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google-api-ruby-client/generated/google/apis/genomics_v1beta2/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 GenomicsV1beta2
# The read group set align request.
class AlignReadGroupSetsRequest
include Google::Apis::Core::Hashable
# The BAM source files for alignment. Exactly one of readGroupSetId,
# bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided.
# The caller must have READ permissions for these files.
# Corresponds to the JSON property `bamSourceUris`
# @return [Array<String>]
attr_accessor :bam_source_uris
# Required. The ID of the dataset the newly aligned 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
# Describes an interleaved FASTQ file source for alignment.
# Corresponds to the JSON property `interleavedFastqSource`
# @return [Google::Apis::GenomicsV1beta2::InterleavedFastqSource]
attr_accessor :interleaved_fastq_source
# Describes a paired-end FASTQ file source for alignment.
# Corresponds to the JSON property `pairedFastqSource`
# @return [Google::Apis::GenomicsV1beta2::PairedFastqSource]
attr_accessor :paired_fastq_source
# The ID of the read group set which will be aligned. A new read group set will
# be generated to hold the aligned data, the originals will not be modified. The
# caller must have READ permissions for this read group set. Exactly one of
# readGroupSetId, bamSourceUris, interleavedFastqSource or pairedFastqSource
# must be provided.
# Corresponds to the JSON property `readGroupSetId`
# @return [String]
attr_accessor :read_group_set_id
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@bam_source_uris = args[:bam_source_uris] unless args[:bam_source_uris].nil?
@dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
@interleaved_fastq_source = args[:interleaved_fastq_source] unless args[:interleaved_fastq_source].nil?
@paired_fastq_source = args[:paired_fastq_source] unless args[:paired_fastq_source].nil?
@read_group_set_id = args[:read_group_set_id] unless args[:read_group_set_id].nil?
end
end
# The read group set align response.
class AlignReadGroupSetsResponse
include Google::Apis::Core::Hashable
# A job ID that can be used to get status information.
# Corresponds to the JSON property `jobId`
# @return [String]
attr_accessor :job_id
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@job_id = args[:job_id] unless args[:job_id].nil?
end
end
# 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. A variant annotation is represented by one or more of these
# canonical types. 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 ID of the containing annotation set.
# Corresponds to the JSON property `annotationSetId`
# @return [String]
attr_accessor :annotation_set_id
# The generated unique ID for this annotation.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# A string which maps to an array of values.
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<String>>]
attr_accessor :info
# The display name of this annotation.
# Corresponds to the JSON property `name`
# @return [String]
attr_accessor :name
# A 0-based half-open genomic coordinate range over a reference sequence, for
# representing the position of a genomic resource.
# Corresponds to the JSON property `position`
# @return [Google::Apis::GenomicsV1beta2::RangePosition]
attr_accessor :position
# 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::GenomicsV1beta2::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.
# Corresponds to the JSON property `variant`
# @return [Google::Apis::GenomicsV1beta2::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] unless args[:annotation_set_id].nil?
@id = args[:id] unless args[:id].nil?
@info = args[:info] unless args[:info].nil?
@name = args[:name] unless args[:name].nil?
@position = args[:position] unless args[:position].nil?
@transcript = args[:transcript] unless args[:transcript].nil?
@type = args[:type] unless args[:type].nil?
@variant = args[:variant] unless args[:variant].nil?
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 ID of the containing dataset.
# Corresponds to the JSON property `datasetId`
# @return [String]
attr_accessor :dataset_id
# The generated unique ID for this annotation set.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# A string which maps to an array of values.
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<String>>]
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] unless args[:dataset_id].nil?
@id = args[:id] unless args[:id].nil?
@info = args[:info] unless args[:info].nil?
@name = args[:name] unless args[:name].nil?
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
@source_uri = args[:source_uri] unless args[:source_uri].nil?
@type = args[:type] unless args[:type].nil?
end
end
#
class BatchAnnotationsResponse
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::GenomicsV1beta2::BatchAnnotationsResponseEntry>]
attr_accessor :entries
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@entries = args[:entries] unless args[:entries].nil?
end
end
#
class BatchAnnotationsResponseEntry
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. A variant annotation is represented by one or more of these
# canonical types. 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::GenomicsV1beta2::Annotation]
attr_accessor :annotation
#
# Corresponds to the JSON property `status`
# @return [Google::Apis::GenomicsV1beta2::BatchAnnotationsResponseEntryStatus]
attr_accessor :status
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@annotation = args[:annotation] unless args[:annotation].nil?
@status = args[:status] unless args[:status].nil?
end
end
#
class BatchAnnotationsResponseEntryStatus
include Google::Apis::Core::Hashable
# The HTTP status code for this operation.
# Corresponds to the JSON property `code`
# @return [Fixnum]
attr_accessor :code
# Error message for this status, if any.
# 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] unless args[:code].nil?
@message = args[:message] unless args[:message].nil?
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::GenomicsV1beta2::Annotation>]
attr_accessor :annotations
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@annotations = args[:annotations] unless args[:annotations].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 Call
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 string which maps to an array of values.
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<String>>]
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] 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?
@genotype_likelihood = args[:genotype_likelihood] unless args[:genotype_likelihood].nil?
@info = args[:info] unless args[:info].nil?
@phaseset = args[:phaseset] unless args[:phaseset].nil?
end
end
# The read group set call request.
class CallReadGroupSetsRequest
include Google::Apis::Core::Hashable
# Required. The ID of the dataset the called variants 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 IDs of the read group sets which will be called. The caller must have READ
# permissions for these read group sets. One of readGroupSetId or sourceUris
# must be provided.
# Corresponds to the JSON property `readGroupSetId`
# @return [String]
attr_accessor :read_group_set_id
# A list of URIs pointing at BAM files in Google Cloud Storage which will be
# called. FASTQ files are not allowed. The caller must have READ permissions for
# these files. One of readGroupSetId or sourceUris must be provided.
# 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] unless args[:dataset_id].nil?
@read_group_set_id = args[:read_group_set_id] unless args[:read_group_set_id].nil?
@source_uris = args[:source_uris] unless args[:source_uris].nil?
end
end
# The read group set call response.
class CallReadGroupSetsResponse
include Google::Apis::Core::Hashable
# A job ID that can be used to get status information.
# Corresponds to the JSON property `jobId`
# @return [String]
attr_accessor :job_id
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@job_id = args[:job_id] unless args[:job_id].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 date this call set was created in milliseconds from the epoch.
# Corresponds to the JSON property `created`
# @return [String]
attr_accessor :created
# The Google generated ID of the call set, immutable.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# A string which maps to an array of values.
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<String>>]
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.
# 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] unless args[:created].nil?
@id = args[:id] unless args[:id].nil?
@info = args[:info] unless args[:info].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?
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 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
# 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 over a reference sequence.
# Corresponds to the JSON property `range`
# @return [Google::Apis::GenomicsV1beta2::Range]
attr_accessor :range
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@mean_coverage = args[:mean_coverage] unless args[:mean_coverage].nil?
@range = args[:range] unless args[:range].nil?
end
end
# A Dataset is a collection of genomic data.
class Dataset
include Google::Apis::Core::Hashable
# The time this dataset was created, in seconds from the epoch.
# Corresponds to the JSON property `createTime`
# @return [String]
attr_accessor :create_time
# The Google generated ID of the dataset, immutable.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# Flag indicating whether or not a dataset is publicly viewable. If a dataset is
# not public, it inherits viewing permissions from its project.
# Corresponds to the JSON property `isPublic`
# @return [Boolean]
attr_accessor :is_public
alias_method :is_public?, :is_public
# The dataset name.
# Corresponds to the JSON property `name`
# @return [String]
attr_accessor :name
# The Google Developers Console project number that this dataset belongs to.
# Corresponds to the JSON property `projectNumber`
# @return [String]
attr_accessor :project_number
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@create_time = args[:create_time] unless args[:create_time].nil?
@id = args[:id] unless args[:id].nil?
@is_public = args[:is_public] unless args[:is_public].nil?
@name = args[:name] unless args[:name].nil?
@project_number = args[:project_number] unless args[:project_number].nil?
end
end
# The job creation request.
class ExperimentalCreateJobRequest
include Google::Apis::Core::Hashable
# Specifies whether or not to run the alignment pipeline. Either align or
# callVariants must be set.
# Corresponds to the JSON property `align`
# @return [Boolean]
attr_accessor :align
alias_method :align?, :align
# Specifies whether or not to run the variant calling pipeline. Either align or
# callVariants must be set.
# Corresponds to the JSON property `callVariants`
# @return [Boolean]
attr_accessor :call_variants
alias_method :call_variants?, :call_variants
# Specifies where to copy the results of certain pipelines. This should be in
# the form of gs://bucket/path.
# Corresponds to the JSON property `gcsOutputPath`
# @return [String]
attr_accessor :gcs_output_path
# A list of Google Cloud Storage URIs of paired end .fastq files to operate upon.
# If specified, this represents the second file of each paired .fastq file. The
# first file of each pair should be specified in sourceUris.
# Corresponds to the JSON property `pairedSourceUris`
# @return [Array<String>]
attr_accessor :paired_source_uris
# Required. The Google Cloud Project ID with which to associate the request.
# Corresponds to the JSON property `projectNumber`
# @return [String]
attr_accessor :project_number
# A list of Google Cloud Storage URIs of data files to operate upon. These can
# be .bam, interleaved .fastq, or paired .fastq. If specifying paired .fastq
# files, the first of each pair of files should be listed here, and the second
# of each pair should be listed in pairedSourceUris.
# 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)
@align = args[:align] unless args[:align].nil?
@call_variants = args[:call_variants] unless args[:call_variants].nil?
@gcs_output_path = args[:gcs_output_path] unless args[:gcs_output_path].nil?
@paired_source_uris = args[:paired_source_uris] unless args[:paired_source_uris].nil?
@project_number = args[:project_number] unless args[:project_number].nil?
@source_uris = args[:source_uris] unless args[:source_uris].nil?
end
end
# The job creation response.
class ExperimentalCreateJobResponse
include Google::Apis::Core::Hashable
# A job ID that can be used to get status information.
# Corresponds to the JSON property `jobId`
# @return [String]
attr_accessor :job_id
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@job_id = args[:job_id] unless args[:job_id].nil?
end
end
# The read group set export request.
class ExportReadGroupSetsRequest
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 Developers Console project number that owns this export.
# Corresponds to the JSON property `projectNumber`
# @return [String]
attr_accessor :project_number
# Required. The IDs of the read group sets to export.
# Corresponds to the JSON property `readGroupSetIds`
# @return [Array<String>]
attr_accessor :read_group_set_ids
# 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] unless args[:export_uri].nil?
@project_number = args[:project_number] unless args[:project_number].nil?
@read_group_set_ids = args[:read_group_set_ids] unless args[:read_group_set_ids].nil?
@reference_names = args[:reference_names] unless args[:reference_names].nil?
end
end
# The read group set export response.
class ExportReadGroupSetsResponse
include Google::Apis::Core::Hashable
# A job ID that can be used to get status information.
# Corresponds to the JSON property `jobId`
# @return [String]
attr_accessor :job_id
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@job_id = args[:job_id] unless args[:job_id].nil?
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 number 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 `projectNumber`
# @return [String]
attr_accessor :project_number
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@bigquery_dataset = args[:bigquery_dataset] unless args[:bigquery_dataset].nil?
@bigquery_table = args[:bigquery_table] unless args[:bigquery_table].nil?
@call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil?
@format = args[:format] unless args[:format].nil?
@project_number = args[:project_number] unless args[:project_number].nil?
end
end
# The variant data export response.
class ExportVariantSetResponse
include Google::Apis::Core::Hashable
# A job ID that can be used to get status information.
# Corresponds to the JSON property `jobId`
# @return [String]
attr_accessor :job_id
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@job_id = args[:job_id] unless args[:job_id].nil?
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] unless args[:id].nil?
@source_name = args[:source_name] unless args[:source_name].nil?
end
end
#
class FastqMetadata
include Google::Apis::Core::Hashable
# Optionally specifies the library name for alignment from FASTQ.
# Corresponds to the JSON property `libraryName`
# @return [String]
attr_accessor :library_name
# Optionally specifies the platform name for alignment from FASTQ. For example:
# CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, PACBIO.
# Corresponds to the JSON property `platformName`
# @return [String]
attr_accessor :platform_name
# Optionally specifies the platform unit for alignment from FASTQ. For example:
# flowcell-barcode.lane for Illumina or slide for SOLID.
# Corresponds to the JSON property `platformUnit`
# @return [String]
attr_accessor :platform_unit
# Optionally specifies the read group name for alignment from FASTQ.
# Corresponds to the JSON property `readGroupName`
# @return [String]
attr_accessor :read_group_name
# Optionally specifies the sample name for alignment from FASTQ.
# Corresponds to the JSON property `sampleName`
# @return [String]
attr_accessor :sample_name
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@library_name = args[:library_name] unless args[:library_name].nil?
@platform_name = args[:platform_name] unless args[:platform_name].nil?
@platform_unit = args[:platform_unit] unless args[:platform_unit].nil?
@read_group_name = args[:read_group_name] unless args[:read_group_name].nil?
@sample_name = args[:sample_name] unless args[:sample_name].nil?
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 in Google Cloud Storage.
# 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] unless args[:dataset_id].nil?
@partition_strategy = args[:partition_strategy] unless args[:partition_strategy].nil?
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
@source_uris = args[:source_uris] unless args[:source_uris].nil?
end
end
# The read group set import response.
class ImportReadGroupSetsResponse
include Google::Apis::Core::Hashable
# A job ID that can be used to get status information.
# Corresponds to the JSON property `jobId`
# @return [String]
attr_accessor :job_id
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@job_id = args[:job_id] unless args[:job_id].nil?
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
# 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. Note that recursive wildcards ('**') are
# not supported.
# 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)
@format = args[:format] unless args[:format].nil?
@normalize_reference_names = args[:normalize_reference_names] unless args[:normalize_reference_names].nil?
@source_uris = args[:source_uris] unless args[:source_uris].nil?
end
end
# The variant data import response.
class ImportVariantsResponse
include Google::Apis::Core::Hashable
# A job ID that can be used to get status information.
# Corresponds to the JSON property `jobId`
# @return [String]
attr_accessor :job_id
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@job_id = args[:job_id] unless args[:job_id].nil?
end
end
# Wrapper message for `int32`.
# The JSON representation for `Int32Value` is JSON number.
class Int32Value
include Google::Apis::Core::Hashable
# The int32 value.
# Corresponds to the JSON property `value`
# @return [Fixnum]
attr_accessor :value
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@value = args[:value] unless args[:value].nil?
end
end
# Describes an interleaved FASTQ file source for alignment.
class InterleavedFastqSource
include Google::Apis::Core::Hashable
# Optionally specifies the metadata to be associated with the final aligned read
# group set.
# Corresponds to the JSON property `metadata`
# @return [Google::Apis::GenomicsV1beta2::FastqMetadata]
attr_accessor :metadata
# A list of URIs pointing at interleaved FASTQ files in Google Cloud Storage
# which will be aligned. The caller must have READ permissions for these files.
# 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)
@metadata = args[:metadata] unless args[:metadata].nil?
@source_uris = args[:source_uris] unless args[:source_uris].nil?
end
end
# A Job represents an ongoing process that can be monitored for status
# information.
class Job
include Google::Apis::Core::Hashable
# The date this job was created, in milliseconds from the epoch.
# Corresponds to the JSON property `created`
# @return [String]
attr_accessor :created
# A more detailed description of this job's current status.
# Corresponds to the JSON property `detailedStatus`
# @return [String]
attr_accessor :detailed_status
# Any errors that occurred during processing.
# Corresponds to the JSON property `errors`
# @return [Array<String>]
attr_accessor :errors
# The job ID.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# If this Job represents an import, this field will contain the IDs of the
# objects that were successfully imported.
# Corresponds to the JSON property `importedIds`
# @return [Array<String>]
attr_accessor :imported_ids
# The Google Developers Console project number to which this job belongs.
# Corresponds to the JSON property `projectNumber`
# @return [String]
attr_accessor :project_number
# A summary representation of the service request that spawned the job.
# Corresponds to the JSON property `request`
# @return [Google::Apis::GenomicsV1beta2::JobRequest]
attr_accessor :request
# The status of this job.
# Corresponds to the JSON property `status`
# @return [String]
attr_accessor :status
# Any warnings that occurred during processing.
# Corresponds to the JSON property `warnings`
# @return [Array<String>]
attr_accessor :warnings
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@created = args[:created] unless args[:created].nil?
@detailed_status = args[:detailed_status] unless args[:detailed_status].nil?
@errors = args[:errors] unless args[:errors].nil?
@id = args[:id] unless args[:id].nil?
@imported_ids = args[:imported_ids] unless args[:imported_ids].nil?
@project_number = args[:project_number] unless args[:project_number].nil?
@request = args[:request] unless args[:request].nil?
@status = args[:status] unless args[:status].nil?
@warnings = args[:warnings] unless args[:warnings].nil?
end
end
# A summary representation of the service request that spawned the job.
class JobRequest
include Google::Apis::Core::Hashable
# The data destination of the request, for example, a Google BigQuery Table or
# Dataset ID.
# Corresponds to the JSON property `destination`
# @return [Array<String>]
attr_accessor :destination
# The data source of the request, for example, a Google Cloud Storage object
# path or Readset ID.
# Corresponds to the JSON property `source`
# @return [Array<String>]
attr_accessor :source
# The original request type.
# 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)
@destination = args[:destination] unless args[:destination].nil?
@source = args[:source] unless args[:source].nil?
@type = args[:type] unless args[:type].nil?
end
end
# Used to hold basic key value information.
class KeyValue
include Google::Apis::Core::Hashable
# A string which maps to an array of values.
# Corresponds to the JSON property `key`
# @return [String]
attr_accessor :key
# The string values.
# Corresponds to the JSON property `value`
# @return [Array<String>]
attr_accessor :value
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?
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::GenomicsV1beta2::CigarUnit>]
attr_accessor :cigar
# 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
# 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::GenomicsV1beta2::Position]
attr_accessor :position
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@cigar = args[:cigar] unless args[:cigar].nil?
@mapping_quality = args[:mapping_quality] unless args[:mapping_quality].nil?
@position = args[:position] unless args[:position].nil?
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 [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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
@offset = args[:offset] unless args[:offset].nil?
@sequence = args[:sequence] unless args[:sequence].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::GenomicsV1beta2::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
# 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::GenomicsV1beta2::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
#
class MergeVariantsRequest
include Google::Apis::Core::Hashable
# The variants to be merged with existing variants.
# Corresponds to the JSON property `variants`
# @return [Array<Google::Apis::GenomicsV1beta2::Variant>]
attr_accessor :variants
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@variants = args[:variants] unless args[:variants].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 Metadata
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
# A string which maps to an array of values.
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<String>>]
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] unless args[:description].nil?
@id = args[:id] unless args[:id].nil?
@info = args[:info] unless args[:info].nil?
@key = args[:key] unless args[:key].nil?
@number = args[:number] unless args[:number].nil?
@type = args[:type] unless args[:type].nil?
@value = args[:value] unless args[:value].nil?
end
end
# Describes a paired-end FASTQ file source for alignment.
class PairedFastqSource
include Google::Apis::Core::Hashable
# A list of URIs pointing at paired end FASTQ files in Google Cloud Storage
# which will be aligned. The first of each paired file should be specified here,
# in an order that matches the second of each paired file specified in
# secondSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq],
# secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ
# permissions for these files.
# Corresponds to the JSON property `firstSourceUris`
# @return [Array<String>]
attr_accessor :first_source_uris
# Optionally specifies the metadata to be associated with the final aligned read
# group set.
# Corresponds to the JSON property `metadata`
# @return [Google::Apis::GenomicsV1beta2::FastqMetadata]
attr_accessor :metadata
# A list of URIs pointing at paired end FASTQ files in Google Cloud Storage
# which will be aligned. The second of each paired file should be specified here,
# in an order that matches the first of each paired file specified in
# firstSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq],
# secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ
# permissions for these files.
# Corresponds to the JSON property `secondSourceUris`
# @return [Array<String>]
attr_accessor :second_source_uris
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@first_source_uris = args[:first_source_uris] unless args[:first_source_uris].nil?
@metadata = args[:metadata] unless args[:metadata].nil?
@second_source_uris = args[:second_source_uris] unless args[:second_source_uris].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 0-based offset from the start of the forward strand for that reference.
# Corresponds to the JSON property `position`
# @return [String]
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] unless args[:position].nil?
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@reverse_strand = args[:reverse_strand] unless args[:reverse_strand].nil?
end
end
# A 0-based half-open genomic coordinate range for search requests.
class QueryRange
include Google::Apis::Core::Hashable
# The end position of the range on the reference, 0-based exclusive. If
# specified, referenceId or referenceName must also be specified. If unset or 0,
# defaults to the length of the reference.
# Corresponds to the JSON property `end`
# @return [String]
attr_accessor :end
# The ID of the reference to query. At most one of referenceId and referenceName
# should be specified.
# 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. At most one of referenceId and referenceName pshould be specified.
# 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 also be specified. Defaults to 0.
# Corresponds to the JSON property `start`
# @return [String]
attr_accessor :start
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@end = args[:end] unless args[:end].nil?
@reference_id = args[:reference_id] unless args[:reference_id].nil?
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@start = args[:start] unless args[:start].nil?
end
end
# A 0-based half-open genomic coordinate range over a reference sequence.
class Range
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 [String]
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. If
# specified, referenceName must also be specified.
# Corresponds to the JSON property `start`
# @return [String]
attr_accessor :start
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@end = args[:end] unless args[:end].nil?
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@start = args[:start] unless args[:start].nil?
end
end
# A 0-based half-open genomic coordinate range over a reference sequence, for
# representing the position of a genomic resource.
class RangePosition
include Google::Apis::Core::Hashable
# The end position of the range on the reference, 0-based exclusive.
# Corresponds to the JSON property `end`
# @return [String]
attr_accessor :end
# 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 [String]
attr_accessor :start
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@end = args[:end] unless args[:end].nil?
@reference_id = args[:reference_id] unless args[:reference_id].nil?
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@reverse_strand = args[:reverse_strand] unless args[:reverse_strand].nil?
@start = args[:start] unless args[:start].nil?
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. 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.
# 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. 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::GenomicsV1beta2::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
# 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 unique ID for this read. This is a generated unique ID, not to be confused
# with fragmentName.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# A string which maps to an array of values.
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<String>>]
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::GenomicsV1beta2::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. (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 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] unless args[:aligned_quality].nil?
@aligned_sequence = args[:aligned_sequence] unless args[:aligned_sequence].nil?
@alignment = args[:alignment] unless args[:alignment].nil?
@duplicate_fragment = args[:duplicate_fragment] unless args[:duplicate_fragment].nil?
@failed_vendor_quality_checks = args[:failed_vendor_quality_checks] unless args[:failed_vendor_quality_checks].nil?
@fragment_length = args[:fragment_length] unless args[:fragment_length].nil?
@fragment_name = args[:fragment_name] unless args[:fragment_name].nil?
@id = args[:id] unless args[:id].nil?
@info = args[:info] unless args[:info].nil?
@next_mate_position = args[:next_mate_position] unless args[:next_mate_position].nil?
@number_reads = args[:number_reads] unless args[:number_reads].nil?
@proper_placement = args[:proper_placement] unless args[:proper_placement].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?
@read_number = args[:read_number] unless args[:read_number].nil?
@secondary_alignment = args[:secondary_alignment] unless args[:secondary_alignment].nil?
@supplementary_alignment = args[:supplementary_alignment] unless args[:supplementary_alignment].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 ID of the dataset this read group belongs to.
# 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::GenomicsV1beta2::ReadGroupExperiment]
attr_accessor :experiment
# The generated unique read group ID. 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
# A string which maps to an array of values.
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<String>>]
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::GenomicsV1beta2::ReadGroupProgram>]
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
# 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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
@description = args[:description] unless args[:description].nil?
@experiment = args[:experiment] unless args[:experiment].nil?
@id = args[:id] unless args[:id].nil?
@info = args[:info] unless args[:info].nil?
@name = args[:name] unless args[:name].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?
@sample_id = args[:sample_id] unless args[:sample_id].nil?
end
end
#
class ReadGroupExperiment
include Google::Apis::Core::Hashable
# 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
# 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
# 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] unless args[:instrument_model].nil?
@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?
end
end
#
class ReadGroupProgram
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
# A read group set is a logical collection of read groups, which are collections
# of reads produced by a sequencer. A read group set typically models reads
# corresponding to one sample, sequenced one way, and aligned one way.
# - A read group set belongs to one dataset.
# - A read group belongs to one read group set.
# - A read belongs to one read group.
class ReadGroupSet
include Google::Apis::Core::Hashable
# The dataset ID.
# 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 read group set ID.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# A string which maps to an array of values.
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<String>>]
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::GenomicsV1beta2::ReadGroup>]
attr_accessor :read_groups
# 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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
@filename = args[:filename] unless args[:filename].nil?
@id = args[:id] unless args[:id].nil?
@info = args[:info] unless args[:info].nil?
@name = args[:name] unless args[:name].nil?
@read_groups = args[:read_groups] unless args[:read_groups].nil?
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].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 Google generated immutable ID of the reference.
# 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
# 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
# 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. Specifies a FASTA format file/
# string with one name, sequence pair.
# 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] 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?
@ncbi_taxon_id = args[:ncbi_taxon_id] unless args[:ncbi_taxon_id].nil?
@source_accessions = args[:source_accessions] unless args[:source_accessions].nil?
@source_uri = args[:source_uri] unless args[:source_uri].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
# A reference set is a set of references which typically comprise a reference
# assembly for a species, such as GRCh38 which is representative of the human
# genome. A reference set defines a common coordinate space for comparing
# reference-aligned experimental data. A reference set contains 1 or more
# references.
class ReferenceSet
include Google::Apis::Core::Hashable
# Public id of this reference set, such as GRCh37.
# Corresponds to the JSON property `assemblyId`
# @return [String]
attr_accessor :assembly_id
# Free text description of this reference set.
# Corresponds to the JSON property `description`
# @return [String]
attr_accessor :description
# The Google generated immutable ID of the reference set.
# 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 (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
# 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] unless args[:assembly_id].nil?
@description = args[:description] unless args[:description].nil?
@id = args[:id] unless args[:id].nil?
@md5checksum = args[:md5checksum] unless args[:md5checksum].nil?
@ncbi_taxon_id = args[:ncbi_taxon_id] unless args[:ncbi_taxon_id].nil?
@reference_ids = args[:reference_ids] unless args[:reference_ids].nil?
@source_accessions = args[:source_accessions] unless args[:source_accessions].nil?
@source_uri = args[:source_uri] unless args[:source_uri].nil?
end
end
#
class SearchAnnotationSetsRequest
include Google::Apis::Core::Hashable
# 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
# Specifies number of results to return in a single page. If unspecified, it
# will default 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] unless args[:dataset_ids].nil?
@name = args[:name] unless args[:name].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
@types = args[:types] unless args[:types].nil?
end
end
#
class SearchAnnotationSetsResponse
include Google::Apis::Core::Hashable
# The matching annotation sets.
# Corresponds to the JSON property `annotationSets`
# @return [Array<Google::Apis::GenomicsV1beta2::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] unless args[:annotation_sets].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
end
end
#
class SearchAnnotationsRequest
include Google::Apis::Core::Hashable
# The annotation sets to search within. The caller must have READ access to
# these annotation sets. Required. All queried annotation sets must have the
# same type.
# Corresponds to the JSON property `annotationSetIds`
# @return [Array<String>]
attr_accessor :annotation_set_ids
# 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
# 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
# A 0-based half-open genomic coordinate range for search requests.
# Corresponds to the JSON property `range`
# @return [Google::Apis::GenomicsV1beta2::QueryRange]
attr_accessor :range
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@annotation_set_ids = args[:annotation_set_ids] unless args[:annotation_set_ids].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@range = args[:range] unless args[:range].nil?
end
end
#
class SearchAnnotationsResponse
include Google::Apis::Core::Hashable
# The matching annotations.
# Corresponds to the JSON property `annotations`
# @return [Array<Google::Apis::GenomicsV1beta2::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] unless args[:annotations].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
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 call sets to return. If unspecified, defaults to 1000.
# 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] unless args[:name].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].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::GenomicsV1beta2::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
# The jobs search request.
class SearchJobsRequest
include Google::Apis::Core::Hashable
# If specified, only jobs created on or after this date, given in milliseconds
# since Unix epoch, will be returned.
# Corresponds to the JSON property `createdAfter`
# @return [String]
attr_accessor :created_after
# If specified, only jobs created prior to this date, given in milliseconds
# since Unix epoch, will be returned.
# Corresponds to the JSON property `createdBefore`
# @return [String]
attr_accessor :created_before
# Specifies the number of results to return in a single page. Defaults to 128.
# The maximum value is 256.
# 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 the nextPageToken
# from the previous response.
# Corresponds to the JSON property `pageToken`
# @return [String]
attr_accessor :page_token
# Required. Only return jobs which belong to this Google Developers Console
# project.
# Corresponds to the JSON property `projectNumber`
# @return [String]
attr_accessor :project_number
# Only return jobs which have a matching status.
# Corresponds to the JSON property `status`
# @return [Array<String>]
attr_accessor :status
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@created_after = args[:created_after] unless args[:created_after].nil?
@created_before = args[:created_before] unless args[:created_before].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@project_number = args[:project_number] unless args[:project_number].nil?
@status = args[:status] unless args[:status].nil?
end
end
# The job search response.
class SearchJobsResponse
include Google::Apis::Core::Hashable
# The list of jobs results, ordered newest to oldest.
# Corresponds to the JSON property `jobs`
# @return [Array<Google::Apis::GenomicsV1beta2::Job>]
attr_accessor :jobs
# The continuation token which is used to page through large result sets.
# Provide this value is a subsequent request to return the next page of results.
# This field will be empty if there are no more 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)
@jobs = args[:jobs] unless args[:jobs].nil?
@next_page_token = args[:next_page_token] unless args[:next_page_token].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
# 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
# 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] unless args[:dataset_ids].nil?
@name = args[:name] unless args[:name].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
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::GenomicsV1beta2::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] unless args[:next_page_token].nil?
@read_group_sets = args[:read_group_sets] unless args[:read_group_sets].nil?
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 [String]
attr_accessor :end
# 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
# 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.
# 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
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@end = args[:end] unless args[:end].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@read_group_ids = args[:read_group_ids] unless args[:read_group_ids].nil?
@read_group_set_ids = args[:read_group_set_ids] unless args[:read_group_set_ids].nil?
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@start = args[:start] unless args[:start].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::GenomicsV1beta2::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
#
class SearchReferenceSetsRequest
include Google::Apis::Core::Hashable
# 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
# 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
# Specifies the maximum number of results to return in a single page.
# 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] unless args[:accessions].nil?
@assembly_id = args[:assembly_id] unless args[:assembly_id].nil?
@md5checksums = args[:md5checksums] unless args[:md5checksums].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
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::GenomicsV1beta2::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] unless args[:next_page_token].nil?
@reference_sets = args[:reference_sets] unless args[:reference_sets].nil?
end
end
#
class SearchReferencesRequest
include Google::Apis::Core::Hashable
# 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 references for which the md5checksum matches. See Reference.
# md5checksum for construction details.
# Corresponds to the JSON property `md5checksums`
# @return [Array<String>]
attr_accessor :md5checksums
# Specifies the maximum number of results to return in a single page.
# 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] unless args[:accessions].nil?
@md5checksums = args[:md5checksums] unless args[:md5checksums].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
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::GenomicsV1beta2::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] unless args[:next_page_token].nil?
@references = args[:references] unless args[:references].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 maximum number of variant sets to return in a request.
# 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] unless args[:dataset_ids].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
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::GenomicsV1beta2::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] unless args[:next_page_token].nil?
@variant_sets = args[:variant_sets] unless args[:variant_sets].nil?
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. 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
# 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 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
# 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 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 [String]
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] unless args[:call_set_ids].nil?
@end = args[:end] unless args[:end].nil?
@max_calls = args[:max_calls] unless args[:max_calls].nil?
@page_size = args[:page_size] unless args[:page_size].nil?
@page_token = args[:page_token] unless args[:page_token].nil?
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@start = args[:start] unless args[:start].nil?
@variant_name = args[:variant_name] unless args[:variant_name].nil?
@variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil?
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::GenomicsV1beta2::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] unless args[:next_page_token].nil?
@variants = args[:variants] unless args[:variants].nil?
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::GenomicsV1beta2::TranscriptCodingSequence]
attr_accessor :coding_sequence
# The exons 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::GenomicsV1beta2::TranscriptExon>]
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] unless args[:coding_sequence].nil?
@exons = args[:exons] unless args[:exons].nil?
@gene_id = args[:gene_id] unless args[:gene_id].nil?
end
end
#
class TranscriptCodingSequence
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 [String]
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 [String]
attr_accessor :start
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@end = args[:end] unless args[:end].nil?
@start = args[:start] unless args[:start].nil?
end
end
#
class TranscriptExon
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 [String]
attr_accessor :end
# Wrapper message for `int32`.
# The JSON representation for `Int32Value` is JSON number.
# Corresponds to the JSON property `frame`
# @return [Google::Apis::GenomicsV1beta2::Int32Value]
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 [String]
attr_accessor :start
def initialize(**args)
update!(**args)
end
# Update properties of this object
def update!(**args)
@end = args[:end] unless args[:end].nil?
@frame = args[:frame] unless args[:frame].nil?
@start = args[:start] unless args[:start].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 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::GenomicsV1beta2::Call>]
attr_accessor :calls
# The date this variant was created, in milliseconds from the epoch.
# Corresponds to the JSON property `created`
# @return [String]
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 [String]
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 Google generated ID of the variant, immutable.
# Corresponds to the JSON property `id`
# @return [String]
attr_accessor :id
# A string which maps to an array of values.
# Corresponds to the JSON property `info`
# @return [Hash<String,Array<String>>]
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 [String]
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] unless args[:alternate_bases].nil?
@calls = args[:calls] unless args[:calls].nil?
@created = args[:created] unless args[:created].nil?
@end = args[:end] unless args[:end].nil?
@filter = args[:filter] unless args[:filter].nil?
@id = args[:id] unless args[:id].nil?
@info = args[:info] unless args[:info].nil?
@names = args[:names] unless args[:names].nil?
@quality = args[:quality] unless args[:quality].nil?
@reference_bases = args[:reference_bases] unless args[:reference_bases].nil?
@reference_name = args[:reference_name] unless args[:reference_name].nil?
@start = args[:start] unless args[:start].nil?
@variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil?
end
end
# A Variant annotation.
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::GenomicsV1beta2::VariantAnnotationCondition>]
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] unless args[:alternate_bases].nil?
@clinical_significance = args[:clinical_significance] unless args[:clinical_significance].nil?
@conditions = args[:conditions] unless args[:conditions].nil?
@effect = args[:effect] unless args[:effect].nil?
@gene_id = args[:gene_id] unless args[:gene_id].nil?
@transcript_ids = args[:transcript_ids] unless args[:transcript_ids].nil?
@type = args[:type] unless args[:type].nil?
end
end
#
class VariantAnnotationCondition
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::GenomicsV1beta2::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] unless args[:concept_id].nil?
@external_ids = args[:external_ids] unless args[:external_ids].nil?
@names = args[:names] unless args[:names].nil?
@omim_id = args[:omim_id] unless args[:omim_id].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. Immutable.
# Corresponds to the JSON property `datasetId`
# @return [String]
attr_accessor :dataset_id
# The Google-generated ID of the variant set. Immutable.
# 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::GenomicsV1beta2::Metadata>]
attr_accessor :metadata
# 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::GenomicsV1beta2::ReferenceBound>]
attr_accessor :reference_bounds
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?
@metadata = args[:metadata] unless args[:metadata].nil?
@reference_bounds = args[:reference_bounds] unless args[:reference_bounds].nil?
end
end
end
end
end
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