|
# A map of additional variant call information. This must be of the form
|
|
# map<string, string[]> (string key mapping to a list of string values).
|
|
# Corresponds to the JSON property `info`
|
|
# @return [Hash<String,Array<Object>>]
|
|
attr_accessor :info
|
|
|
|
# If this field is present, this variant call's genotype ordering implies
|
|
# the phase of the bases and is consistent with any other variant calls in
|
|
# the same reference sequence which have the same phaseset value.
|
|
# When importing data from VCF, if the genotype data was phased but no
|
|
# phase set was specified this field will be set to `*`.
|
|
# Corresponds to the JSON property `phaseset`
|
|
# @return [String]
|
|
attr_accessor :phaseset
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@call_set_id = args[:call_set_id] if args.key?(:call_set_id)
|
|
@call_set_name = args[:call_set_name] if args.key?(:call_set_name)
|
|
@genotype = args[:genotype] if args.key?(:genotype)
|
|
@genotype_likelihood = args[:genotype_likelihood] if args.key?(:genotype_likelihood)
|
|
@info = args[:info] if args.key?(:info)
|
|
@phaseset = args[:phaseset] if args.key?(:phaseset)
|
|
end
|
|
end
|
|
|
|
# A variant set is a collection of call sets and variants. It contains summary
|
|
# statistics of those contents. A variant set belongs to a dataset.
|
|
class VariantSet
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The dataset to which this variant set belongs.
|
|
# Corresponds to the JSON property `datasetId`
|
|
# @return [String]
|
|
attr_accessor :dataset_id
|
|
|
|
# A textual description of this variant set.
|
|
# Corresponds to the JSON property `description`
|
|
# @return [String]
|
|
attr_accessor :description
|
|
|
|
# The server-generated variant set ID, unique across all variant sets.
|
|
# Corresponds to the JSON property `id`
|
|
# @return [String]
|
|
attr_accessor :id
|
|
|
|
# The metadata associated with this variant set.
|
|
# Corresponds to the JSON property `metadata`
|
|
# @return [Array<Google::Apis::GenomicsV1::VariantSetMetadata>]
|
|
attr_accessor :metadata
|
|
|
|
# User-specified, mutable name.
|
|
# Corresponds to the JSON property `name`
|
|
# @return [String]
|
|
attr_accessor :name
|
|
|
|
# A list of all references used by the variants in a variant set
|
|
# with associated coordinate upper bounds for each one.
|
|
# Corresponds to the JSON property `referenceBounds`
|
|
# @return [Array<Google::Apis::GenomicsV1::ReferenceBound>]
|
|
attr_accessor :reference_bounds
|
|
|
|
# The reference set to which the variant set is mapped. The reference set
|
|
# describes the alignment provenance of the variant set, while the
|
|
# `referenceBounds` describe the shape of the actual variant data. The
|
|
# reference set's reference names are a superset of those found in the
|
|
# `referenceBounds`.
|
|
# For example, given a variant set that is mapped to the GRCh38 reference set
|
|
# and contains a single variant on reference 'X', `referenceBounds` would
|
|
# contain only an entry for 'X', while the associated reference set
|
|
# enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
|
|
# Corresponds to the JSON property `referenceSetId`
|
|
# @return [String]
|
|
attr_accessor :reference_set_id
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
@description = args[:description] if args.key?(:description)
|
|
@id = args[:id] if args.key?(:id)
|
|
@metadata = args[:metadata] if args.key?(:metadata)
|
|
@name = args[:name] if args.key?(:name)
|
|
@reference_bounds = args[:reference_bounds] if args.key?(:reference_bounds)
|
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
end
|
|
end
|
|
|
|
# Metadata describes a single piece of variant call metadata.
|
|
# These data include a top level key and either a single value string (value)
|
|
# or a list of key-value pairs (info.)
|
|
# Value and info are mutually exclusive.
|
|
class VariantSetMetadata
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# A textual description of this metadata.
|
|
# Corresponds to the JSON property `description`
|
|
# @return [String]
|
|
attr_accessor :description
|
|
|
|
# User-provided ID field, not enforced by this API.
|
|
# Two or more pieces of structured metadata with identical
|
|
# id and key fields are considered equivalent.
|
|
# Corresponds to the JSON property `id`
|
|
# @return [String]
|
|
attr_accessor :id
|
|
|
|
# Remaining structured metadata key-value pairs. This must be of the form
|
|
# map<string, string[]> (string key mapping to a list of string values).
|
|
# Corresponds to the JSON property `info`
|
|
# @return [Hash<String,Array<Object>>]
|
|
attr_accessor :info
|
|
|
|
# The top-level key.
|
|
# Corresponds to the JSON property `key`
|
|
# @return [String]
|
|
attr_accessor :key
|
|
|
|
# The number of values that can be included in a field described by this
|
|
# metadata.
|
|
# Corresponds to the JSON property `number`
|
|
# @return [String]
|
|
attr_accessor :number
|
|
|
|
# The type of data. Possible types include: Integer, Float,
|
|
# Flag, Character, and String.
|
|
# Corresponds to the JSON property `type`
|
|
# @return [String]
|
|
attr_accessor :type
|
|
|
|
# The value field for simple metadata
|
|
# Corresponds to the JSON property `value`
|
|
# @return [String]
|
|
attr_accessor :value
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@description = args[:description] if args.key?(:description)
|
|
@id = args[:id] if args.key?(:id)
|
|
@info = args[:info] if args.key?(:info)
|
|
@key = args[:key] if args.key?(:key)
|
|
@number = args[:number] if args.key?(:number)
|
|
@type = args[:type] if args.key?(:type)
|
|
@value = args[:value] if args.key?(:value)
|
|
end
|
|
end
|
|
|
|
# This event is generated once a worker VM has been assigned to run the
|
|
# pipeline.
|
|
class WorkerAssignedEvent
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The worker's instance name.
|
|
# Corresponds to the JSON property `instance`
|
|
# @return [String]
|
|
attr_accessor :instance
|
|
|
|
# The zone the worker is running in.
|
|
# Corresponds to the JSON property `zone`
|
|
# @return [String]
|
|
attr_accessor :zone
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@instance = args[:instance] if args.key?(:instance)
|
|
@zone = args[:zone] if args.key?(:zone)
|
|
end
|
|
end
|
|
|
|
# This event is generated when the worker VM that was assigned to the pipeline
|
|
# has been released (i.e., deleted).
|
|
class WorkerReleasedEvent
|
|
include Google::Apis::Core::Hashable
|
|
|
|
# The worker's instance name.
|
|
# Corresponds to the JSON property `instance`
|
|
# @return [String]
|
|
attr_accessor :instance
|
|
|
|
# The zone the worker was running in.
|
|
# Corresponds to the JSON property `zone`
|
|
# @return [String]
|
|
attr_accessor :zone
|
|
|
|
def initialize(**args)
|
|
update!(**args)
|
|
end
|
|
|
|
# Update properties of this object
|
|
def update!(**args)
|
|
@instance = args[:instance] if args.key?(:instance)
|
|
@zone = args[:zone] if args.key?(:zone)
|
|
end
|
|
end
|
|
end
|
|
end
|
|
end
|