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google-api-ruby-client/generated/google/apis/genomics_v1/classes.rb

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# Copyright 2015 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
require 'date'
require 'google/apis/core/base_service'
require 'google/apis/core/json_representation'
require 'google/apis/core/hashable'
require 'google/apis/errors'
module Google
module Apis
module GenomicsV1
# 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`.
class Annotation
include Google::Apis::Core::Hashable
# The annotation set to which this annotation belongs.
# Corresponds to the JSON property `annotationSetId`
# @return [String]
attr_accessor :annotation_set_id
# The end position of the range on the reference, 0-based exclusive.
# Corresponds to the JSON property `end`
# @return [Fixnum]
attr_accessor :end
# The server-generated annotation ID, unique across all annotations.
# 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
# The display name of this annotation.
# Corresponds to the JSON property `name`
# @return [String]
attr_accessor :name
# The ID of the Google Genomics reference associated with this range.
# Corresponds to the JSON property `referenceId`
# @return [String]
attr_accessor :reference_id
# The display name corresponding to the reference specified by
# `referenceId`, for example `chr1`, `1`, or `chrX`.
# Corresponds to the JSON property `referenceName`
# @return [String]
attr_accessor :reference_name
# Whether this range refers to the reverse strand, as opposed to the forward
# strand. Note that regardless of this field, the start/end position of the
# range always refer to the forward strand.
# Corresponds to the JSON property `reverseStrand`
# @return [Boolean]
attr_accessor :reverse_strand
alias_method :reverse_strand?, :reverse_strand
# The start position of the range on the reference, 0-based inclusive.
# Corresponds to the JSON property `start`
# @return [Fixnum]
attr_accessor :start
# A transcript represents the assertion that a particular region of the
# reference genome may be transcribed as RNA.
# Corresponds to the JSON property `transcript`
# @return [Google::Apis::GenomicsV1::Transcript]
attr_accessor :transcript
# The data type for this annotation. Must match the containing annotation
# set's type.
# Corresponds to the JSON property `type`
# @return [String]
attr_accessor :type
# A variant annotation, which describes the effect of a variant on the
# genome, the coding sequence, and/or higher level consequences at the
# organism level e.g. pathogenicity. This field is only set for annotations
# of type `VARIANT`.
# Corresponds to the JSON property `variant`
# @return [Google::Apis::GenomicsV1::VariantAnnotation]
attr_accessor :variant
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@annotation_set_id = args[:annotation_set_id] if args.key?(:annotation_set_id)
@end = args[:end] if args.key?(:end)
@id = args[:id] if args.key?(:id)
@info = args[:info] if args.key?(:info)
@name = args[:name] if args.key?(:name)
@reference_id = args[:reference_id] if args.key?(:reference_id)
@reference_name = args[:reference_name] if args.key?(:reference_name)
@reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
@start = args[:start] if args.key?(:start)
@transcript = args[:transcript] if args.key?(:transcript)
@type = args[:type] if args.key?(:type)
@variant = args[:variant] if args.key?(:variant)
end
end
# An annotation set is a logical grouping of annotations that share consistent
# type information and provenance. Examples of annotation sets include 'all
# genes from refseq', and 'all variant annotations from ClinVar'.
class AnnotationSet
include Google::Apis::Core::Hashable
# The dataset to which this annotation set belongs.
# Corresponds to the JSON property `datasetId`
# @return [String]
attr_accessor :dataset_id
# The server-generated annotation set ID, unique across all annotation sets.
# 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
# The display name for this annotation set.
# Corresponds to the JSON property `name`
# @return [String]
attr_accessor :name
# The ID of the reference set that defines the coordinate space for this
# set's annotations.
# Corresponds to the JSON property `referenceSetId`
# @return [String]
attr_accessor :reference_set_id
# The source URI describing the file from which this annotation set was
# generated, if any.
# Corresponds to the JSON property `sourceUri`
# @return [String]
attr_accessor :source_uri
# The type of annotations contained within this set.
# 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)
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
@id = args[:id] if args.key?(:id)
@info = args[:info] if args.key?(:info)
@name = args[:name] if args.key?(:name)
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
@source_uri = args[:source_uri] if args.key?(:source_uri)
@type = args[:type] if args.key?(:type)
end
end
#
class BatchCreateAnnotationsRequest
include Google::Apis::Core::Hashable
# The annotations to be created. At most 4096 can be specified in a single
# request.
# Corresponds to the JSON property `annotations`
# @return [Array<Google::Apis::GenomicsV1::Annotation>]
attr_accessor :annotations
# A unique request ID which enables the server to detect duplicated requests.
# If provided, duplicated requests will result in the same response; if not
# provided, duplicated requests may result in duplicated data. For a given
# annotation set, callers should not reuse `request_id`s when writing
# different batches of annotations - behavior in this case is undefined.
# A common approach is to use a UUID. For batch jobs where worker crashes are
# a possibility, consider using some unique variant of a worker or run ID.
# Corresponds to the JSON property `requestId`
# @return [String]
attr_accessor :request_id
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@annotations = args[:annotations] if args.key?(:annotations)
@request_id = args[:request_id] if args.key?(:request_id)
end
end
#
class BatchCreateAnnotationsResponse
include Google::Apis::Core::Hashable
# The resulting per-annotation entries, ordered consistently with the
# original request.
# Corresponds to the JSON property `entries`
# @return [Array<Google::Apis::GenomicsV1::Entry>]
attr_accessor :entries
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@entries = args[:entries] if args.key?(:entries)
end
end
# Associates `members` with a `role`.
class Binding
include Google::Apis::Core::Hashable
# Specifies the identities requesting access for a Cloud Platform resource.
# `members` can have the following values:
# * `allUsers`: A special identifier that represents anyone who is
# on the internet; with or without a Google account.
# * `allAuthenticatedUsers`: A special identifier that represents anyone
# who is authenticated with a Google account or a service account.
# * `user:`emailid``: An email address that represents a specific Google
# account. For example, `alice@gmail.com` or `joe@example.com`.
# * `serviceAccount:`emailid``: An email address that represents a service
# account. For example, `my-other-app@appspot.gserviceaccount.com`.
# * `group:`emailid``: An email address that represents a Google group.
# For example, `admins@example.com`.
# * `domain:`domain``: A Google Apps domain name that represents all the
# users of that domain. For example, `google.com` or `example.com`.
# Corresponds to the JSON property `members`
# @return [Array<String>]
attr_accessor :members
# Role that is assigned to `members`.
# For example, `roles/viewer`, `roles/editor`, or `roles/owner`.
# Required
# Corresponds to the JSON property `role`
# @return [String]
attr_accessor :role
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@members = args[:members] if args.key?(:members)
@role = args[:role] if args.key?(:role)
end
end
# A call set is a collection of variant calls, typically for one sample. It
# belongs to a variant set.
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
class CallSet
include Google::Apis::Core::Hashable
# The date this call set was created in milliseconds from the epoch.
# Corresponds to the JSON property `created`
# @return [Fixnum]
attr_accessor :created
# The server-generated call set ID, unique across all call sets.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# A map of additional call set 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 call set name.
# Corresponds to the JSON property `name`
# @return [String]
attr_accessor :name
# The sample ID this call set corresponds to.
# Corresponds to the JSON property `sampleId`
# @return [String]
attr_accessor :sample_id
# The IDs of the variant sets this call set belongs to. This field must
# have exactly length one, as a call set belongs to a single variant set.
# This field is repeated for compatibility with the
# [GA4GH 0.5.1
# API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/
# variants.avdl#L76).
# 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)
@created = args[:created] if args.key?(:created)
@id = args[:id] if args.key?(:id)
@info = args[:info] if args.key?(:info)
@name = args[:name] if args.key?(:name)
@sample_id = args[:sample_id] if args.key?(:sample_id)
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
end
end
# The request message for Operations.CancelOperation.
class CancelOperationRequest
include Google::Apis::Core::Hashable
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
end
end
# A single CIGAR operation.
class CigarUnit
include Google::Apis::Core::Hashable
#
# Corresponds to the JSON property `operation`
# @return [String]
attr_accessor :operation
# The number of genomic bases that the operation runs for. Required.
# Corresponds to the JSON property `operationLength`
# @return [Fixnum]
attr_accessor :operation_length
# `referenceSequence` is only used at mismatches
# (`SEQUENCE_MISMATCH`) and deletions (`DELETE`).
# Filling this field replaces SAM's MD tag. If the relevant information is
# not available, this field is unset.
# Corresponds to the JSON property `referenceSequence`
# @return [String]
attr_accessor :reference_sequence
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@operation = args[:operation] if args.key?(:operation)
@operation_length = args[:operation_length] if args.key?(:operation_length)
@reference_sequence = args[:reference_sequence] if args.key?(:reference_sequence)
end
end
#
class ClinicalCondition
include Google::Apis::Core::Hashable
# The MedGen concept id associated with this gene.
# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
# Corresponds to the JSON property `conceptId`
# @return [String]
attr_accessor :concept_id
# The set of external IDs for this condition.
# Corresponds to the JSON property `externalIds`
# @return [Array<Google::Apis::GenomicsV1::ExternalId>]
attr_accessor :external_ids
# A set of names for the condition.
# Corresponds to the JSON property `names`
# @return [Array<String>]
attr_accessor :names
# The OMIM id for this condition.
# Search for these IDs at http://omim.org/
# Corresponds to the JSON property `omimId`
# @return [String]
attr_accessor :omim_id
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@concept_id = args[:concept_id] if args.key?(:concept_id)
@external_ids = args[:external_ids] if args.key?(:external_ids)
@names = args[:names] if args.key?(:names)
@omim_id = args[:omim_id] if args.key?(:omim_id)
end
end
#
class CodingSequence
include Google::Apis::Core::Hashable
# The end of the coding sequence on this annotation's reference sequence,
# 0-based exclusive. Note that this position is relative to the reference
# start, and *not* the containing annotation start.
# Corresponds to the JSON property `end`
# @return [Fixnum]
attr_accessor :end
# The start of the coding sequence on this annotation's reference sequence,
# 0-based inclusive. Note that this position 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)
@start = args[:start] if args.key?(:start)
end
end
# Describes a Compute Engine resource that is being managed by a running
# pipeline.
class ComputeEngine
include Google::Apis::Core::Hashable
# The names of the disks that were created for this pipeline.
# Corresponds to the JSON property `diskNames`
# @return [Array<String>]
attr_accessor :disk_names
# The instance on which the operation is running.
# Corresponds to the JSON property `instanceName`
# @return [String]
attr_accessor :instance_name
# The machine type of the instance.
# Corresponds to the JSON property `machineType`
# @return [String]
attr_accessor :machine_type
# The availability zone in which the instance resides.
# 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)
@disk_names = args[:disk_names] if args.key?(:disk_names)
@instance_name = args[:instance_name] if args.key?(:instance_name)
@machine_type = args[:machine_type] if args.key?(:machine_type)
@zone = args[:zone] if args.key?(:zone)
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.
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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
# 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
#
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
# 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 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&#58; `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.
# **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"]
# `
# ]
# `
# 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
# 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.
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
# ### 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.
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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.
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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.
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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.
# **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"]
# `
# ]
# `
# 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&#58;
# * `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
# 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.
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
# 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.
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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
end
end
end
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