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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
# 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] unless args[:datasets].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
end
end
# A Dataset is a collection of genomic data.
class Dataset
include Google::Apis::Core::Hashable
# The server-generated dataset ID, unique across all datasets.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# The Google Developers Console project ID that this dataset belongs to.
# Corresponds to the JSON property `projectId`
# @return [String]
attr_accessor :project_id
# The dataset name.
# Corresponds to the JSON property `name`
# @return [String]
attr_accessor :name
# The time this dataset was created, in seconds from the epoch.
# Corresponds to the JSON property `createTime`
# @return [String]
attr_accessor :create_time
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@id = args[:id] unless args[:id].nil?
@project_id = args[:project_id] unless args[:project_id].nil?
@name = args[:name] unless args[:name].nil?
@create_time = args[:create_time] unless args[:create_time].nil?
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 UndeleteDatasetRequest
include Google::Apis::Core::Hashable
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
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
# The server-assigned name, which is only unique within the same service that
# originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-
# qzoWAgEw`
# Corresponds to the JSON property `name`
# @return [String]
attr_accessor :name
# An [OperationMetadata][google.genomics.v1.OperationMetadata] object. This will
# always be returned with the [Operation][google.longrunning.Operation].
# Corresponds to the JSON property `metadata`
# @return [Hash<String,Object>]
attr_accessor :metadata
# If the value is `false`, it means the operation is still in progress. If true,
# the operation is completed and the `result` is available.
# Corresponds to the JSON property `done`
# @return [Boolean]
attr_accessor :done
alias_method :done?, :done
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# The `Status` type defines a logical error model that is suitable for different
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# 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
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# use and understand for most users - Flexible enough to meet unexpected needs #
# Overview The `Status` message contains three pieces of data: error code, error
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# message, and error details. The error code should be an enum value of [google.
# rpc.Code][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
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# 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` which 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 purpose. - 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.
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# Corresponds to the JSON property `error`
# @return [Google::Apis::GenomicsV1::Status]
attr_accessor :error
# If importing [ReadGroupSets][google.genomics.v1.ReadGroupSet], an [
# ImportReadGroupSetsResponse][google.genomics.v1.ImportReadGroupSetsResponse]
# is returned. If importing [Variants][google.genomics.v1.Variant], an [
# ImportVariantsResponse][google.genomics.v1.ImportVariantsResponse] is returned.
# For 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)
@name = args[:name] unless args[:name].nil?
@metadata = args[:metadata] unless args[:metadata].nil?
@done = args[:done] unless args[:done].nil?
@error = args[:error] unless args[:error].nil?
@response = args[:response] unless args[:response].nil?
end
end
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# The `Status` type defines a logical error model that is suitable for different
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# 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
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# use and understand for most users - Flexible enough to meet unexpected needs #
# Overview The `Status` message contains three pieces of data: error code, error
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# message, and error details. The error code should be an enum value of [google.
# rpc.Code][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
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# 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` which 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 purpose. - 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.
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class Status
include Google::Apis::Core::Hashable
# The status code, which should be an enum value of [google.rpc.Code][google.rpc.
# Code].
# Corresponds to the JSON property `code`
# @return [Fixnum]
attr_accessor :code
# 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][
# google.rpc.Status.details] field, or localized by the client.
# Corresponds to the JSON property `message`
# @return [String]
attr_accessor :message
# A list of messages that carry the error details. There will be a common set of
# message types for APIs to use.
# Corresponds to the JSON property `details`
# @return [Array<Hash<String,Object>>]
attr_accessor :details
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@code = args[:code] unless args[:code].nil?
@message = args[:message] unless args[:message].nil?
@details = args[:details] unless args[:details].nil?
end
end
# The response message for [Operations.ListOperations][google.longrunning.
# Operations.ListOperations].
class ListOperationsResponse
include Google::Apis::Core::Hashable
# 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
# The standard List next-page token.
# 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)
@operations = args[:operations] unless args[:operations].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
end
end
# The request message for [Operations.CancelOperation][google.longrunning.
# 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
# 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 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 in Google Cloud Storage.
# Corresponds to the JSON property `sourceUris`
# @return [Array<String>]
attr_accessor :source_uris
# 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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
@source_uris = args[:source_uris] unless args[:source_uris].nil?
@partition_strategy = args[:partition_strategy] unless args[:partition_strategy].nil?
end
end
# The read group set export request.
class ExportReadGroupSetRequest
include Google::Apis::Core::Hashable
# Required. The Google Developers Console project ID that owns this export.
# Corresponds to the JSON property `projectId`
# @return [String]
attr_accessor :project_id
# 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
# 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)
@project_id = args[:project_id] unless args[:project_id].nil?
@export_uri = args[:export_uri] unless args[:export_uri].nil?
@reference_names = args[:reference_names] unless args[:reference_names].nil?
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 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
# Specifies number of results to return in a single page. If unspecified, it
# will default to 256. The maximum value is 1024.
# Corresponds to the JSON property `pageSize`
# @return [Fixnum]
attr_accessor :page_size
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@dataset_ids = args[:dataset_ids] unless args[:dataset_ids].nil?
@name = args[:name] unless args[:name].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
end
end
# The read group set search response.
class SearchReadGroupSetsResponse
include Google::Apis::Core::Hashable
# The list of matching read group sets.
# Corresponds to the JSON property `readGroupSets`
# @return [Array<Google::Apis::GenomicsV1::ReadGroupSet>]
attr_accessor :read_group_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)
@read_group_sets = args[:read_group_sets] unless args[:read_group_sets].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
end
end
# A read group set is a logical collection of read groups, which are collections
# of reads produced by a sequencer. A read group set typically models reads
# corresponding to one sample, sequenced one way, and aligned one way. * A read
# group set belongs to one dataset. * A read group belongs to one read group set.
# * A read belongs to one read group.
class ReadGroupSet
include Google::Apis::Core::Hashable
# The server-generated read group set ID, unique for all read group sets.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# The dataset ID.
# Corresponds to the JSON property `datasetId`
# @return [String]
attr_accessor :dataset_id
# The reference set the reads in this read group set are aligned to.
# Corresponds to the JSON property `referenceSetId`
# @return [String]
attr_accessor :reference_set_id
# 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 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 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
# A map of additional read group set information.
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<Object>>]
attr_accessor :info
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@id = args[:id] unless args[:id].nil?
@dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
@name = args[:name] unless args[:name].nil?
@filename = args[:filename] unless args[:filename].nil?
@read_groups = args[:read_groups] unless args[:read_groups].nil?
@info = args[:info] unless args[:info].nil?
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 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 the `
# name` field.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# The ID of the dataset this read group belongs to.
# Corresponds to the JSON property `datasetId`
# @return [String]
attr_accessor :dataset_id
# 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
# A free-form text description of this read group.
# Corresponds to the JSON property `description`
# @return [String]
attr_accessor :description
# The sample this read group's data was generated from. Note: This is not an
# actual ID within this repository, but rather an identifier for a sample which
# may be meaningful to some external system.
# Corresponds to the JSON property `sampleId`
# @return [String]
attr_accessor :sample_id
# The experiment used to generate this read group.
# Corresponds to the JSON property `experiment`
# @return [Google::Apis::GenomicsV1::Experiment]
attr_accessor :experiment
# 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. Required if
# there are any read alignments.
# Corresponds to the JSON property `referenceSetId`
# @return [String]
attr_accessor :reference_set_id
# A map of additional read group information. This must be of the form map (
# string key mapping to a list of string values).
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<Object>>]
attr_accessor :info
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@id = args[:id] unless args[:id].nil?
@dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
@name = args[:name] unless args[:name].nil?
@description = args[:description] unless args[:description].nil?
@sample_id = args[:sample_id] unless args[:sample_id].nil?
@experiment = args[:experiment] unless args[:experiment].nil?
@predicted_insert_size = args[:predicted_insert_size] unless args[:predicted_insert_size].nil?
@programs = args[:programs] unless args[:programs].nil?
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
@info = args[:info] unless args[:info].nil?
end
end
#
class Experiment
include Google::Apis::Core::Hashable
# The library used as part of this experiment. Note: This is not an actual ID
# within this repository, but rather an identifier for a library which may be
# meaningful to some external system.
# Corresponds to the JSON property `libraryId`
# @return [String]
attr_accessor :library_id
# The platform unit used as part of this experiment e.g. 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
# The instrument model used as part of this experiment. This maps to sequencing
# technology in BAM.
# Corresponds to the JSON property `instrumentModel`
# @return [String]
attr_accessor :instrument_model
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@library_id = args[:library_id] unless args[:library_id].nil?
@platform_unit = args[:platform_unit] unless args[:platform_unit].nil?
@sequencing_center = args[:sequencing_center] unless args[:sequencing_center].nil?
@instrument_model = args[:instrument_model] unless args[:instrument_model].nil?
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 name of the program.
# 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] unless args[:command_line].nil?
@id = args[:id] unless args[:id].nil?
@name = args[:name] unless args[:name].nil?
@prev_program_id = args[:prev_program_id] unless args[:prev_program_id].nil?
@version = args[:version] unless args[:version].nil?
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 [String]
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] unless args[:bucket_width].nil?
@coverage_buckets = args[:coverage_buckets] unless args[:coverage_buckets].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
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
# 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
# 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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@range = args[:range] unless args[:range].nil?
@mean_coverage = args[:mean_coverage] unless args[:mean_coverage].nil?
end
end
# A 0-based half-open genomic coordinate range for search requests.
class Range
include Google::Apis::Core::Hashable
# 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 [String]
attr_accessor :start
# The end position of the range on the reference, 0-based exclusive.
# Corresponds to the JSON property `end`
# @return [String]
attr_accessor :end
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@start = args[:start] unless args[:start].nil?
@end = args[:end] unless args[:end].nil?
end
end
# The read search request.
class SearchReadsRequest
include Google::Apis::Core::Hashable
# 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 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 reference sequence name, for example `chr1`, `1`, or `chrX`. If set to *,
# only unmapped reads 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 [String]
attr_accessor :start
# 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 [String]
attr_accessor :end
# 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
# Specifies number of results to return in a single page. If unspecified, it
# will default to 256. The maximum value is 2048.
# Corresponds to the JSON property `pageSize`
# @return [Fixnum]
attr_accessor :page_size
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@read_group_set_ids = args[:read_group_set_ids] unless args[:read_group_set_ids].nil?
@read_group_ids = args[:read_group_ids] unless args[:read_group_ids].nil?
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@start = args[:start] unless args[:start].nil?
@end = args[:end] unless args[:end].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
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 last and are further 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] unless args[:alignments].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
end
end
# A read alignment describes a linear alignment of a string of DNA to a [
# reference sequence][google.genomics.v1.Reference], 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]
# [google.genomics.v1.ReadGroupSet]. ### 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 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
# The ID of the read group this read belongs to. (Every read must belong to
# exactly one read group.)
# Corresponds to the JSON property `readGroupId`
# @return [String]
attr_accessor :read_group_id
# The ID of the read group set this read belongs to. (Every read must belong to
# exactly one read group set.)
# Corresponds to the JSON property `readGroupSetId`
# @return [String]
attr_accessor :read_group_set_id
# The fragment name. Equivalent to QNAME (query template name) in SAM.
# Corresponds to the JSON property `fragmentName`
# @return [String]
attr_accessor :fragment_name
# 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 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
# The observed length of the fragment, equivalent to TLEN in SAM.
# Corresponds to the JSON property `fragmentLength`
# @return [Fixnum]
attr_accessor :fragment_length
# 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
# The number of reads in the fragment (extension to SAM flag 0x1).
# Corresponds to the JSON property `numberReads`
# @return [Fixnum]
attr_accessor :number_reads
# 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
# 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
# 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
# The bases of the read sequence contained in this alignment record, *without
# CIGAR operations applied*. `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
# The quality of the read sequence contained in this alignment record. `
# 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
# 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
# A map of additional read alignment information. This must be of the form map (
# string key mapping to a list of string values).
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<Object>>]
attr_accessor :info
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@id = args[:id] unless args[:id].nil?
@read_group_id = args[:read_group_id] unless args[:read_group_id].nil?
@read_group_set_id = args[:read_group_set_id] unless args[:read_group_set_id].nil?
@fragment_name = args[:fragment_name] unless args[:fragment_name].nil?
@proper_placement = args[:proper_placement] unless args[:proper_placement].nil?
@duplicate_fragment = args[:duplicate_fragment] unless args[:duplicate_fragment].nil?
@fragment_length = args[:fragment_length] unless args[:fragment_length].nil?
@read_number = args[:read_number] unless args[:read_number].nil?
@number_reads = args[:number_reads] unless args[:number_reads].nil?
@failed_vendor_quality_checks = args[:failed_vendor_quality_checks] unless args[:failed_vendor_quality_checks].nil?
@alignment = args[:alignment] unless args[:alignment].nil?
@secondary_alignment = args[:secondary_alignment] unless args[:secondary_alignment].nil?
@supplementary_alignment = args[:supplementary_alignment] unless args[:supplementary_alignment].nil?
@aligned_sequence = args[:aligned_sequence] unless args[:aligned_sequence].nil?
@aligned_quality = args[:aligned_quality] unless args[:aligned_quality].nil?
@next_mate_position = args[:next_mate_position] unless args[:next_mate_position].nil?
@info = args[:info] unless args[:info].nil?
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
# 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
# The mapping quality of this alignment. Represents how likely the read maps to
# this position as opposed to other locations.
# Corresponds to the JSON property `mappingQuality`
# @return [Fixnum]
attr_accessor :mapping_quality
# 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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@position = args[:position] unless args[:position].nil?
@mapping_quality = args[:mapping_quality] unless args[:mapping_quality].nil?
@cigar = args[:cigar] unless args[:cigar].nil?
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 name of the reference in whatever reference set is being used.
# Corresponds to the JSON property `referenceName`
# @return [String]
attr_accessor :reference_name
# The 0-based offset from the start of the forward strand for that reference.
# Corresponds to the JSON property `position`
# @return [String]
attr_accessor :position
# 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)
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@position = args[:position] unless args[:position].nil?
@reverse_strand = args[:reverse_strand] unless args[:reverse_strand].nil?
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 [String]
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] unless args[:operation].nil?
@operation_length = args[:operation_length] unless args[:operation_length].nil?
@reference_sequence = args[:reference_sequence] unless args[:reference_sequence].nil?
end
end
#
class SearchReferenceSetsRequest
include Google::Apis::Core::Hashable
# If present, return references for which the `md5checksum` matches. See `
# ReferenceSet.md5checksum` for details.
# Corresponds to the JSON property `md5checksums`
# @return [Array<String>]
attr_accessor :md5checksums
# If present, return references for which the accession matches any of these
# strings. Best to give a version number, for example `GCF_000001405.26`. If
# only the main accession number is given then all records with that main
# accession will be returned, whichever version. Note that different versions
# will have different sequences.
# 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
# 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
# Specifies the maximum number of results to return in a single page.
# Corresponds to the JSON property `pageSize`
# @return [Fixnum]
attr_accessor :page_size
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@md5checksums = args[:md5checksums] unless args[:md5checksums].nil?
@accessions = args[:accessions] unless args[:accessions].nil?
@assembly_id = args[:assembly_id] unless args[:assembly_id].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
end
end
#
class SearchReferenceSetsResponse
include Google::Apis::Core::Hashable
# The matching references sets.
# Corresponds to the JSON property `referenceSets`
# @return [Array<Google::Apis::GenomicsV1::ReferenceSet>]
attr_accessor :reference_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)
@reference_sets = args[:reference_sets] unless args[:reference_sets].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
end
end
# A reference set is a set of references which typically comprise a reference
# assembly for a species, such as `GRCh38` which is representative of the human
# genome. A reference set defines a common coordinate space for comparing
# reference-aligned experimental data. A reference set contains 1 or more
# references.
class ReferenceSet
include Google::Apis::Core::Hashable
# The server-generated reference set ID, unique across all reference sets.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :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
# 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 (e.g. 9606->human) indicating the
# species which this assembly 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, e.g. EBV in a
# human reference genome.
# Corresponds to the JSON property `ncbiTaxonId`
# @return [Fixnum]
attr_accessor :ncbi_taxon_id
# Free text description of this reference set.
# Corresponds to the JSON property `description`
# @return [String]
attr_accessor :description
# Public id of this reference set, such as `GRCh37`.
# Corresponds to the JSON property `assemblyId`
# @return [String]
attr_accessor :assembly_id
# The URI from which the references were obtained.
# Corresponds to the JSON property `sourceUri`
# @return [String]
attr_accessor :source_uri
# 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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@id = args[:id] unless args[:id].nil?
@reference_ids = args[:reference_ids] unless args[:reference_ids].nil?
@md5checksum = args[:md5checksum] unless args[:md5checksum].nil?
@ncbi_taxon_id = args[:ncbi_taxon_id] unless args[:ncbi_taxon_id].nil?
@description = args[:description] unless args[:description].nil?
@assembly_id = args[:assembly_id] unless args[:assembly_id].nil?
@source_uri = args[:source_uri] unless args[:source_uri].nil?
@source_accessions = args[:source_accessions] unless args[:source_accessions].nil?
end
end
#
class SearchReferencesRequest
include Google::Apis::Core::Hashable
# If present, return references for which the `md5checksum` matches. See `
# Reference.md5checksum` for construction details.
# Corresponds to the JSON property `md5checksums`
# @return [Array<String>]
attr_accessor :md5checksums
# If present, return references for which the accession matches this string.
# Best to give a version number, for example `GCF_000001405.26`. If only the
# main accession number is given then all records with that main accession will
# be returned, whichever version. Note that different versions will have
# different sequences.
# Corresponds to the JSON property `accessions`
# @return [Array<String>]
attr_accessor :accessions
# If present, return only references which belong to this reference set.
# Corresponds to the JSON property `referenceSetId`
# @return [String]
attr_accessor :reference_set_id
# 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
# Specifies the maximum number of results to return in a single page.
# Corresponds to the JSON property `pageSize`
# @return [Fixnum]
attr_accessor :page_size
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@md5checksums = args[:md5checksums] unless args[:md5checksums].nil?
@accessions = args[:accessions] unless args[:accessions].nil?
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
end
end
#
class SearchReferencesResponse
include Google::Apis::Core::Hashable
# The matching references.
# Corresponds to the JSON property `references`
# @return [Array<Google::Apis::GenomicsV1::Reference>]
attr_accessor :references
# 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)
@references = args[:references] unless args[:references].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
end
end
# A reference is a canonical assembled DNA sequence, intended to act as a
# reference coordinate space for other genomic annotations. A single reference
# might represent the human chromosome 1 or mitochandrial DNA, for instance. A
# reference belongs to one or more reference sets.
class Reference
include Google::Apis::Core::Hashable
# The server-generated reference ID, unique across all references.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# The length of this reference's sequence.
# Corresponds to the JSON property `length`
# @return [String]
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
# The URI from which the sequence was obtained. Specifies a FASTA format file/
# string with one name, sequence pair.
# Corresponds to the JSON property `sourceUri`
# @return [String]
attr_accessor :source_uri
# 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
# ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not
# specified by the containing reference set.
# Corresponds to the JSON property `ncbiTaxonId`
# @return [Fixnum]
attr_accessor :ncbi_taxon_id
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@id = args[:id] unless args[:id].nil?
@length = args[:length] unless args[:length].nil?
@md5checksum = args[:md5checksum] unless args[:md5checksum].nil?
@name = args[:name] unless args[:name].nil?
@source_uri = args[:source_uri] unless args[:source_uri].nil?
@source_accessions = args[:source_accessions] unless args[:source_accessions].nil?
@ncbi_taxon_id = args[:ncbi_taxon_id] unless args[:ncbi_taxon_id].nil?
end
end
#
class ListBasesResponse
include Google::Apis::Core::Hashable
# 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 [String]
attr_accessor :offset
# A substring of the bases that make up this reference.
# Corresponds to the JSON property `sequence`
# @return [String]
attr_accessor :sequence
# 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)
@offset = args[:offset] unless args[:offset].nil?
@sequence = args[:sequence] unless args[:sequence].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
end
end
# The variant data import request.
class ImportVariantsRequest
include Google::Apis::Core::Hashable
# Required. The variant set to which variant data should be imported.
# Corresponds to the JSON property `variantSetId`
# @return [String]
attr_accessor :variant_set_id
# 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
# 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
# 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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil?
@source_uris = args[:source_uris] unless args[:source_uris].nil?
@format = args[:format] unless args[:format].nil?
@normalize_reference_names = args[:normalize_reference_names] unless args[:normalize_reference_names].nil?
end
end
# A variant set is a collection of call sets and variants. It contains summary
# statistics of those contents. A variant set belongs to a dataset.
class VariantSet
include Google::Apis::Core::Hashable
# The dataset to which this variant set belongs.
# Corresponds to the JSON property `datasetId`
# @return [String]
attr_accessor :dataset_id
# The server-generated variant set ID, unique across all variant sets.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# 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 metadata associated with this variant set.
# Corresponds to the JSON property `metadata`
# @return [Array<Google::Apis::GenomicsV1::VariantSetMetadata>]
attr_accessor :metadata
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
@id = args[:id] unless args[:id].nil?
@reference_bounds = args[:reference_bounds] unless args[:reference_bounds].nil?
@metadata = args[:metadata] unless args[:metadata].nil?
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 reference the bound is associate with.
# 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 [String]
attr_accessor :upper_bound
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@upper_bound = args[:upper_bound] unless args[:upper_bound].nil?
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
# The top-level key.
# Corresponds to the JSON property `key`
# @return [String]
attr_accessor :key
# The value field for simple metadata
# Corresponds to the JSON property `value`
# @return [String]
attr_accessor :value
# 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
# 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 number of values that can be included in a field described by this
# metadata.
# Corresponds to the JSON property `number`
# @return [Fixnum]
attr_accessor :number
# A textual description of this metadata.
# Corresponds to the JSON property `description`
# @return [String]
attr_accessor :description
# Remaining structured metadata key-value pairs. This must be of the form map (
# string key mapping to a list of string values).
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<Object>>]
attr_accessor :info
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@key = args[:key] unless args[:key].nil?
@value = args[:value] unless args[:value].nil?
@id = args[:id] unless args[:id].nil?
@type = args[:type] unless args[:type].nil?
@number = args[:number] unless args[:number].nil?
@description = args[:description] unless args[:description].nil?
@info = args[:info] unless args[:info].nil?
end
end
# The variant data export request.
class ExportVariantSetRequest
include Google::Apis::Core::Hashable
# 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
# 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
# The format for the exported data.
# Corresponds to the JSON property `format`
# @return [String]
attr_accessor :format
# 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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil?
@project_id = args[:project_id] unless args[:project_id].nil?
@format = args[:format] unless args[:format].nil?
@bigquery_dataset = args[:bigquery_dataset] unless args[:bigquery_dataset].nil?
@bigquery_table = args[:bigquery_table] unless args[:bigquery_table].nil?
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 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 maximum number of variant sets to return in a request.
# Corresponds to the JSON property `pageSize`
# @return [Fixnum]
attr_accessor :page_size
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@dataset_ids = args[:dataset_ids] unless args[:dataset_ids].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
end
end
# The search variant sets response.
class SearchVariantSetsResponse
include Google::Apis::Core::Hashable
# The variant sets belonging to the requested dataset.
# Corresponds to the JSON property `variantSets`
# @return [Array<Google::Apis::GenomicsV1::VariantSet>]
attr_accessor :variant_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)
@variant_sets = args[:variant_sets] unless args[:variant_sets].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
end
end
# The variant search request.
class SearchVariantsRequest
include Google::Apis::Core::Hashable
# 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
# Only return variants which have exactly this name.
# Corresponds to the JSON property `variantName`
# @return [String]
attr_accessor :variant_name
# 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. Currently, variants with
# no calls from any call set will never be returned.
# Corresponds to the JSON property `callSetIds`
# @return [Array<String>]
attr_accessor :call_set_ids
# 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 [String]
attr_accessor :start
# 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 [String]
attr_accessor :end
# 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 maximum number of variants to return. If unspecified, defaults to 5000.
# Corresponds to the JSON property `pageSize`
# @return [Fixnum]
attr_accessor :page_size
# The maximum number of calls to return. However, at least one variant will
# always be returned, even if it has more calls than this limit. If unspecified,
# defaults to 5000.
# Corresponds to the JSON property `maxCalls`
# @return [Fixnum]
attr_accessor :max_calls
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil?
@variant_name = args[:variant_name] unless args[:variant_name].nil?
@call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil?
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@start = args[:start] unless args[:start].nil?
@end = args[:end] unless args[:end].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
@max_calls = args[:max_calls] unless args[:max_calls].nil?
end
end
# The variant search response.
class SearchVariantsResponse
include Google::Apis::Core::Hashable
# The list of matching Variants.
# Corresponds to the JSON property `variants`
# @return [Array<Google::Apis::GenomicsV1::Variant>]
attr_accessor :variants
# 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)
@variants = args[:variants] unless args[:variants].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
end
end
# A variant represents a change in DNA sequence relative to a reference sequence.
# For example, a variant could represent a SNP or an insertion. Variants belong
# to a variant set. Each of the calls on a variant represent a determination of
# genotype with respect to that variant. For example, a call might assign
# probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named
# NA12345. A call belongs to a call set, which contains related calls typically
# from one sample.
class Variant
include Google::Apis::Core::Hashable
# The ID of the variant set this variant belongs to.
# Corresponds to the JSON property `variantSetId`
# @return [String]
attr_accessor :variant_set_id
# The server-generated variant ID, unique across all variants.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# Names for the variant, for example a RefSNP ID.
# Corresponds to the JSON property `names`
# @return [Array<String>]
attr_accessor :names
# The date this variant was created, in milliseconds from the epoch.
# Corresponds to the JSON property `created`
# @return [String]
attr_accessor :created
# 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 [String]
attr_accessor :start
# 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 [String]
attr_accessor :end
# 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 bases that appear instead of the reference bases.
# Corresponds to the JSON property `alternateBases`
# @return [Array<String>]
attr_accessor :alternate_bases
# 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
# 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
# A map of additional variant information. This must be of the form map (string
# key mapping to a list of string values).
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<Object>>]
attr_accessor :info
# 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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil?
@id = args[:id] unless args[:id].nil?
@names = args[:names] unless args[:names].nil?
@created = args[:created] unless args[:created].nil?
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@start = args[:start] unless args[:start].nil?
@end = args[:end] unless args[:end].nil?
@reference_bases = args[:reference_bases] unless args[:reference_bases].nil?
@alternate_bases = args[:alternate_bases] unless args[:alternate_bases].nil?
@quality = args[:quality] unless args[:quality].nil?
@filter = args[:filter] unless args[:filter].nil?
@info = args[:info] unless args[:info].nil?
@calls = args[:calls] unless args[:calls].nil?
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
# 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
# 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 key mapping to a list of string values).
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<Object>>]
attr_accessor :info
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@call_set_id = args[:call_set_id] unless args[:call_set_id].nil?
@call_set_name = args[:call_set_name] unless args[:call_set_name].nil?
@genotype = args[:genotype] unless args[:genotype].nil?
@phaseset = args[:phaseset] unless args[:phaseset].nil?
@genotype_likelihood = args[:genotype_likelihood] unless args[:genotype_likelihood].nil?
@info = args[:info] unless args[:info].nil?
end
end
#
class MergeVariantsRequest
include Google::Apis::Core::Hashable
# 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)
@variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil?
@variants = args[:variants] unless args[:variants].nil?
end
end
# The call set search request.
class SearchCallSetsRequest
include Google::Apis::Core::Hashable
# 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
# 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 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 maximum number of call sets to return. If unspecified, defaults to 1000.
# Corresponds to the JSON property `pageSize`
# @return [Fixnum]
attr_accessor :page_size
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil?
@name = args[:name] unless args[:name].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
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] unless args[:call_sets].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
end
end
# A call set is a collection of variant calls, typically for one sample. It
# belongs to a variant set.
class CallSet
include Google::Apis::Core::Hashable
# The server-generated call set ID, unique across all call sets.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# 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
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# 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).
Regen APIs
2015-07-20 21:49:34 +00:00
# Corresponds to the JSON property `variantSetIds`
# @return [Array<String>]
attr_accessor :variant_set_ids
# The date this call set was created in milliseconds from the epoch.
# Corresponds to the JSON property `created`
# @return [String]
attr_accessor :created
# A map of additional call set information. This must be of the form map (string
# key mapping to a list of string values).
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<Object>>]
attr_accessor :info
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@id = args[:id] unless args[:id].nil?
@name = args[:name] unless args[:name].nil?
@sample_id = args[:sample_id] unless args[:sample_id].nil?
@variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil?
@created = args[:created] unless args[:created].nil?
@info = args[:info] unless args[:info].nil?
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] unless args[:read_group_set_ids].nil?
end
end
# The variant data import response.
class ImportVariantsResponse
include Google::Apis::Core::Hashable
# IDs of the call sets that were created.
# 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] unless args[:call_set_ids].nil?
end
end
# Metadata describing an [Operation][google.longrunning.Operation].
class OperationMetadata
include Google::Apis::Core::Hashable
# The Google Cloud Project in which the job is scoped.
# Corresponds to the JSON property `projectId`
# @return [String]
attr_accessor :project_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 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
# 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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@project_id = args[:project_id] unless args[:project_id].nil?
@create_time = args[:create_time] unless args[:create_time].nil?
@request = args[:request] unless args[:request].nil?
@events = args[:events] unless args[:events].nil?
end
end
# An event that occurred during an [Operation][google.longrunning.Operation].
class OperationEvent
include Google::Apis::Core::Hashable
# Required description of event.
# Corresponds to the JSON property `description`
# @return [String]
attr_accessor :description
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@description = args[:description] unless args[:description].nil?
end
end
end
end
end