google-api-client 0.10.1 → 0.10.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/CHANGELOG.md +3 -0
- data/api_names.yaml +395 -0
- data/generated/google/apis/adexchangebuyer2_v2beta1.rb +1 -1
- data/generated/google/apis/adexchangebuyer2_v2beta1/classes.rb +254 -254
- data/generated/google/apis/adexchangebuyer2_v2beta1/representations.rb +65 -65
- data/generated/google/apis/adexchangebuyer2_v2beta1/service.rb +220 -220
- data/generated/google/apis/admin_directory_v1.rb +1 -1
- data/generated/google/apis/admin_directory_v1/classes.rb +106 -0
- data/generated/google/apis/admin_directory_v1/representations.rb +37 -0
- data/generated/google/apis/admin_reports_v1.rb +3 -3
- data/generated/google/apis/admin_reports_v1/service.rb +6 -6
- data/generated/google/apis/adsense_v1_4.rb +1 -1
- data/generated/google/apis/adsensehost_v4_1.rb +1 -1
- data/generated/google/apis/analytics_v3.rb +1 -1
- data/generated/google/apis/analytics_v3/service.rb +39 -0
- data/generated/google/apis/analyticsreporting_v4/classes.rb +920 -920
- data/generated/google/apis/analyticsreporting_v4/representations.rb +197 -197
- data/generated/google/apis/analyticsreporting_v4/service.rb +4 -4
- data/generated/google/apis/androidenterprise_v1.rb +1 -1
- data/generated/google/apis/androidenterprise_v1/classes.rb +8 -13
- data/generated/google/apis/androidenterprise_v1/service.rb +3 -3
- data/generated/google/apis/appengine_v1beta5.rb +1 -1
- data/generated/google/apis/appengine_v1beta5/classes.rb +115 -5
- data/generated/google/apis/appengine_v1beta5/representations.rb +37 -0
- data/generated/google/apis/appengine_v1beta5/service.rb +12 -9
- data/generated/google/apis/appstate_v1.rb +1 -1
- data/generated/google/apis/bigquery_v2.rb +1 -1
- data/generated/google/apis/bigquery_v2/classes.rb +32 -37
- data/generated/google/apis/bigquery_v2/service.rb +10 -2
- data/generated/google/apis/calendar_v3.rb +1 -1
- data/generated/google/apis/calendar_v3/classes.rb +205 -0
- data/generated/google/apis/calendar_v3/representations.rb +97 -0
- data/generated/google/apis/classroom_v1.rb +22 -25
- data/generated/google/apis/classroom_v1/classes.rb +998 -907
- data/generated/google/apis/classroom_v1/representations.rb +240 -240
- data/generated/google/apis/classroom_v1/service.rb +1269 -1061
- data/generated/google/apis/cloudbuild_v1.rb +1 -1
- data/generated/google/apis/cloudbuild_v1/classes.rb +164 -163
- data/generated/google/apis/cloudbuild_v1/representations.rb +31 -31
- data/generated/google/apis/cloudbuild_v1/service.rb +114 -114
- data/generated/google/apis/clouddebugger_v2.rb +1 -1
- data/generated/google/apis/clouddebugger_v2/classes.rb +687 -687
- data/generated/google/apis/clouddebugger_v2/representations.rb +147 -147
- data/generated/google/apis/clouddebugger_v2/service.rb +132 -132
- data/generated/google/apis/cloudkms_v1.rb +1 -1
- data/generated/google/apis/cloudkms_v1/classes.rb +231 -248
- data/generated/google/apis/cloudkms_v1/representations.rb +74 -74
- data/generated/google/apis/cloudkms_v1/service.rb +228 -228
- data/generated/google/apis/cloudmonitoring_v2beta2.rb +1 -1
- data/generated/google/apis/cloudresourcemanager_v1.rb +1 -1
- data/generated/google/apis/cloudresourcemanager_v1/classes.rb +738 -128
- data/generated/google/apis/cloudresourcemanager_v1/representations.rb +245 -23
- data/generated/google/apis/cloudresourcemanager_v1/service.rb +1293 -249
- data/generated/google/apis/cloudresourcemanager_v1beta1.rb +4 -4
- data/generated/google/apis/cloudresourcemanager_v1beta1/classes.rb +982 -372
- data/generated/google/apis/cloudresourcemanager_v1beta1/representations.rb +293 -71
- data/generated/google/apis/cloudresourcemanager_v1beta1/service.rb +626 -277
- data/generated/google/apis/cloudtrace_v1.rb +1 -1
- data/generated/google/apis/cloudtrace_v1/classes.rb +19 -19
- data/generated/google/apis/cloudtrace_v1/representations.rb +2 -2
- data/generated/google/apis/cloudtrace_v1/service.rb +30 -30
- data/generated/google/apis/compute_beta.rb +1 -1
- data/generated/google/apis/compute_beta/classes.rb +116 -0
- data/generated/google/apis/compute_beta/representations.rb +48 -0
- data/generated/google/apis/compute_beta/service.rb +46 -1
- data/generated/google/apis/compute_v1.rb +1 -1
- data/generated/google/apis/dataflow_v1b3.rb +1 -1
- data/generated/google/apis/dataflow_v1b3/classes.rb +3276 -3320
- data/generated/google/apis/dataflow_v1b3/representations.rb +779 -781
- data/generated/google/apis/dataflow_v1b3/service.rb +225 -225
- data/generated/google/apis/dataproc_v1.rb +1 -1
- data/generated/google/apis/dataproc_v1/classes.rb +1221 -1207
- data/generated/google/apis/dataproc_v1/representations.rb +255 -253
- data/generated/google/apis/dataproc_v1/service.rb +100 -100
- data/generated/google/apis/deploymentmanager_v2.rb +1 -1
- data/generated/google/apis/deploymentmanager_v2/classes.rb +5 -5
- data/generated/google/apis/dns_v1.rb +1 -1
- data/generated/google/apis/dns_v2beta1.rb +1 -1
- data/generated/google/apis/doubleclicksearch_v2.rb +1 -1
- data/generated/google/apis/drive_v2.rb +1 -1
- data/generated/google/apis/drive_v2/classes.rb +3 -1
- data/generated/google/apis/drive_v3.rb +1 -1
- data/generated/google/apis/drive_v3/classes.rb +3 -1
- data/generated/google/apis/fusiontables_v2.rb +1 -1
- data/generated/google/apis/games_configuration_v1configuration.rb +1 -1
- data/generated/google/apis/games_management_v1management.rb +1 -1
- data/generated/google/apis/games_v1.rb +1 -1
- data/generated/google/apis/genomics_v1.rb +7 -7
- data/generated/google/apis/genomics_v1/classes.rb +959 -959
- data/generated/google/apis/genomics_v1/representations.rb +238 -238
- data/generated/google/apis/genomics_v1/service.rb +996 -996
- data/generated/google/apis/iam_v1.rb +1 -1
- data/generated/google/apis/iam_v1/classes.rb +440 -440
- data/generated/google/apis/iam_v1/representations.rb +94 -94
- data/generated/google/apis/iam_v1/service.rb +170 -173
- data/generated/google/apis/identitytoolkit_v3.rb +1 -1
- data/generated/google/apis/identitytoolkit_v3/classes.rb +55 -0
- data/generated/google/apis/identitytoolkit_v3/representations.rb +8 -0
- data/generated/google/apis/kgsearch_v1/service.rb +4 -4
- data/generated/google/apis/language_v1beta1.rb +1 -1
- data/generated/google/apis/language_v1beta1/classes.rb +427 -427
- data/generated/google/apis/language_v1beta1/representations.rb +113 -113
- data/generated/google/apis/language_v1beta1/service.rb +25 -24
- data/generated/google/apis/licensing_v1.rb +2 -2
- data/generated/google/apis/licensing_v1/classes.rb +14 -2
- data/generated/google/apis/licensing_v1/representations.rb +2 -0
- data/generated/google/apis/licensing_v1/service.rb +1 -1
- data/generated/google/apis/logging_v2beta1.rb +1 -1
- data/generated/google/apis/logging_v2beta1/classes.rb +864 -864
- data/generated/google/apis/logging_v2beta1/representations.rb +168 -168
- data/generated/google/apis/logging_v2beta1/service.rb +261 -261
- data/generated/google/apis/manufacturers_v1.rb +1 -1
- data/generated/google/apis/manufacturers_v1/classes.rb +452 -105
- data/generated/google/apis/manufacturers_v1/representations.rb +138 -18
- data/generated/google/apis/manufacturers_v1/service.rb +11 -11
- data/generated/google/apis/mirror_v1.rb +1 -1
- data/generated/google/apis/monitoring_v3.rb +7 -7
- data/generated/google/apis/monitoring_v3/classes.rb +668 -670
- data/generated/google/apis/monitoring_v3/representations.rb +140 -140
- data/generated/google/apis/monitoring_v3/service.rb +208 -208
- data/generated/google/apis/partners_v2.rb +1 -1
- data/generated/google/apis/partners_v2/classes.rb +505 -505
- data/generated/google/apis/partners_v2/representations.rb +118 -118
- data/generated/google/apis/partners_v2/service.rb +275 -275
- data/generated/google/apis/people_v1.rb +1 -1
- data/generated/google/apis/people_v1/classes.rb +1037 -1031
- data/generated/google/apis/people_v1/representations.rb +247 -246
- data/generated/google/apis/people_v1/service.rb +20 -20
- data/generated/google/apis/plus_domains_v1.rb +1 -1
- data/generated/google/apis/plus_v1.rb +1 -1
- data/generated/google/apis/proximitybeacon_v1beta1.rb +1 -1
- data/generated/google/apis/proximitybeacon_v1beta1/classes.rb +392 -392
- data/generated/google/apis/proximitybeacon_v1beta1/representations.rb +93 -93
- data/generated/google/apis/proximitybeacon_v1beta1/service.rb +381 -381
- data/generated/google/apis/pubsub_v1.rb +4 -4
- data/generated/google/apis/pubsub_v1/classes.rb +131 -132
- data/generated/google/apis/pubsub_v1/representations.rb +35 -35
- data/generated/google/apis/pubsub_v1/service.rb +399 -408
- data/generated/google/apis/reseller_v1.rb +1 -1
- data/generated/google/apis/reseller_v1/classes.rb +9 -0
- data/generated/google/apis/reseller_v1/representations.rb +1 -0
- data/generated/google/apis/script_v1.rb +9 -9
- data/generated/google/apis/script_v1/classes.rb +110 -110
- data/generated/google/apis/script_v1/representations.rb +26 -26
- data/generated/google/apis/sheets_v4.rb +4 -4
- data/generated/google/apis/sheets_v4/classes.rb +4329 -4329
- data/generated/google/apis/sheets_v4/representations.rb +856 -856
- data/generated/google/apis/sheets_v4/service.rb +106 -106
- data/generated/google/apis/slides_v1.rb +4 -4
- data/generated/google/apis/slides_v1/classes.rb +2923 -2841
- data/generated/google/apis/slides_v1/representations.rb +722 -691
- data/generated/google/apis/slides_v1/service.rb +58 -15
- data/generated/google/apis/speech_v1beta1.rb +1 -1
- data/generated/google/apis/speech_v1beta1/classes.rb +191 -191
- data/generated/google/apis/speech_v1beta1/representations.rb +57 -57
- data/generated/google/apis/speech_v1beta1/service.rb +70 -70
- data/generated/google/apis/storage_v1.rb +1 -1
- data/generated/google/apis/storage_v1/classes.rb +151 -0
- data/generated/google/apis/storage_v1/representations.rb +45 -0
- data/generated/google/apis/storage_v1/service.rb +248 -0
- data/generated/google/apis/vision_v1.rb +1 -1
- data/generated/google/apis/vision_v1/classes.rb +1227 -1221
- data/generated/google/apis/vision_v1/representations.rb +217 -215
- data/generated/google/apis/webmasters_v3.rb +1 -1
- data/generated/google/apis/youtube_analytics_v1.rb +1 -1
- data/generated/google/apis/youtube_partner_v1.rb +1 -1
- data/generated/google/apis/youtube_partner_v1/classes.rb +78 -0
- data/generated/google/apis/youtube_partner_v1/representations.rb +34 -0
- data/generated/google/apis/youtube_partner_v1/service.rb +40 -0
- data/generated/google/apis/youtubereporting_v1.rb +4 -4
- data/generated/google/apis/youtubereporting_v1/classes.rb +65 -65
- data/generated/google/apis/youtubereporting_v1/representations.rb +18 -18
- data/generated/google/apis/youtubereporting_v1/service.rb +111 -111
- data/lib/google/apis/version.rb +1 -1
- metadata +2 -2
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# @see https://developers.google.com/cloud-dns
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module DnsV1
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VERSION = 'V1'
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REVISION = '20170322'
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# View and manage your data across Google Cloud Platform services
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AUTH_CLOUD_PLATFORM = 'https://www.googleapis.com/auth/cloud-platform'
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# @see https://developers.google.com/cloud-dns
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module DnsV2beta1
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VERSION = 'V2beta1'
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# View and manage your data across Google Cloud Platform services
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AUTH_CLOUD_PLATFORM = 'https://www.googleapis.com/auth/cloud-platform'
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# @see https://developers.google.com/doubleclick-search/
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module DoubleclicksearchV2
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VERSION = 'V2'
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# View and manage your advertising data in DoubleClick Search
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AUTH_DOUBLECLICKSEARCH = 'https://www.googleapis.com/auth/doubleclicksearch'
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# The title of this file. Note that for immutable items such as the top level
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# folders of Team Drives, My Drive root folder, and Application Data folder the
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# title is constant.
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module FusiontablesV2
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# Manage your Fusion Tables
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AUTH_FUSIONTABLES = 'https://www.googleapis.com/auth/fusiontables'
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module GamesConfigurationV1configuration
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# View and manage your Google Play Developer account
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module GamesManagementV1management
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# Share your Google+ profile information and view and manage your game activity
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# View and manage its own configuration data in your Google Drive
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module GenomicsV1
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# Response message for `TestIamPermissions` method.
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class TestIamPermissionsResponse
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# A subset of `TestPermissionsRequest.permissions` that the caller is
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# Request message for `GetIamPolicy` method.
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class GetIamPolicyRequest
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end
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#
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class SearchReferencesResponse
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# The matching references.
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# @return [Array<Google::Apis::GenomicsV1::Reference>]
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# The continuation token, which is used to page through large result sets.
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# results. This field will be empty if there aren't any additional results.
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attr_accessor :next_page_token
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update!(**args)
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end
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end
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#
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class SearchAnnotationSetsRequest
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include Google::Apis::Core::Hashable
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# Only return annotations sets for which a substring of the name matches this
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# string (case insensitive).
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# Corresponds to the JSON property `name`
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# @return [String]
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attr_accessor :name
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# If specified, only annotation sets associated with the given reference set
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# The continuation token, which is used to page through large result sets.
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# To get the next page of results, set this parameter to the value of
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# `nextPageToken` from the previous response.
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# Corresponds to the JSON property `pageToken`
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# The maximum number of results to return in a single page. If unspecified,
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attr_accessor :page_size
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# Required. The dataset IDs to search within. Caller must have `READ` access
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# to these datasets.
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# Corresponds to the JSON property `datasetIds`
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attr_accessor :dataset_ids
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# If specified, only annotation sets that have any of these types are
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# returned.
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# Corresponds to the JSON property `types`
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# @return [Array<String>]
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attr_accessor :types
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end
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end
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# The read group set search response.
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class SearchReadGroupSetsResponse
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include Google::Apis::Core::Hashable
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# The list of matching read group sets.
|
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# Corresponds to the JSON property `readGroupSets`
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# @return [Array<Google::Apis::GenomicsV1::ReadGroupSet>]
|
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attr_accessor :read_group_sets
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# The continuation token, which is used to page through large result sets.
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# Provide this value in a subsequent request to return the next page of
|
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|
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# results. This field will be empty if there aren't any additional results.
|
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# Corresponds to the JSON property `nextPageToken`
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# @return [String]
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attr_accessor :next_page_token
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|
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|
-
end
|
|
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|
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|
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|
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# Update properties of this object
|
|
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|
-
def update!(**args)
|
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|
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|
|
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|
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@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
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|
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end
|
|
166
|
-
end
|
|
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|
-
|
|
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|
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#
|
|
169
|
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class SearchReferencesRequest
|
|
170
|
-
include Google::Apis::Core::Hashable
|
|
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|
-
|
|
172
|
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# If present, return references for which the
|
|
173
|
-
# md5checksum matches exactly.
|
|
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|
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# Corresponds to the JSON property `md5checksums`
|
|
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|
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# @return [Array<String>]
|
|
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|
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attr_accessor :md5checksums
|
|
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|
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|
|
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|
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# If present, return references for which a prefix of any of
|
|
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|
-
# sourceAccessions match
|
|
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|
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# any of these strings. Accession numbers typically have a main number and a
|
|
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|
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# version, for example `GCF_000001405.26`.
|
|
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|
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# Corresponds to the JSON property `accessions`
|
|
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|
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# @return [Array<String>]
|
|
184
|
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attr_accessor :accessions
|
|
185
|
-
|
|
186
|
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# The continuation token, which is used to page through large result sets.
|
|
187
|
-
# To get the next page of results, set this parameter to the value of
|
|
188
|
-
# `nextPageToken` from the previous response.
|
|
189
|
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# Corresponds to the JSON property `pageToken`
|
|
190
|
-
# @return [String]
|
|
191
|
-
attr_accessor :page_token
|
|
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|
-
|
|
193
|
-
# If present, return only references which belong to this reference set.
|
|
194
|
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# Corresponds to the JSON property `referenceSetId`
|
|
195
|
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# @return [String]
|
|
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|
-
attr_accessor :reference_set_id
|
|
197
|
-
|
|
198
|
-
# The maximum number of results to return in a single page. If unspecified,
|
|
199
|
-
# defaults to 1024. The maximum value is 4096.
|
|
200
|
-
# Corresponds to the JSON property `pageSize`
|
|
201
|
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# @return [Fixnum]
|
|
202
|
-
attr_accessor :page_size
|
|
203
|
-
|
|
204
|
-
def initialize(**args)
|
|
205
|
-
update!(**args)
|
|
206
|
-
end
|
|
207
|
-
|
|
208
|
-
# Update properties of this object
|
|
209
|
-
def update!(**args)
|
|
210
|
-
@md5checksums = args[:md5checksums] if args.key?(:md5checksums)
|
|
211
|
-
@accessions = args[:accessions] if args.key?(:accessions)
|
|
212
|
-
@page_token = args[:page_token] if args.key?(:page_token)
|
|
213
|
-
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
214
|
-
@page_size = args[:page_size] if args.key?(:page_size)
|
|
215
|
-
end
|
|
216
|
-
end
|
|
217
|
-
|
|
218
|
-
# A linear alignment can be represented by one CIGAR string. Describes the
|
|
219
|
-
# mapped position and local alignment of the read to the reference.
|
|
220
|
-
class LinearAlignment
|
|
221
|
-
include Google::Apis::Core::Hashable
|
|
222
|
-
|
|
223
|
-
# An abstraction for referring to a genomic position, in relation to some
|
|
224
|
-
# already known reference. For now, represents a genomic position as a
|
|
225
|
-
# reference name, a base number on that reference (0-based), and a
|
|
226
|
-
# determination of forward or reverse strand.
|
|
227
|
-
# Corresponds to the JSON property `position`
|
|
228
|
-
# @return [Google::Apis::GenomicsV1::Position]
|
|
229
|
-
attr_accessor :position
|
|
230
|
-
|
|
231
|
-
# Represents the local alignment of this sequence (alignment matches, indels,
|
|
232
|
-
# etc) against the reference.
|
|
233
|
-
# Corresponds to the JSON property `cigar`
|
|
234
|
-
# @return [Array<Google::Apis::GenomicsV1::CigarUnit>]
|
|
235
|
-
attr_accessor :cigar
|
|
236
|
-
|
|
237
|
-
# The mapping quality of this alignment. Represents how likely
|
|
238
|
-
# the read maps to this position as opposed to other locations.
|
|
239
|
-
# Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
|
|
240
|
-
# the nearest integer.
|
|
241
|
-
# Corresponds to the JSON property `mappingQuality`
|
|
242
|
-
# @return [Fixnum]
|
|
243
|
-
attr_accessor :mapping_quality
|
|
244
|
-
|
|
245
|
-
def initialize(**args)
|
|
246
|
-
update!(**args)
|
|
247
|
-
end
|
|
248
|
-
|
|
249
|
-
# Update properties of this object
|
|
250
|
-
def update!(**args)
|
|
251
|
-
@position = args[:position] if args.key?(:position)
|
|
252
|
-
@cigar = args[:cigar] if args.key?(:cigar)
|
|
253
|
-
@mapping_quality = args[:mapping_quality] if args.key?(:mapping_quality)
|
|
254
|
-
end
|
|
255
|
-
end
|
|
256
|
-
|
|
257
25
|
# A Dataset is a collection of genomic data.
|
|
258
26
|
# For more genomics resource definitions, see [Fundamentals of Google
|
|
259
27
|
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
@@ -339,12 +107,6 @@ module Google
|
|
|
339
107
|
# @return [String]
|
|
340
108
|
attr_accessor :id
|
|
341
109
|
|
|
342
|
-
# The predicted insert size of this read group. The insert size is the length
|
|
343
|
-
# the sequenced DNA fragment from end-to-end, not including the adapters.
|
|
344
|
-
# Corresponds to the JSON property `predictedInsertSize`
|
|
345
|
-
# @return [Fixnum]
|
|
346
|
-
attr_accessor :predicted_insert_size
|
|
347
|
-
|
|
348
110
|
# The programs used to generate this read group. Programs are always
|
|
349
111
|
# identical for all read groups within a read group set. For this reason,
|
|
350
112
|
# only the first read group in a returned set will have this field
|
|
@@ -353,6 +115,12 @@ module Google
|
|
|
353
115
|
# @return [Array<Google::Apis::GenomicsV1::Program>]
|
|
354
116
|
attr_accessor :programs
|
|
355
117
|
|
|
118
|
+
# The predicted insert size of this read group. The insert size is the length
|
|
119
|
+
# the sequenced DNA fragment from end-to-end, not including the adapters.
|
|
120
|
+
# Corresponds to the JSON property `predictedInsertSize`
|
|
121
|
+
# @return [Fixnum]
|
|
122
|
+
attr_accessor :predicted_insert_size
|
|
123
|
+
|
|
356
124
|
# A free-form text description of this read group.
|
|
357
125
|
# Corresponds to the JSON property `description`
|
|
358
126
|
# @return [String]
|
|
@@ -383,8 +151,8 @@ module Google
|
|
|
383
151
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
384
152
|
@info = args[:info] if args.key?(:info)
|
|
385
153
|
@id = args[:id] if args.key?(:id)
|
|
386
|
-
@predicted_insert_size = args[:predicted_insert_size] if args.key?(:predicted_insert_size)
|
|
387
154
|
@programs = args[:programs] if args.key?(:programs)
|
|
155
|
+
@predicted_insert_size = args[:predicted_insert_size] if args.key?(:predicted_insert_size)
|
|
388
156
|
@description = args[:description] if args.key?(:description)
|
|
389
157
|
@sample_id = args[:sample_id] if args.key?(:sample_id)
|
|
390
158
|
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
@@ -404,27 +172,17 @@ module Google
|
|
|
404
172
|
class ReadGroupSet
|
|
405
173
|
include Google::Apis::Core::Hashable
|
|
406
174
|
|
|
407
|
-
# The
|
|
408
|
-
#
|
|
409
|
-
#
|
|
410
|
-
|
|
411
|
-
|
|
412
|
-
# The dataset to which this read group set belongs.
|
|
413
|
-
# Corresponds to the JSON property `datasetId`
|
|
414
|
-
# @return [String]
|
|
415
|
-
attr_accessor :dataset_id
|
|
175
|
+
# The read groups in this set. There are typically 1-10 read groups in a read
|
|
176
|
+
# group set.
|
|
177
|
+
# Corresponds to the JSON property `readGroups`
|
|
178
|
+
# @return [Array<Google::Apis::GenomicsV1::ReadGroup>]
|
|
179
|
+
attr_accessor :read_groups
|
|
416
180
|
|
|
417
181
|
# The filename of the original source file for this read group set, if any.
|
|
418
182
|
# Corresponds to the JSON property `filename`
|
|
419
183
|
# @return [String]
|
|
420
184
|
attr_accessor :filename
|
|
421
185
|
|
|
422
|
-
# The read groups in this set. There are typically 1-10 read groups in a read
|
|
423
|
-
# group set.
|
|
424
|
-
# Corresponds to the JSON property `readGroups`
|
|
425
|
-
# @return [Array<Google::Apis::GenomicsV1::ReadGroup>]
|
|
426
|
-
attr_accessor :read_groups
|
|
427
|
-
|
|
428
186
|
# The read group set name. By default this will be initialized to the sample
|
|
429
187
|
# name of the sequenced data contained in this set.
|
|
430
188
|
# Corresponds to the JSON property `name`
|
|
@@ -441,19 +199,29 @@ module Google
|
|
|
441
199
|
# @return [Hash<String,Array<Object>>]
|
|
442
200
|
attr_accessor :info
|
|
443
201
|
|
|
202
|
+
# The server-generated read group set ID, unique for all read group sets.
|
|
203
|
+
# Corresponds to the JSON property `id`
|
|
204
|
+
# @return [String]
|
|
205
|
+
attr_accessor :id
|
|
206
|
+
|
|
207
|
+
# The dataset to which this read group set belongs.
|
|
208
|
+
# Corresponds to the JSON property `datasetId`
|
|
209
|
+
# @return [String]
|
|
210
|
+
attr_accessor :dataset_id
|
|
211
|
+
|
|
444
212
|
def initialize(**args)
|
|
445
213
|
update!(**args)
|
|
446
214
|
end
|
|
447
215
|
|
|
448
216
|
# Update properties of this object
|
|
449
217
|
def update!(**args)
|
|
450
|
-
@id = args[:id] if args.key?(:id)
|
|
451
|
-
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
452
|
-
@filename = args[:filename] if args.key?(:filename)
|
|
453
218
|
@read_groups = args[:read_groups] if args.key?(:read_groups)
|
|
219
|
+
@filename = args[:filename] if args.key?(:filename)
|
|
454
220
|
@name = args[:name] if args.key?(:name)
|
|
455
221
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
456
222
|
@info = args[:info] if args.key?(:info)
|
|
223
|
+
@id = args[:id] if args.key?(:id)
|
|
224
|
+
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
457
225
|
end
|
|
458
226
|
end
|
|
459
227
|
|
|
@@ -461,11 +229,6 @@ module Google
|
|
|
461
229
|
class SearchVariantSetsResponse
|
|
462
230
|
include Google::Apis::Core::Hashable
|
|
463
231
|
|
|
464
|
-
# The variant sets belonging to the requested dataset.
|
|
465
|
-
# Corresponds to the JSON property `variantSets`
|
|
466
|
-
# @return [Array<Google::Apis::GenomicsV1::VariantSet>]
|
|
467
|
-
attr_accessor :variant_sets
|
|
468
|
-
|
|
469
232
|
# The continuation token, which is used to page through large result sets.
|
|
470
233
|
# Provide this value in a subsequent request to return the next page of
|
|
471
234
|
# results. This field will be empty if there aren't any additional results.
|
|
@@ -473,14 +236,19 @@ module Google
|
|
|
473
236
|
# @return [String]
|
|
474
237
|
attr_accessor :next_page_token
|
|
475
238
|
|
|
239
|
+
# The variant sets belonging to the requested dataset.
|
|
240
|
+
# Corresponds to the JSON property `variantSets`
|
|
241
|
+
# @return [Array<Google::Apis::GenomicsV1::VariantSet>]
|
|
242
|
+
attr_accessor :variant_sets
|
|
243
|
+
|
|
476
244
|
def initialize(**args)
|
|
477
245
|
update!(**args)
|
|
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246
|
end
|
|
479
247
|
|
|
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|
# Update properties of this object
|
|
481
249
|
def update!(**args)
|
|
482
|
-
@variant_sets = args[:variant_sets] if args.key?(:variant_sets)
|
|
483
250
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
251
|
+
@variant_sets = args[:variant_sets] if args.key?(:variant_sets)
|
|
484
252
|
end
|
|
485
253
|
end
|
|
486
254
|
|
|
@@ -578,13 +346,6 @@ module Google
|
|
|
578
346
|
class Position
|
|
579
347
|
include Google::Apis::Core::Hashable
|
|
580
348
|
|
|
581
|
-
# Whether this position is on the reverse strand, as opposed to the forward
|
|
582
|
-
# strand.
|
|
583
|
-
# Corresponds to the JSON property `reverseStrand`
|
|
584
|
-
# @return [Boolean]
|
|
585
|
-
attr_accessor :reverse_strand
|
|
586
|
-
alias_method :reverse_strand?, :reverse_strand
|
|
587
|
-
|
|
588
349
|
# The 0-based offset from the start of the forward strand for that reference.
|
|
589
350
|
# Corresponds to the JSON property `position`
|
|
590
351
|
# @return [String]
|
|
@@ -595,15 +356,22 @@ module Google
|
|
|
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356
|
# @return [String]
|
|
596
357
|
attr_accessor :reference_name
|
|
597
358
|
|
|
359
|
+
# Whether this position is on the reverse strand, as opposed to the forward
|
|
360
|
+
# strand.
|
|
361
|
+
# Corresponds to the JSON property `reverseStrand`
|
|
362
|
+
# @return [Boolean]
|
|
363
|
+
attr_accessor :reverse_strand
|
|
364
|
+
alias_method :reverse_strand?, :reverse_strand
|
|
365
|
+
|
|
598
366
|
def initialize(**args)
|
|
599
367
|
update!(**args)
|
|
600
368
|
end
|
|
601
369
|
|
|
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370
|
# Update properties of this object
|
|
603
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|
def update!(**args)
|
|
604
|
-
@reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
|
|
605
372
|
@position = args[:position] if args.key?(:position)
|
|
606
373
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
374
|
+
@reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
|
|
607
375
|
end
|
|
608
376
|
end
|
|
609
377
|
|
|
@@ -638,6 +406,12 @@ module Google
|
|
|
638
406
|
class SearchCallSetsRequest
|
|
639
407
|
include Google::Apis::Core::Hashable
|
|
640
408
|
|
|
409
|
+
# Restrict the query to call sets within the given variant sets. At least one
|
|
410
|
+
# ID must be provided.
|
|
411
|
+
# Corresponds to the JSON property `variantSetIds`
|
|
412
|
+
# @return [Array<String>]
|
|
413
|
+
attr_accessor :variant_set_ids
|
|
414
|
+
|
|
641
415
|
# Only return call sets for which a substring of the name matches this
|
|
642
416
|
# string.
|
|
643
417
|
# Corresponds to the JSON property `name`
|
|
@@ -657,22 +431,16 @@ module Google
|
|
|
657
431
|
# @return [Fixnum]
|
|
658
432
|
attr_accessor :page_size
|
|
659
433
|
|
|
660
|
-
# Restrict the query to call sets within the given variant sets. At least one
|
|
661
|
-
# ID must be provided.
|
|
662
|
-
# Corresponds to the JSON property `variantSetIds`
|
|
663
|
-
# @return [Array<String>]
|
|
664
|
-
attr_accessor :variant_set_ids
|
|
665
|
-
|
|
666
434
|
def initialize(**args)
|
|
667
435
|
update!(**args)
|
|
668
436
|
end
|
|
669
437
|
|
|
670
438
|
# Update properties of this object
|
|
671
439
|
def update!(**args)
|
|
440
|
+
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
|
672
441
|
@name = args[:name] if args.key?(:name)
|
|
673
442
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
674
443
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
675
|
-
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
|
676
444
|
end
|
|
677
445
|
end
|
|
678
446
|
|
|
@@ -796,14 +564,6 @@ module Google
|
|
|
796
564
|
class SearchReadsRequest
|
|
797
565
|
include Google::Apis::Core::Hashable
|
|
798
566
|
|
|
799
|
-
# The IDs of the read groups sets within which to search for reads. All
|
|
800
|
-
# specified read group sets must be aligned against a common set of reference
|
|
801
|
-
# sequences; this defines the genomic coordinates for the query. Must specify
|
|
802
|
-
# one of `readGroupSetIds` or `readGroupIds`.
|
|
803
|
-
# Corresponds to the JSON property `readGroupSetIds`
|
|
804
|
-
# @return [Array<String>]
|
|
805
|
-
attr_accessor :read_group_set_ids
|
|
806
|
-
|
|
807
567
|
# The IDs of the read groups within which to search for reads. All specified
|
|
808
568
|
# read groups must belong to the same read group sets. Must specify one of
|
|
809
569
|
# `readGroupSetIds` or `readGroupIds`.
|
|
@@ -843,19 +603,40 @@ module Google
|
|
|
843
603
|
# @return [String]
|
|
844
604
|
attr_accessor :reference_name
|
|
845
605
|
|
|
606
|
+
# The IDs of the read groups sets within which to search for reads. All
|
|
607
|
+
# specified read group sets must be aligned against a common set of reference
|
|
608
|
+
# sequences; this defines the genomic coordinates for the query. Must specify
|
|
609
|
+
# one of `readGroupSetIds` or `readGroupIds`.
|
|
610
|
+
# Corresponds to the JSON property `readGroupSetIds`
|
|
611
|
+
# @return [Array<String>]
|
|
612
|
+
attr_accessor :read_group_set_ids
|
|
613
|
+
|
|
846
614
|
def initialize(**args)
|
|
847
615
|
update!(**args)
|
|
848
616
|
end
|
|
849
617
|
|
|
850
618
|
# Update properties of this object
|
|
851
619
|
def update!(**args)
|
|
852
|
-
@read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids)
|
|
853
620
|
@read_group_ids = args[:read_group_ids] if args.key?(:read_group_ids)
|
|
854
621
|
@end = args[:end] if args.key?(:end)
|
|
855
622
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
856
623
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
857
624
|
@start = args[:start] if args.key?(:start)
|
|
858
625
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
626
|
+
@read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids)
|
|
627
|
+
end
|
|
628
|
+
end
|
|
629
|
+
|
|
630
|
+
# The request message for Operations.CancelOperation.
|
|
631
|
+
class CancelOperationRequest
|
|
632
|
+
include Google::Apis::Core::Hashable
|
|
633
|
+
|
|
634
|
+
def initialize(**args)
|
|
635
|
+
update!(**args)
|
|
636
|
+
end
|
|
637
|
+
|
|
638
|
+
# Update properties of this object
|
|
639
|
+
def update!(**args)
|
|
859
640
|
end
|
|
860
641
|
end
|
|
861
642
|
|
|
@@ -868,24 +649,32 @@ module Google
|
|
|
868
649
|
class Annotation
|
|
869
650
|
include Google::Apis::Core::Hashable
|
|
870
651
|
|
|
652
|
+
# Whether this range refers to the reverse strand, as opposed to the forward
|
|
653
|
+
# strand. Note that regardless of this field, the start/end position of the
|
|
654
|
+
# range always refer to the forward strand.
|
|
655
|
+
# Corresponds to the JSON property `reverseStrand`
|
|
656
|
+
# @return [Boolean]
|
|
657
|
+
attr_accessor :reverse_strand
|
|
658
|
+
alias_method :reverse_strand?, :reverse_strand
|
|
659
|
+
|
|
871
660
|
# The display name corresponding to the reference specified by
|
|
872
661
|
# `referenceId`, for example `chr1`, `1`, or `chrX`.
|
|
873
662
|
# Corresponds to the JSON property `referenceName`
|
|
874
663
|
# @return [String]
|
|
875
664
|
attr_accessor :reference_name
|
|
876
665
|
|
|
877
|
-
# The data type for this annotation. Must match the containing annotation
|
|
878
|
-
# set's type.
|
|
879
|
-
# Corresponds to the JSON property `type`
|
|
880
|
-
# @return [String]
|
|
881
|
-
attr_accessor :type
|
|
882
|
-
|
|
883
666
|
# A map of additional read alignment information. This must be of the form
|
|
884
667
|
# map<string, string[]> (string key mapping to a list of string values).
|
|
885
668
|
# Corresponds to the JSON property `info`
|
|
886
669
|
# @return [Hash<String,Array<Object>>]
|
|
887
670
|
attr_accessor :info
|
|
888
671
|
|
|
672
|
+
# The data type for this annotation. Must match the containing annotation
|
|
673
|
+
# set's type.
|
|
674
|
+
# Corresponds to the JSON property `type`
|
|
675
|
+
# @return [String]
|
|
676
|
+
attr_accessor :type
|
|
677
|
+
|
|
889
678
|
# The end position of the range on the reference, 0-based exclusive.
|
|
890
679
|
# Corresponds to the JSON property `end`
|
|
891
680
|
# @return [String]
|
|
@@ -920,23 +709,15 @@ module Google
|
|
|
920
709
|
# @return [Google::Apis::GenomicsV1::VariantAnnotation]
|
|
921
710
|
attr_accessor :variant
|
|
922
711
|
|
|
923
|
-
# The server-generated annotation ID, unique across all annotations.
|
|
924
|
-
# Corresponds to the JSON property `id`
|
|
925
|
-
# @return [String]
|
|
926
|
-
attr_accessor :id
|
|
927
|
-
|
|
928
712
|
# The ID of the Google Genomics reference associated with this range.
|
|
929
713
|
# Corresponds to the JSON property `referenceId`
|
|
930
714
|
# @return [String]
|
|
931
715
|
attr_accessor :reference_id
|
|
932
716
|
|
|
933
|
-
#
|
|
934
|
-
#
|
|
935
|
-
#
|
|
936
|
-
|
|
937
|
-
# @return [Boolean]
|
|
938
|
-
attr_accessor :reverse_strand
|
|
939
|
-
alias_method :reverse_strand?, :reverse_strand
|
|
717
|
+
# The server-generated annotation ID, unique across all annotations.
|
|
718
|
+
# Corresponds to the JSON property `id`
|
|
719
|
+
# @return [String]
|
|
720
|
+
attr_accessor :id
|
|
940
721
|
|
|
941
722
|
def initialize(**args)
|
|
942
723
|
update!(**args)
|
|
@@ -944,53 +725,18 @@ module Google
|
|
|
944
725
|
|
|
945
726
|
# Update properties of this object
|
|
946
727
|
def update!(**args)
|
|
728
|
+
@reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
|
|
947
729
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
948
|
-
@type = args[:type] if args.key?(:type)
|
|
949
730
|
@info = args[:info] if args.key?(:info)
|
|
731
|
+
@type = args[:type] if args.key?(:type)
|
|
950
732
|
@end = args[:end] if args.key?(:end)
|
|
951
733
|
@transcript = args[:transcript] if args.key?(:transcript)
|
|
952
734
|
@start = args[:start] if args.key?(:start)
|
|
953
735
|
@annotation_set_id = args[:annotation_set_id] if args.key?(:annotation_set_id)
|
|
954
736
|
@name = args[:name] if args.key?(:name)
|
|
955
737
|
@variant = args[:variant] if args.key?(:variant)
|
|
956
|
-
@id = args[:id] if args.key?(:id)
|
|
957
738
|
@reference_id = args[:reference_id] if args.key?(:reference_id)
|
|
958
|
-
@
|
|
959
|
-
end
|
|
960
|
-
end
|
|
961
|
-
|
|
962
|
-
# The request message for Operations.CancelOperation.
|
|
963
|
-
class CancelOperationRequest
|
|
964
|
-
include Google::Apis::Core::Hashable
|
|
965
|
-
|
|
966
|
-
def initialize(**args)
|
|
967
|
-
update!(**args)
|
|
968
|
-
end
|
|
969
|
-
|
|
970
|
-
# Update properties of this object
|
|
971
|
-
def update!(**args)
|
|
972
|
-
end
|
|
973
|
-
end
|
|
974
|
-
|
|
975
|
-
# Runtime metadata that will be populated in the
|
|
976
|
-
# runtimeMetadata
|
|
977
|
-
# field of the Operation associated with a RunPipeline execution.
|
|
978
|
-
class RuntimeMetadata
|
|
979
|
-
include Google::Apis::Core::Hashable
|
|
980
|
-
|
|
981
|
-
# Describes a Compute Engine resource that is being managed by a running
|
|
982
|
-
# pipeline.
|
|
983
|
-
# Corresponds to the JSON property `computeEngine`
|
|
984
|
-
# @return [Google::Apis::GenomicsV1::ComputeEngine]
|
|
985
|
-
attr_accessor :compute_engine
|
|
986
|
-
|
|
987
|
-
def initialize(**args)
|
|
988
|
-
update!(**args)
|
|
989
|
-
end
|
|
990
|
-
|
|
991
|
-
# Update properties of this object
|
|
992
|
-
def update!(**args)
|
|
993
|
-
@compute_engine = args[:compute_engine] if args.key?(:compute_engine)
|
|
739
|
+
@id = args[:id] if args.key?(:id)
|
|
994
740
|
end
|
|
995
741
|
end
|
|
996
742
|
|
|
@@ -999,14 +745,6 @@ module Google
|
|
|
999
745
|
class Operation
|
|
1000
746
|
include Google::Apis::Core::Hashable
|
|
1001
747
|
|
|
1002
|
-
# If the value is `false`, it means the operation is still in progress.
|
|
1003
|
-
# If true, the operation is completed, and either `error` or `response` is
|
|
1004
|
-
# available.
|
|
1005
|
-
# Corresponds to the JSON property `done`
|
|
1006
|
-
# @return [Boolean]
|
|
1007
|
-
attr_accessor :done
|
|
1008
|
-
alias_method :done?, :done
|
|
1009
|
-
|
|
1010
748
|
# If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If
|
|
1011
749
|
# importing Variants, an ImportVariantsResponse is returned. For pipelines and
|
|
1012
750
|
# exports, an empty response is returned.
|
|
@@ -1069,17 +807,47 @@ module Google
|
|
|
1069
807
|
# @return [Hash<String,Object>]
|
|
1070
808
|
attr_accessor :metadata
|
|
1071
809
|
|
|
810
|
+
# If the value is `false`, it means the operation is still in progress.
|
|
811
|
+
# If true, the operation is completed, and either `error` or `response` is
|
|
812
|
+
# available.
|
|
813
|
+
# Corresponds to the JSON property `done`
|
|
814
|
+
# @return [Boolean]
|
|
815
|
+
attr_accessor :done
|
|
816
|
+
alias_method :done?, :done
|
|
817
|
+
|
|
1072
818
|
def initialize(**args)
|
|
1073
819
|
update!(**args)
|
|
1074
820
|
end
|
|
1075
821
|
|
|
1076
822
|
# Update properties of this object
|
|
1077
823
|
def update!(**args)
|
|
1078
|
-
@done = args[:done] if args.key?(:done)
|
|
1079
824
|
@response = args[:response] if args.key?(:response)
|
|
1080
825
|
@name = args[:name] if args.key?(:name)
|
|
1081
826
|
@error = args[:error] if args.key?(:error)
|
|
1082
827
|
@metadata = args[:metadata] if args.key?(:metadata)
|
|
828
|
+
@done = args[:done] if args.key?(:done)
|
|
829
|
+
end
|
|
830
|
+
end
|
|
831
|
+
|
|
832
|
+
# Runtime metadata that will be populated in the
|
|
833
|
+
# runtimeMetadata
|
|
834
|
+
# field of the Operation associated with a RunPipeline execution.
|
|
835
|
+
class RuntimeMetadata
|
|
836
|
+
include Google::Apis::Core::Hashable
|
|
837
|
+
|
|
838
|
+
# Describes a Compute Engine resource that is being managed by a running
|
|
839
|
+
# pipeline.
|
|
840
|
+
# Corresponds to the JSON property `computeEngine`
|
|
841
|
+
# @return [Google::Apis::GenomicsV1::ComputeEngine]
|
|
842
|
+
attr_accessor :compute_engine
|
|
843
|
+
|
|
844
|
+
def initialize(**args)
|
|
845
|
+
update!(**args)
|
|
846
|
+
end
|
|
847
|
+
|
|
848
|
+
# Update properties of this object
|
|
849
|
+
def update!(**args)
|
|
850
|
+
@compute_engine = args[:compute_engine] if args.key?(:compute_engine)
|
|
1083
851
|
end
|
|
1084
852
|
end
|
|
1085
853
|
|
|
@@ -1109,6 +877,26 @@ module Google
|
|
|
1109
877
|
class VariantCall
|
|
1110
878
|
include Google::Apis::Core::Hashable
|
|
1111
879
|
|
|
880
|
+
# The name of the call set this variant call belongs to.
|
|
881
|
+
# Corresponds to the JSON property `callSetName`
|
|
882
|
+
# @return [String]
|
|
883
|
+
attr_accessor :call_set_name
|
|
884
|
+
|
|
885
|
+
# The genotype likelihoods for this variant call. Each array entry
|
|
886
|
+
# represents how likely a specific genotype is for this call. The value
|
|
887
|
+
# ordering is defined by the GL tag in the VCF spec.
|
|
888
|
+
# If Phred-scaled genotype likelihood scores (PL) are available and
|
|
889
|
+
# log10(P) genotype likelihood scores (GL) are not, PL scores are converted
|
|
890
|
+
# to GL scores. If both are available, PL scores are stored in `info`.
|
|
891
|
+
# Corresponds to the JSON property `genotypeLikelihood`
|
|
892
|
+
# @return [Array<Float>]
|
|
893
|
+
attr_accessor :genotype_likelihood
|
|
894
|
+
|
|
895
|
+
# The ID of the call set this variant call belongs to.
|
|
896
|
+
# Corresponds to the JSON property `callSetId`
|
|
897
|
+
# @return [String]
|
|
898
|
+
attr_accessor :call_set_id
|
|
899
|
+
|
|
1112
900
|
# The genotype of this variant call. Each value represents either the value
|
|
1113
901
|
# of the `referenceBases` field or a 1-based index into
|
|
1114
902
|
# `alternateBases`. If a variant had a `referenceBases`
|
|
@@ -1140,38 +928,18 @@ module Google
|
|
|
1140
928
|
# @return [Hash<String,Array<Object>>]
|
|
1141
929
|
attr_accessor :info
|
|
1142
930
|
|
|
1143
|
-
# The name of the call set this variant call belongs to.
|
|
1144
|
-
# Corresponds to the JSON property `callSetName`
|
|
1145
|
-
# @return [String]
|
|
1146
|
-
attr_accessor :call_set_name
|
|
1147
|
-
|
|
1148
|
-
# The genotype likelihoods for this variant call. Each array entry
|
|
1149
|
-
# represents how likely a specific genotype is for this call. The value
|
|
1150
|
-
# ordering is defined by the GL tag in the VCF spec.
|
|
1151
|
-
# If Phred-scaled genotype likelihood scores (PL) are available and
|
|
1152
|
-
# log10(P) genotype likelihood scores (GL) are not, PL scores are converted
|
|
1153
|
-
# to GL scores. If both are available, PL scores are stored in `info`.
|
|
1154
|
-
# Corresponds to the JSON property `genotypeLikelihood`
|
|
1155
|
-
# @return [Array<Float>]
|
|
1156
|
-
attr_accessor :genotype_likelihood
|
|
1157
|
-
|
|
1158
|
-
# The ID of the call set this variant call belongs to.
|
|
1159
|
-
# Corresponds to the JSON property `callSetId`
|
|
1160
|
-
# @return [String]
|
|
1161
|
-
attr_accessor :call_set_id
|
|
1162
|
-
|
|
1163
931
|
def initialize(**args)
|
|
1164
932
|
update!(**args)
|
|
1165
933
|
end
|
|
1166
934
|
|
|
1167
935
|
# Update properties of this object
|
|
1168
936
|
def update!(**args)
|
|
1169
|
-
@genotype = args[:genotype] if args.key?(:genotype)
|
|
1170
|
-
@phaseset = args[:phaseset] if args.key?(:phaseset)
|
|
1171
|
-
@info = args[:info] if args.key?(:info)
|
|
1172
937
|
@call_set_name = args[:call_set_name] if args.key?(:call_set_name)
|
|
1173
938
|
@genotype_likelihood = args[:genotype_likelihood] if args.key?(:genotype_likelihood)
|
|
1174
939
|
@call_set_id = args[:call_set_id] if args.key?(:call_set_id)
|
|
940
|
+
@genotype = args[:genotype] if args.key?(:genotype)
|
|
941
|
+
@phaseset = args[:phaseset] if args.key?(:phaseset)
|
|
942
|
+
@info = args[:info] if args.key?(:info)
|
|
1175
943
|
end
|
|
1176
944
|
end
|
|
1177
945
|
|
|
@@ -1206,13 +974,6 @@ module Google
|
|
|
1206
974
|
class ListBasesResponse
|
|
1207
975
|
include Google::Apis::Core::Hashable
|
|
1208
976
|
|
|
1209
|
-
# The offset position (0-based) of the given `sequence` from the
|
|
1210
|
-
# start of this `Reference`. This value will differ for each page
|
|
1211
|
-
# in a paginated request.
|
|
1212
|
-
# Corresponds to the JSON property `offset`
|
|
1213
|
-
# @return [String]
|
|
1214
|
-
attr_accessor :offset
|
|
1215
|
-
|
|
1216
977
|
# The continuation token, which is used to page through large result sets.
|
|
1217
978
|
# Provide this value in a subsequent request to return the next page of
|
|
1218
979
|
# results. This field will be empty if there aren't any additional results.
|
|
@@ -1225,15 +986,22 @@ module Google
|
|
|
1225
986
|
# @return [String]
|
|
1226
987
|
attr_accessor :sequence
|
|
1227
988
|
|
|
989
|
+
# The offset position (0-based) of the given `sequence` from the
|
|
990
|
+
# start of this `Reference`. This value will differ for each page
|
|
991
|
+
# in a paginated request.
|
|
992
|
+
# Corresponds to the JSON property `offset`
|
|
993
|
+
# @return [String]
|
|
994
|
+
attr_accessor :offset
|
|
995
|
+
|
|
1228
996
|
def initialize(**args)
|
|
1229
997
|
update!(**args)
|
|
1230
998
|
end
|
|
1231
999
|
|
|
1232
1000
|
# Update properties of this object
|
|
1233
1001
|
def update!(**args)
|
|
1234
|
-
@offset = args[:offset] if args.key?(:offset)
|
|
1235
1002
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
1236
1003
|
@sequence = args[:sequence] if args.key?(:sequence)
|
|
1004
|
+
@offset = args[:offset] if args.key?(:offset)
|
|
1237
1005
|
end
|
|
1238
1006
|
end
|
|
1239
1007
|
|
|
@@ -1309,19 +1077,6 @@ module Google
|
|
|
1309
1077
|
end
|
|
1310
1078
|
end
|
|
1311
1079
|
|
|
1312
|
-
#
|
|
1313
|
-
class UndeleteDatasetRequest
|
|
1314
|
-
include Google::Apis::Core::Hashable
|
|
1315
|
-
|
|
1316
|
-
def initialize(**args)
|
|
1317
|
-
update!(**args)
|
|
1318
|
-
end
|
|
1319
|
-
|
|
1320
|
-
# Update properties of this object
|
|
1321
|
-
def update!(**args)
|
|
1322
|
-
end
|
|
1323
|
-
end
|
|
1324
|
-
|
|
1325
1080
|
# Associates `members` with a `role`.
|
|
1326
1081
|
class Binding
|
|
1327
1082
|
include Google::Apis::Core::Hashable
|
|
@@ -1362,10 +1117,29 @@ module Google
|
|
|
1362
1117
|
end
|
|
1363
1118
|
end
|
|
1364
1119
|
|
|
1120
|
+
#
|
|
1121
|
+
class UndeleteDatasetRequest
|
|
1122
|
+
include Google::Apis::Core::Hashable
|
|
1123
|
+
|
|
1124
|
+
def initialize(**args)
|
|
1125
|
+
update!(**args)
|
|
1126
|
+
end
|
|
1127
|
+
|
|
1128
|
+
# Update properties of this object
|
|
1129
|
+
def update!(**args)
|
|
1130
|
+
end
|
|
1131
|
+
end
|
|
1132
|
+
|
|
1365
1133
|
# A 0-based half-open genomic coordinate range for search requests.
|
|
1366
1134
|
class Range
|
|
1367
1135
|
include Google::Apis::Core::Hashable
|
|
1368
1136
|
|
|
1137
|
+
# The reference sequence name, for example `chr1`,
|
|
1138
|
+
# `1`, or `chrX`.
|
|
1139
|
+
# Corresponds to the JSON property `referenceName`
|
|
1140
|
+
# @return [String]
|
|
1141
|
+
attr_accessor :reference_name
|
|
1142
|
+
|
|
1369
1143
|
# The start position of the range on the reference, 0-based inclusive.
|
|
1370
1144
|
# Corresponds to the JSON property `start`
|
|
1371
1145
|
# @return [String]
|
|
@@ -1376,21 +1150,15 @@ module Google
|
|
|
1376
1150
|
# @return [String]
|
|
1377
1151
|
attr_accessor :end
|
|
1378
1152
|
|
|
1379
|
-
# The reference sequence name, for example `chr1`,
|
|
1380
|
-
# `1`, or `chrX`.
|
|
1381
|
-
# Corresponds to the JSON property `referenceName`
|
|
1382
|
-
# @return [String]
|
|
1383
|
-
attr_accessor :reference_name
|
|
1384
|
-
|
|
1385
1153
|
def initialize(**args)
|
|
1386
1154
|
update!(**args)
|
|
1387
1155
|
end
|
|
1388
1156
|
|
|
1389
1157
|
# Update properties of this object
|
|
1390
1158
|
def update!(**args)
|
|
1159
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
1391
1160
|
@start = args[:start] if args.key?(:start)
|
|
1392
1161
|
@end = args[:end] if args.key?(:end)
|
|
1393
|
-
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
1394
1162
|
end
|
|
1395
1163
|
end
|
|
1396
1164
|
|
|
@@ -1512,11 +1280,6 @@ module Google
|
|
|
1512
1280
|
class SearchCallSetsResponse
|
|
1513
1281
|
include Google::Apis::Core::Hashable
|
|
1514
1282
|
|
|
1515
|
-
# The list of matching call sets.
|
|
1516
|
-
# Corresponds to the JSON property `callSets`
|
|
1517
|
-
# @return [Array<Google::Apis::GenomicsV1::CallSet>]
|
|
1518
|
-
attr_accessor :call_sets
|
|
1519
|
-
|
|
1520
1283
|
# The continuation token, which is used to page through large result sets.
|
|
1521
1284
|
# Provide this value in a subsequent request to return the next page of
|
|
1522
1285
|
# results. This field will be empty if there aren't any additional results.
|
|
@@ -1524,14 +1287,19 @@ module Google
|
|
|
1524
1287
|
# @return [String]
|
|
1525
1288
|
attr_accessor :next_page_token
|
|
1526
1289
|
|
|
1290
|
+
# The list of matching call sets.
|
|
1291
|
+
# Corresponds to the JSON property `callSets`
|
|
1292
|
+
# @return [Array<Google::Apis::GenomicsV1::CallSet>]
|
|
1293
|
+
attr_accessor :call_sets
|
|
1294
|
+
|
|
1527
1295
|
def initialize(**args)
|
|
1528
1296
|
update!(**args)
|
|
1529
1297
|
end
|
|
1530
1298
|
|
|
1531
1299
|
# Update properties of this object
|
|
1532
1300
|
def update!(**args)
|
|
1533
|
-
@call_sets = args[:call_sets] if args.key?(:call_sets)
|
|
1534
1301
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
1302
|
+
@call_sets = args[:call_sets] if args.key?(:call_sets)
|
|
1535
1303
|
end
|
|
1536
1304
|
end
|
|
1537
1305
|
|
|
@@ -1548,6 +1316,12 @@ module Google
|
|
|
1548
1316
|
class Variant
|
|
1549
1317
|
include Google::Apis::Core::Hashable
|
|
1550
1318
|
|
|
1319
|
+
# The reference on which this variant occurs.
|
|
1320
|
+
# (such as `chr20` or `X`)
|
|
1321
|
+
# Corresponds to the JSON property `referenceName`
|
|
1322
|
+
# @return [String]
|
|
1323
|
+
attr_accessor :reference_name
|
|
1324
|
+
|
|
1551
1325
|
# A map of additional variant information. This must be of the form
|
|
1552
1326
|
# map<string, string[]> (string key mapping to a list of string values).
|
|
1553
1327
|
# Corresponds to the JSON property `info`
|
|
@@ -1560,15 +1334,21 @@ module Google
|
|
|
1560
1334
|
# @return [String]
|
|
1561
1335
|
attr_accessor :reference_bases
|
|
1562
1336
|
|
|
1337
|
+
# The bases that appear instead of the reference bases.
|
|
1338
|
+
# Corresponds to the JSON property `alternateBases`
|
|
1339
|
+
# @return [Array<String>]
|
|
1340
|
+
attr_accessor :alternate_bases
|
|
1341
|
+
|
|
1563
1342
|
# Names for the variant, for example a RefSNP ID.
|
|
1564
1343
|
# Corresponds to the JSON property `names`
|
|
1565
1344
|
# @return [Array<String>]
|
|
1566
1345
|
attr_accessor :names
|
|
1567
1346
|
|
|
1568
|
-
#
|
|
1569
|
-
#
|
|
1347
|
+
# A list of filters (normally quality filters) this variant has failed.
|
|
1348
|
+
# `PASS` indicates this variant has passed all filters.
|
|
1349
|
+
# Corresponds to the JSON property `filter`
|
|
1570
1350
|
# @return [Array<String>]
|
|
1571
|
-
attr_accessor :
|
|
1351
|
+
attr_accessor :filter
|
|
1572
1352
|
|
|
1573
1353
|
# The end position (0-based) of this variant. This corresponds to the first
|
|
1574
1354
|
# base after the last base in the reference allele. So, the length of
|
|
@@ -1578,12 +1358,6 @@ module Google
|
|
|
1578
1358
|
# @return [String]
|
|
1579
1359
|
attr_accessor :end
|
|
1580
1360
|
|
|
1581
|
-
# A list of filters (normally quality filters) this variant has failed.
|
|
1582
|
-
# `PASS` indicates this variant has passed all filters.
|
|
1583
|
-
# Corresponds to the JSON property `filter`
|
|
1584
|
-
# @return [Array<String>]
|
|
1585
|
-
attr_accessor :filter
|
|
1586
|
-
|
|
1587
1361
|
# The variant calls for this particular variant. Each one represents the
|
|
1588
1362
|
# determination of genotype with respect to this variant.
|
|
1589
1363
|
# Corresponds to the JSON property `calls`
|
|
@@ -1617,31 +1391,25 @@ module Google
|
|
|
1617
1391
|
# @return [String]
|
|
1618
1392
|
attr_accessor :variant_set_id
|
|
1619
1393
|
|
|
1620
|
-
# The reference on which this variant occurs.
|
|
1621
|
-
# (such as `chr20` or `X`)
|
|
1622
|
-
# Corresponds to the JSON property `referenceName`
|
|
1623
|
-
# @return [String]
|
|
1624
|
-
attr_accessor :reference_name
|
|
1625
|
-
|
|
1626
1394
|
def initialize(**args)
|
|
1627
1395
|
update!(**args)
|
|
1628
1396
|
end
|
|
1629
1397
|
|
|
1630
1398
|
# Update properties of this object
|
|
1631
1399
|
def update!(**args)
|
|
1400
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
1632
1401
|
@info = args[:info] if args.key?(:info)
|
|
1633
1402
|
@reference_bases = args[:reference_bases] if args.key?(:reference_bases)
|
|
1634
|
-
@names = args[:names] if args.key?(:names)
|
|
1635
1403
|
@alternate_bases = args[:alternate_bases] if args.key?(:alternate_bases)
|
|
1636
|
-
@
|
|
1404
|
+
@names = args[:names] if args.key?(:names)
|
|
1637
1405
|
@filter = args[:filter] if args.key?(:filter)
|
|
1406
|
+
@end = args[:end] if args.key?(:end)
|
|
1638
1407
|
@calls = args[:calls] if args.key?(:calls)
|
|
1639
1408
|
@created = args[:created] if args.key?(:created)
|
|
1640
1409
|
@start = args[:start] if args.key?(:start)
|
|
1641
1410
|
@quality = args[:quality] if args.key?(:quality)
|
|
1642
1411
|
@id = args[:id] if args.key?(:id)
|
|
1643
1412
|
@variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
|
|
1644
|
-
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
1645
1413
|
end
|
|
1646
1414
|
end
|
|
1647
1415
|
|
|
@@ -1649,87 +1417,15 @@ module Google
|
|
|
1649
1417
|
class ListOperationsResponse
|
|
1650
1418
|
include Google::Apis::Core::Hashable
|
|
1651
1419
|
|
|
1652
|
-
# A list of operations that matches the specified filter in the request.
|
|
1653
|
-
# Corresponds to the JSON property `operations`
|
|
1654
|
-
# @return [Array<Google::Apis::GenomicsV1::Operation>]
|
|
1655
|
-
attr_accessor :operations
|
|
1656
|
-
|
|
1657
1420
|
# The standard List next-page token.
|
|
1658
1421
|
# Corresponds to the JSON property `nextPageToken`
|
|
1659
1422
|
# @return [String]
|
|
1660
1423
|
attr_accessor :next_page_token
|
|
1661
1424
|
|
|
1662
|
-
|
|
1663
|
-
|
|
1664
|
-
|
|
1665
|
-
|
|
1666
|
-
# Update properties of this object
|
|
1667
|
-
def update!(**args)
|
|
1668
|
-
@operations = args[:operations] if args.key?(:operations)
|
|
1669
|
-
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
1670
|
-
end
|
|
1671
|
-
end
|
|
1672
|
-
|
|
1673
|
-
# The variant search request.
|
|
1674
|
-
class SearchVariantsRequest
|
|
1675
|
-
include Google::Apis::Core::Hashable
|
|
1676
|
-
|
|
1677
|
-
# At most one variant set ID must be provided. Only variants from this
|
|
1678
|
-
# variant set will be returned. If omitted, a call set id must be included in
|
|
1679
|
-
# the request.
|
|
1680
|
-
# Corresponds to the JSON property `variantSetIds`
|
|
1681
|
-
# @return [Array<String>]
|
|
1682
|
-
attr_accessor :variant_set_ids
|
|
1683
|
-
|
|
1684
|
-
# The end of the window, 0-based exclusive. If unspecified or 0, defaults to
|
|
1685
|
-
# the length of the reference.
|
|
1686
|
-
# Corresponds to the JSON property `end`
|
|
1687
|
-
# @return [String]
|
|
1688
|
-
attr_accessor :end
|
|
1689
|
-
|
|
1690
|
-
# The maximum number of calls to return in a single page. Note that this
|
|
1691
|
-
# limit may be exceeded in the event that a matching variant contains more
|
|
1692
|
-
# calls than the requested maximum. If unspecified, defaults to 5000. The
|
|
1693
|
-
# maximum value is 10000.
|
|
1694
|
-
# Corresponds to the JSON property `maxCalls`
|
|
1695
|
-
# @return [Fixnum]
|
|
1696
|
-
attr_accessor :max_calls
|
|
1697
|
-
|
|
1698
|
-
# The continuation token, which is used to page through large result sets.
|
|
1699
|
-
# To get the next page of results, set this parameter to the value of
|
|
1700
|
-
# `nextPageToken` from the previous response.
|
|
1701
|
-
# Corresponds to the JSON property `pageToken`
|
|
1702
|
-
# @return [String]
|
|
1703
|
-
attr_accessor :page_token
|
|
1704
|
-
|
|
1705
|
-
# The maximum number of variants to return in a single page. If unspecified,
|
|
1706
|
-
# defaults to 5000. The maximum value is 10000.
|
|
1707
|
-
# Corresponds to the JSON property `pageSize`
|
|
1708
|
-
# @return [Fixnum]
|
|
1709
|
-
attr_accessor :page_size
|
|
1710
|
-
|
|
1711
|
-
# Only return variant calls which belong to call sets with these ids.
|
|
1712
|
-
# Leaving this blank returns all variant calls. If a variant has no
|
|
1713
|
-
# calls belonging to any of these call sets, it won't be returned at all.
|
|
1714
|
-
# Corresponds to the JSON property `callSetIds`
|
|
1715
|
-
# @return [Array<String>]
|
|
1716
|
-
attr_accessor :call_set_ids
|
|
1717
|
-
|
|
1718
|
-
# The beginning of the window (0-based, inclusive) for which
|
|
1719
|
-
# overlapping variants should be returned. If unspecified, defaults to 0.
|
|
1720
|
-
# Corresponds to the JSON property `start`
|
|
1721
|
-
# @return [String]
|
|
1722
|
-
attr_accessor :start
|
|
1723
|
-
|
|
1724
|
-
# Only return variants which have exactly this name.
|
|
1725
|
-
# Corresponds to the JSON property `variantName`
|
|
1726
|
-
# @return [String]
|
|
1727
|
-
attr_accessor :variant_name
|
|
1728
|
-
|
|
1729
|
-
# Required. Only return variants in this reference sequence.
|
|
1730
|
-
# Corresponds to the JSON property `referenceName`
|
|
1731
|
-
# @return [String]
|
|
1732
|
-
attr_accessor :reference_name
|
|
1425
|
+
# A list of operations that matches the specified filter in the request.
|
|
1426
|
+
# Corresponds to the JSON property `operations`
|
|
1427
|
+
# @return [Array<Google::Apis::GenomicsV1::Operation>]
|
|
1428
|
+
attr_accessor :operations
|
|
1733
1429
|
|
|
1734
1430
|
def initialize(**args)
|
|
1735
1431
|
update!(**args)
|
|
@@ -1737,15 +1433,8 @@ module Google
|
|
|
1737
1433
|
|
|
1738
1434
|
# Update properties of this object
|
|
1739
1435
|
def update!(**args)
|
|
1740
|
-
@
|
|
1741
|
-
@
|
|
1742
|
-
@max_calls = args[:max_calls] if args.key?(:max_calls)
|
|
1743
|
-
@page_token = args[:page_token] if args.key?(:page_token)
|
|
1744
|
-
@page_size = args[:page_size] if args.key?(:page_size)
|
|
1745
|
-
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
|
1746
|
-
@start = args[:start] if args.key?(:start)
|
|
1747
|
-
@variant_name = args[:variant_name] if args.key?(:variant_name)
|
|
1748
|
-
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
1436
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
1437
|
+
@operations = args[:operations] if args.key?(:operations)
|
|
1749
1438
|
end
|
|
1750
1439
|
end
|
|
1751
1440
|
|
|
@@ -1822,15 +1511,22 @@ module Google
|
|
|
1822
1511
|
end
|
|
1823
1512
|
end
|
|
1824
1513
|
|
|
1825
|
-
# The
|
|
1826
|
-
class
|
|
1514
|
+
# The variant search request.
|
|
1515
|
+
class SearchVariantsRequest
|
|
1827
1516
|
include Google::Apis::Core::Hashable
|
|
1828
1517
|
|
|
1829
|
-
#
|
|
1830
|
-
#
|
|
1831
|
-
#
|
|
1518
|
+
# At most one variant set ID must be provided. Only variants from this
|
|
1519
|
+
# variant set will be returned. If omitted, a call set id must be included in
|
|
1520
|
+
# the request.
|
|
1521
|
+
# Corresponds to the JSON property `variantSetIds`
|
|
1522
|
+
# @return [Array<String>]
|
|
1523
|
+
attr_accessor :variant_set_ids
|
|
1524
|
+
|
|
1525
|
+
# The end of the window, 0-based exclusive. If unspecified or 0, defaults to
|
|
1526
|
+
# the length of the reference.
|
|
1527
|
+
# Corresponds to the JSON property `end`
|
|
1832
1528
|
# @return [String]
|
|
1833
|
-
attr_accessor :
|
|
1529
|
+
attr_accessor :end
|
|
1834
1530
|
|
|
1835
1531
|
# The continuation token, which is used to page through large result sets.
|
|
1836
1532
|
# To get the next page of results, set this parameter to the value of
|
|
@@ -1839,30 +1535,102 @@ module Google
|
|
|
1839
1535
|
# @return [String]
|
|
1840
1536
|
attr_accessor :page_token
|
|
1841
1537
|
|
|
1842
|
-
# The maximum number of
|
|
1843
|
-
#
|
|
1538
|
+
# The maximum number of calls to return in a single page. Note that this
|
|
1539
|
+
# limit may be exceeded in the event that a matching variant contains more
|
|
1540
|
+
# calls than the requested maximum. If unspecified, defaults to 5000. The
|
|
1541
|
+
# maximum value is 10000.
|
|
1542
|
+
# Corresponds to the JSON property `maxCalls`
|
|
1543
|
+
# @return [Fixnum]
|
|
1544
|
+
attr_accessor :max_calls
|
|
1545
|
+
|
|
1546
|
+
# The maximum number of variants to return in a single page. If unspecified,
|
|
1547
|
+
# defaults to 5000. The maximum value is 10000.
|
|
1844
1548
|
# Corresponds to the JSON property `pageSize`
|
|
1845
1549
|
# @return [Fixnum]
|
|
1846
1550
|
attr_accessor :page_size
|
|
1847
1551
|
|
|
1848
|
-
#
|
|
1849
|
-
#
|
|
1850
|
-
#
|
|
1552
|
+
# Only return variant calls which belong to call sets with these ids.
|
|
1553
|
+
# Leaving this blank returns all variant calls. If a variant has no
|
|
1554
|
+
# calls belonging to any of these call sets, it won't be returned at all.
|
|
1555
|
+
# Corresponds to the JSON property `callSetIds`
|
|
1851
1556
|
# @return [Array<String>]
|
|
1852
|
-
attr_accessor :
|
|
1557
|
+
attr_accessor :call_set_ids
|
|
1853
1558
|
|
|
1854
|
-
|
|
1855
|
-
|
|
1856
|
-
|
|
1559
|
+
# Only return variants which have exactly this name.
|
|
1560
|
+
# Corresponds to the JSON property `variantName`
|
|
1561
|
+
# @return [String]
|
|
1562
|
+
attr_accessor :variant_name
|
|
1857
1563
|
|
|
1858
|
-
#
|
|
1859
|
-
|
|
1860
|
-
|
|
1861
|
-
|
|
1862
|
-
|
|
1863
|
-
|
|
1864
|
-
|
|
1865
|
-
|
|
1564
|
+
# The beginning of the window (0-based, inclusive) for which
|
|
1565
|
+
# overlapping variants should be returned. If unspecified, defaults to 0.
|
|
1566
|
+
# Corresponds to the JSON property `start`
|
|
1567
|
+
# @return [String]
|
|
1568
|
+
attr_accessor :start
|
|
1569
|
+
|
|
1570
|
+
# Required. Only return variants in this reference sequence.
|
|
1571
|
+
# Corresponds to the JSON property `referenceName`
|
|
1572
|
+
# @return [String]
|
|
1573
|
+
attr_accessor :reference_name
|
|
1574
|
+
|
|
1575
|
+
def initialize(**args)
|
|
1576
|
+
update!(**args)
|
|
1577
|
+
end
|
|
1578
|
+
|
|
1579
|
+
# Update properties of this object
|
|
1580
|
+
def update!(**args)
|
|
1581
|
+
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
|
1582
|
+
@end = args[:end] if args.key?(:end)
|
|
1583
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
|
1584
|
+
@max_calls = args[:max_calls] if args.key?(:max_calls)
|
|
1585
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
|
1586
|
+
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
|
1587
|
+
@variant_name = args[:variant_name] if args.key?(:variant_name)
|
|
1588
|
+
@start = args[:start] if args.key?(:start)
|
|
1589
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
1590
|
+
end
|
|
1591
|
+
end
|
|
1592
|
+
|
|
1593
|
+
# The read group set search request.
|
|
1594
|
+
class SearchReadGroupSetsRequest
|
|
1595
|
+
include Google::Apis::Core::Hashable
|
|
1596
|
+
|
|
1597
|
+
# Restricts this query to read group sets within the given datasets. At least
|
|
1598
|
+
# one ID must be provided.
|
|
1599
|
+
# Corresponds to the JSON property `datasetIds`
|
|
1600
|
+
# @return [Array<String>]
|
|
1601
|
+
attr_accessor :dataset_ids
|
|
1602
|
+
|
|
1603
|
+
# Only return read group sets for which a substring of the name matches this
|
|
1604
|
+
# string.
|
|
1605
|
+
# Corresponds to the JSON property `name`
|
|
1606
|
+
# @return [String]
|
|
1607
|
+
attr_accessor :name
|
|
1608
|
+
|
|
1609
|
+
# The continuation token, which is used to page through large result sets.
|
|
1610
|
+
# To get the next page of results, set this parameter to the value of
|
|
1611
|
+
# `nextPageToken` from the previous response.
|
|
1612
|
+
# Corresponds to the JSON property `pageToken`
|
|
1613
|
+
# @return [String]
|
|
1614
|
+
attr_accessor :page_token
|
|
1615
|
+
|
|
1616
|
+
# The maximum number of results to return in a single page. If unspecified,
|
|
1617
|
+
# defaults to 256. The maximum value is 1024.
|
|
1618
|
+
# Corresponds to the JSON property `pageSize`
|
|
1619
|
+
# @return [Fixnum]
|
|
1620
|
+
attr_accessor :page_size
|
|
1621
|
+
|
|
1622
|
+
def initialize(**args)
|
|
1623
|
+
update!(**args)
|
|
1624
|
+
end
|
|
1625
|
+
|
|
1626
|
+
# Update properties of this object
|
|
1627
|
+
def update!(**args)
|
|
1628
|
+
@dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
|
|
1629
|
+
@name = args[:name] if args.key?(:name)
|
|
1630
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
|
1631
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
|
1632
|
+
end
|
|
1633
|
+
end
|
|
1866
1634
|
|
|
1867
1635
|
#
|
|
1868
1636
|
class SearchAnnotationsResponse
|
|
@@ -1895,6 +1663,13 @@ module Google
|
|
|
1895
1663
|
class SearchReadsResponse
|
|
1896
1664
|
include Google::Apis::Core::Hashable
|
|
1897
1665
|
|
|
1666
|
+
# The continuation token, which is used to page through large result sets.
|
|
1667
|
+
# Provide this value in a subsequent request to return the next page of
|
|
1668
|
+
# results. This field will be empty if there aren't any additional results.
|
|
1669
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
1670
|
+
# @return [String]
|
|
1671
|
+
attr_accessor :next_page_token
|
|
1672
|
+
|
|
1898
1673
|
# The list of matching alignments sorted by mapped genomic coordinate,
|
|
1899
1674
|
# if any, ascending in position within the same reference. Unmapped reads,
|
|
1900
1675
|
# which have no position, are returned contiguously and are sorted in
|
|
@@ -1903,21 +1678,14 @@ module Google
|
|
|
1903
1678
|
# @return [Array<Google::Apis::GenomicsV1::Read>]
|
|
1904
1679
|
attr_accessor :alignments
|
|
1905
1680
|
|
|
1906
|
-
# The continuation token, which is used to page through large result sets.
|
|
1907
|
-
# Provide this value in a subsequent request to return the next page of
|
|
1908
|
-
# results. This field will be empty if there aren't any additional results.
|
|
1909
|
-
# Corresponds to the JSON property `nextPageToken`
|
|
1910
|
-
# @return [String]
|
|
1911
|
-
attr_accessor :next_page_token
|
|
1912
|
-
|
|
1913
1681
|
def initialize(**args)
|
|
1914
1682
|
update!(**args)
|
|
1915
1683
|
end
|
|
1916
1684
|
|
|
1917
1685
|
# Update properties of this object
|
|
1918
1686
|
def update!(**args)
|
|
1919
|
-
@alignments = args[:alignments] if args.key?(:alignments)
|
|
1920
1687
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
1688
|
+
@alignments = args[:alignments] if args.key?(:alignments)
|
|
1921
1689
|
end
|
|
1922
1690
|
end
|
|
1923
1691
|
|
|
@@ -1925,6 +1693,12 @@ module Google
|
|
|
1925
1693
|
class ClinicalCondition
|
|
1926
1694
|
include Google::Apis::Core::Hashable
|
|
1927
1695
|
|
|
1696
|
+
# The MedGen concept id associated with this gene.
|
|
1697
|
+
# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
|
|
1698
|
+
# Corresponds to the JSON property `conceptId`
|
|
1699
|
+
# @return [String]
|
|
1700
|
+
attr_accessor :concept_id
|
|
1701
|
+
|
|
1928
1702
|
# A set of names for the condition.
|
|
1929
1703
|
# Corresponds to the JSON property `names`
|
|
1930
1704
|
# @return [Array<String>]
|
|
@@ -1941,22 +1715,16 @@ module Google
|
|
|
1941
1715
|
# @return [Array<Google::Apis::GenomicsV1::ExternalId>]
|
|
1942
1716
|
attr_accessor :external_ids
|
|
1943
1717
|
|
|
1944
|
-
# The MedGen concept id associated with this gene.
|
|
1945
|
-
# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
|
|
1946
|
-
# Corresponds to the JSON property `conceptId`
|
|
1947
|
-
# @return [String]
|
|
1948
|
-
attr_accessor :concept_id
|
|
1949
|
-
|
|
1950
1718
|
def initialize(**args)
|
|
1951
1719
|
update!(**args)
|
|
1952
1720
|
end
|
|
1953
1721
|
|
|
1954
1722
|
# Update properties of this object
|
|
1955
1723
|
def update!(**args)
|
|
1724
|
+
@concept_id = args[:concept_id] if args.key?(:concept_id)
|
|
1956
1725
|
@names = args[:names] if args.key?(:names)
|
|
1957
1726
|
@omim_id = args[:omim_id] if args.key?(:omim_id)
|
|
1958
1727
|
@external_ids = args[:external_ids] if args.key?(:external_ids)
|
|
1959
|
-
@concept_id = args[:concept_id] if args.key?(:concept_id)
|
|
1960
1728
|
end
|
|
1961
1729
|
end
|
|
1962
1730
|
|
|
@@ -1964,6 +1732,16 @@ module Google
|
|
|
1964
1732
|
class Program
|
|
1965
1733
|
include Google::Apis::Core::Hashable
|
|
1966
1734
|
|
|
1735
|
+
# The command line used to run this program.
|
|
1736
|
+
# Corresponds to the JSON property `commandLine`
|
|
1737
|
+
# @return [String]
|
|
1738
|
+
attr_accessor :command_line
|
|
1739
|
+
|
|
1740
|
+
# The ID of the program run before this one.
|
|
1741
|
+
# Corresponds to the JSON property `prevProgramId`
|
|
1742
|
+
# @return [String]
|
|
1743
|
+
attr_accessor :prev_program_id
|
|
1744
|
+
|
|
1967
1745
|
# The user specified locally unique ID of the program. Used along with
|
|
1968
1746
|
# `prevProgramId` to define an ordering between programs.
|
|
1969
1747
|
# Corresponds to the JSON property `id`
|
|
@@ -1981,15 +1759,44 @@ module Google
|
|
|
1981
1759
|
# @return [String]
|
|
1982
1760
|
attr_accessor :name
|
|
1983
1761
|
|
|
1984
|
-
|
|
1985
|
-
|
|
1762
|
+
def initialize(**args)
|
|
1763
|
+
update!(**args)
|
|
1764
|
+
end
|
|
1765
|
+
|
|
1766
|
+
# Update properties of this object
|
|
1767
|
+
def update!(**args)
|
|
1768
|
+
@command_line = args[:command_line] if args.key?(:command_line)
|
|
1769
|
+
@prev_program_id = args[:prev_program_id] if args.key?(:prev_program_id)
|
|
1770
|
+
@id = args[:id] if args.key?(:id)
|
|
1771
|
+
@version = args[:version] if args.key?(:version)
|
|
1772
|
+
@name = args[:name] if args.key?(:name)
|
|
1773
|
+
end
|
|
1774
|
+
end
|
|
1775
|
+
|
|
1776
|
+
# Describes a Compute Engine resource that is being managed by a running
|
|
1777
|
+
# pipeline.
|
|
1778
|
+
class ComputeEngine
|
|
1779
|
+
include Google::Apis::Core::Hashable
|
|
1780
|
+
|
|
1781
|
+
# The machine type of the instance.
|
|
1782
|
+
# Corresponds to the JSON property `machineType`
|
|
1986
1783
|
# @return [String]
|
|
1987
|
-
attr_accessor :
|
|
1784
|
+
attr_accessor :machine_type
|
|
1988
1785
|
|
|
1989
|
-
# The
|
|
1990
|
-
# Corresponds to the JSON property `
|
|
1786
|
+
# The names of the disks that were created for this pipeline.
|
|
1787
|
+
# Corresponds to the JSON property `diskNames`
|
|
1788
|
+
# @return [Array<String>]
|
|
1789
|
+
attr_accessor :disk_names
|
|
1790
|
+
|
|
1791
|
+
# The instance on which the operation is running.
|
|
1792
|
+
# Corresponds to the JSON property `instanceName`
|
|
1991
1793
|
# @return [String]
|
|
1992
|
-
attr_accessor :
|
|
1794
|
+
attr_accessor :instance_name
|
|
1795
|
+
|
|
1796
|
+
# The availability zone in which the instance resides.
|
|
1797
|
+
# Corresponds to the JSON property `zone`
|
|
1798
|
+
# @return [String]
|
|
1799
|
+
attr_accessor :zone
|
|
1993
1800
|
|
|
1994
1801
|
def initialize(**args)
|
|
1995
1802
|
update!(**args)
|
|
@@ -1997,11 +1804,10 @@ module Google
|
|
|
1997
1804
|
|
|
1998
1805
|
# Update properties of this object
|
|
1999
1806
|
def update!(**args)
|
|
2000
|
-
@
|
|
2001
|
-
@
|
|
2002
|
-
@
|
|
2003
|
-
@
|
|
2004
|
-
@prev_program_id = args[:prev_program_id] if args.key?(:prev_program_id)
|
|
1807
|
+
@machine_type = args[:machine_type] if args.key?(:machine_type)
|
|
1808
|
+
@disk_names = args[:disk_names] if args.key?(:disk_names)
|
|
1809
|
+
@instance_name = args[:instance_name] if args.key?(:instance_name)
|
|
1810
|
+
@zone = args[:zone] if args.key?(:zone)
|
|
2005
1811
|
end
|
|
2006
1812
|
end
|
|
2007
1813
|
|
|
@@ -2032,66 +1838,28 @@ module Google
|
|
|
2032
1838
|
end
|
|
2033
1839
|
end
|
|
2034
1840
|
|
|
2035
|
-
# Describes a Compute Engine resource that is being managed by a running
|
|
2036
|
-
# pipeline.
|
|
2037
|
-
class ComputeEngine
|
|
2038
|
-
include Google::Apis::Core::Hashable
|
|
2039
|
-
|
|
2040
|
-
# The instance on which the operation is running.
|
|
2041
|
-
# Corresponds to the JSON property `instanceName`
|
|
2042
|
-
# @return [String]
|
|
2043
|
-
attr_accessor :instance_name
|
|
2044
|
-
|
|
2045
|
-
# The availability zone in which the instance resides.
|
|
2046
|
-
# Corresponds to the JSON property `zone`
|
|
2047
|
-
# @return [String]
|
|
2048
|
-
attr_accessor :zone
|
|
2049
|
-
|
|
2050
|
-
# The machine type of the instance.
|
|
2051
|
-
# Corresponds to the JSON property `machineType`
|
|
2052
|
-
# @return [String]
|
|
2053
|
-
attr_accessor :machine_type
|
|
2054
|
-
|
|
2055
|
-
# The names of the disks that were created for this pipeline.
|
|
2056
|
-
# Corresponds to the JSON property `diskNames`
|
|
2057
|
-
# @return [Array<String>]
|
|
2058
|
-
attr_accessor :disk_names
|
|
2059
|
-
|
|
2060
|
-
def initialize(**args)
|
|
2061
|
-
update!(**args)
|
|
2062
|
-
end
|
|
2063
|
-
|
|
2064
|
-
# Update properties of this object
|
|
2065
|
-
def update!(**args)
|
|
2066
|
-
@instance_name = args[:instance_name] if args.key?(:instance_name)
|
|
2067
|
-
@zone = args[:zone] if args.key?(:zone)
|
|
2068
|
-
@machine_type = args[:machine_type] if args.key?(:machine_type)
|
|
2069
|
-
@disk_names = args[:disk_names] if args.key?(:disk_names)
|
|
2070
|
-
end
|
|
2071
|
-
end
|
|
2072
|
-
|
|
2073
1841
|
#
|
|
2074
1842
|
class ExternalId
|
|
2075
1843
|
include Google::Apis::Core::Hashable
|
|
2076
1844
|
|
|
2077
|
-
# The id used by the source of this data.
|
|
2078
|
-
# Corresponds to the JSON property `id`
|
|
2079
|
-
# @return [String]
|
|
2080
|
-
attr_accessor :id
|
|
2081
|
-
|
|
2082
1845
|
# The name of the source of this data.
|
|
2083
1846
|
# Corresponds to the JSON property `sourceName`
|
|
2084
1847
|
# @return [String]
|
|
2085
1848
|
attr_accessor :source_name
|
|
2086
1849
|
|
|
1850
|
+
# The id used by the source of this data.
|
|
1851
|
+
# Corresponds to the JSON property `id`
|
|
1852
|
+
# @return [String]
|
|
1853
|
+
attr_accessor :id
|
|
1854
|
+
|
|
2087
1855
|
def initialize(**args)
|
|
2088
1856
|
update!(**args)
|
|
2089
1857
|
end
|
|
2090
1858
|
|
|
2091
1859
|
# Update properties of this object
|
|
2092
1860
|
def update!(**args)
|
|
2093
|
-
@id = args[:id] if args.key?(:id)
|
|
2094
1861
|
@source_name = args[:source_name] if args.key?(:source_name)
|
|
1862
|
+
@id = args[:id] if args.key?(:id)
|
|
2095
1863
|
end
|
|
2096
1864
|
end
|
|
2097
1865
|
|
|
@@ -2137,18 +1905,6 @@ module Google
|
|
|
2137
1905
|
class VariantSetMetadata
|
|
2138
1906
|
include Google::Apis::Core::Hashable
|
|
2139
1907
|
|
|
2140
|
-
# The type of data. Possible types include: Integer, Float,
|
|
2141
|
-
# Flag, Character, and String.
|
|
2142
|
-
# Corresponds to the JSON property `type`
|
|
2143
|
-
# @return [String]
|
|
2144
|
-
attr_accessor :type
|
|
2145
|
-
|
|
2146
|
-
# Remaining structured metadata key-value pairs. This must be of the form
|
|
2147
|
-
# map<string, string[]> (string key mapping to a list of string values).
|
|
2148
|
-
# Corresponds to the JSON property `info`
|
|
2149
|
-
# @return [Hash<String,Array<Object>>]
|
|
2150
|
-
attr_accessor :info
|
|
2151
|
-
|
|
2152
1908
|
# The number of values that can be included in a field described by this
|
|
2153
1909
|
# metadata.
|
|
2154
1910
|
# Corresponds to the JSON property `number`
|
|
@@ -2177,19 +1933,31 @@ module Google
|
|
|
2177
1933
|
# @return [String]
|
|
2178
1934
|
attr_accessor :description
|
|
2179
1935
|
|
|
1936
|
+
# Remaining structured metadata key-value pairs. This must be of the form
|
|
1937
|
+
# map<string, string[]> (string key mapping to a list of string values).
|
|
1938
|
+
# Corresponds to the JSON property `info`
|
|
1939
|
+
# @return [Hash<String,Array<Object>>]
|
|
1940
|
+
attr_accessor :info
|
|
1941
|
+
|
|
1942
|
+
# The type of data. Possible types include: Integer, Float,
|
|
1943
|
+
# Flag, Character, and String.
|
|
1944
|
+
# Corresponds to the JSON property `type`
|
|
1945
|
+
# @return [String]
|
|
1946
|
+
attr_accessor :type
|
|
1947
|
+
|
|
2180
1948
|
def initialize(**args)
|
|
2181
1949
|
update!(**args)
|
|
2182
1950
|
end
|
|
2183
1951
|
|
|
2184
1952
|
# Update properties of this object
|
|
2185
1953
|
def update!(**args)
|
|
2186
|
-
@type = args[:type] if args.key?(:type)
|
|
2187
|
-
@info = args[:info] if args.key?(:info)
|
|
2188
1954
|
@number = args[:number] if args.key?(:number)
|
|
2189
1955
|
@id = args[:id] if args.key?(:id)
|
|
2190
1956
|
@value = args[:value] if args.key?(:value)
|
|
2191
1957
|
@key = args[:key] if args.key?(:key)
|
|
2192
1958
|
@description = args[:description] if args.key?(:description)
|
|
1959
|
+
@info = args[:info] if args.key?(:info)
|
|
1960
|
+
@type = args[:type] if args.key?(:type)
|
|
2193
1961
|
end
|
|
2194
1962
|
end
|
|
2195
1963
|
|
|
@@ -2202,26 +1970,36 @@ module Google
|
|
|
2202
1970
|
class Reference
|
|
2203
1971
|
include Google::Apis::Core::Hashable
|
|
2204
1972
|
|
|
1973
|
+
# The server-generated reference ID, unique across all references.
|
|
1974
|
+
# Corresponds to the JSON property `id`
|
|
1975
|
+
# @return [String]
|
|
1976
|
+
attr_accessor :id
|
|
1977
|
+
|
|
1978
|
+
# The length of this reference's sequence.
|
|
1979
|
+
# Corresponds to the JSON property `length`
|
|
1980
|
+
# @return [String]
|
|
1981
|
+
attr_accessor :length
|
|
1982
|
+
|
|
2205
1983
|
# All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
|
2206
1984
|
# with a version number, for example `GCF_000001405.26`.
|
|
2207
1985
|
# Corresponds to the JSON property `sourceAccessions`
|
|
2208
1986
|
# @return [Array<String>]
|
|
2209
1987
|
attr_accessor :source_accessions
|
|
2210
1988
|
|
|
2211
|
-
# ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
|
|
2212
|
-
# Corresponds to the JSON property `ncbiTaxonId`
|
|
2213
|
-
# @return [Fixnum]
|
|
2214
|
-
attr_accessor :ncbi_taxon_id
|
|
2215
|
-
|
|
2216
1989
|
# The URI from which the sequence was obtained. Typically specifies a FASTA
|
|
2217
1990
|
# format file.
|
|
2218
1991
|
# Corresponds to the JSON property `sourceUri`
|
|
2219
1992
|
# @return [String]
|
|
2220
1993
|
attr_accessor :source_uri
|
|
2221
1994
|
|
|
2222
|
-
#
|
|
2223
|
-
# Corresponds to the JSON property `
|
|
2224
|
-
# @return [
|
|
1995
|
+
# ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
|
|
1996
|
+
# Corresponds to the JSON property `ncbiTaxonId`
|
|
1997
|
+
# @return [Fixnum]
|
|
1998
|
+
attr_accessor :ncbi_taxon_id
|
|
1999
|
+
|
|
2000
|
+
# The name of this reference, for example `22`.
|
|
2001
|
+
# Corresponds to the JSON property `name`
|
|
2002
|
+
# @return [String]
|
|
2225
2003
|
attr_accessor :name
|
|
2226
2004
|
|
|
2227
2005
|
# MD5 of the upper-case sequence excluding all whitespace characters (this
|
|
@@ -2231,29 +2009,19 @@ module Google
|
|
|
2231
2009
|
# @return [String]
|
|
2232
2010
|
attr_accessor :md5checksum
|
|
2233
2011
|
|
|
2234
|
-
# The server-generated reference ID, unique across all references.
|
|
2235
|
-
# Corresponds to the JSON property `id`
|
|
2236
|
-
# @return [String]
|
|
2237
|
-
attr_accessor :id
|
|
2238
|
-
|
|
2239
|
-
# The length of this reference's sequence.
|
|
2240
|
-
# Corresponds to the JSON property `length`
|
|
2241
|
-
# @return [String]
|
|
2242
|
-
attr_accessor :length
|
|
2243
|
-
|
|
2244
2012
|
def initialize(**args)
|
|
2245
2013
|
update!(**args)
|
|
2246
2014
|
end
|
|
2247
2015
|
|
|
2248
2016
|
# Update properties of this object
|
|
2249
2017
|
def update!(**args)
|
|
2018
|
+
@id = args[:id] if args.key?(:id)
|
|
2019
|
+
@length = args[:length] if args.key?(:length)
|
|
2250
2020
|
@source_accessions = args[:source_accessions] if args.key?(:source_accessions)
|
|
2251
|
-
@ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
|
|
2252
2021
|
@source_uri = args[:source_uri] if args.key?(:source_uri)
|
|
2022
|
+
@ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
|
|
2253
2023
|
@name = args[:name] if args.key?(:name)
|
|
2254
2024
|
@md5checksum = args[:md5checksum] if args.key?(:md5checksum)
|
|
2255
|
-
@id = args[:id] if args.key?(:id)
|
|
2256
|
-
@length = args[:length] if args.key?(:length)
|
|
2257
2025
|
end
|
|
2258
2026
|
end
|
|
2259
2027
|
|
|
@@ -2261,6 +2029,12 @@ module Google
|
|
|
2261
2029
|
class SearchReferenceSetsRequest
|
|
2262
2030
|
include Google::Apis::Core::Hashable
|
|
2263
2031
|
|
|
2032
|
+
# If present, return reference sets for which the
|
|
2033
|
+
# md5checksum matches exactly.
|
|
2034
|
+
# Corresponds to the JSON property `md5checksums`
|
|
2035
|
+
# @return [Array<String>]
|
|
2036
|
+
attr_accessor :md5checksums
|
|
2037
|
+
|
|
2264
2038
|
# If present, return reference sets for which a prefix of any of
|
|
2265
2039
|
# sourceAccessions
|
|
2266
2040
|
# match any of these strings. Accession numbers typically have a main number
|
|
@@ -2288,23 +2062,17 @@ module Google
|
|
|
2288
2062
|
# @return [String]
|
|
2289
2063
|
attr_accessor :assembly_id
|
|
2290
2064
|
|
|
2291
|
-
# If present, return reference sets for which the
|
|
2292
|
-
# md5checksum matches exactly.
|
|
2293
|
-
# Corresponds to the JSON property `md5checksums`
|
|
2294
|
-
# @return [Array<String>]
|
|
2295
|
-
attr_accessor :md5checksums
|
|
2296
|
-
|
|
2297
2065
|
def initialize(**args)
|
|
2298
2066
|
update!(**args)
|
|
2299
2067
|
end
|
|
2300
2068
|
|
|
2301
2069
|
# Update properties of this object
|
|
2302
2070
|
def update!(**args)
|
|
2071
|
+
@md5checksums = args[:md5checksums] if args.key?(:md5checksums)
|
|
2303
2072
|
@accessions = args[:accessions] if args.key?(:accessions)
|
|
2304
2073
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
2305
2074
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
2306
2075
|
@assembly_id = args[:assembly_id] if args.key?(:assembly_id)
|
|
2307
|
-
@md5checksums = args[:md5checksums] if args.key?(:md5checksums)
|
|
2308
2076
|
end
|
|
2309
2077
|
end
|
|
2310
2078
|
|
|
@@ -2384,38 +2152,6 @@ module Google
|
|
|
2384
2152
|
end
|
|
2385
2153
|
end
|
|
2386
2154
|
|
|
2387
|
-
#
|
|
2388
|
-
class BatchCreateAnnotationsRequest
|
|
2389
|
-
include Google::Apis::Core::Hashable
|
|
2390
|
-
|
|
2391
|
-
# The annotations to be created. At most 4096 can be specified in a single
|
|
2392
|
-
# request.
|
|
2393
|
-
# Corresponds to the JSON property `annotations`
|
|
2394
|
-
# @return [Array<Google::Apis::GenomicsV1::Annotation>]
|
|
2395
|
-
attr_accessor :annotations
|
|
2396
|
-
|
|
2397
|
-
# A unique request ID which enables the server to detect duplicated requests.
|
|
2398
|
-
# If provided, duplicated requests will result in the same response; if not
|
|
2399
|
-
# provided, duplicated requests may result in duplicated data. For a given
|
|
2400
|
-
# annotation set, callers should not reuse `request_id`s when writing
|
|
2401
|
-
# different batches of annotations - behavior in this case is undefined.
|
|
2402
|
-
# A common approach is to use a UUID. For batch jobs where worker crashes are
|
|
2403
|
-
# a possibility, consider using some unique variant of a worker or run ID.
|
|
2404
|
-
# Corresponds to the JSON property `requestId`
|
|
2405
|
-
# @return [String]
|
|
2406
|
-
attr_accessor :request_id
|
|
2407
|
-
|
|
2408
|
-
def initialize(**args)
|
|
2409
|
-
update!(**args)
|
|
2410
|
-
end
|
|
2411
|
-
|
|
2412
|
-
# Update properties of this object
|
|
2413
|
-
def update!(**args)
|
|
2414
|
-
@annotations = args[:annotations] if args.key?(:annotations)
|
|
2415
|
-
@request_id = args[:request_id] if args.key?(:request_id)
|
|
2416
|
-
end
|
|
2417
|
-
end
|
|
2418
|
-
|
|
2419
2155
|
# A read alignment describes a linear alignment of a string of DNA to a
|
|
2420
2156
|
# reference sequence, in addition to metadata
|
|
2421
2157
|
# about the fragment (the molecule of DNA sequenced) and the read (the bases
|
|
@@ -2491,6 +2227,39 @@ module Google
|
|
|
2491
2227
|
class Read
|
|
2492
2228
|
include Google::Apis::Core::Hashable
|
|
2493
2229
|
|
|
2230
|
+
# A linear alignment can be represented by one CIGAR string. Describes the
|
|
2231
|
+
# mapped position and local alignment of the read to the reference.
|
|
2232
|
+
# Corresponds to the JSON property `alignment`
|
|
2233
|
+
# @return [Google::Apis::GenomicsV1::LinearAlignment]
|
|
2234
|
+
attr_accessor :alignment
|
|
2235
|
+
|
|
2236
|
+
# The server-generated read ID, unique across all reads. This is different
|
|
2237
|
+
# from the `fragmentName`.
|
|
2238
|
+
# Corresponds to the JSON property `id`
|
|
2239
|
+
# @return [String]
|
|
2240
|
+
attr_accessor :id
|
|
2241
|
+
|
|
2242
|
+
# The number of reads in the fragment (extension to SAM flag 0x1).
|
|
2243
|
+
# Corresponds to the JSON property `numberReads`
|
|
2244
|
+
# @return [Fixnum]
|
|
2245
|
+
attr_accessor :number_reads
|
|
2246
|
+
|
|
2247
|
+
# Whether this alignment is secondary. Equivalent to SAM flag 0x100.
|
|
2248
|
+
# A secondary alignment represents an alternative to the primary alignment
|
|
2249
|
+
# for this read. Aligners may return secondary alignments if a read can map
|
|
2250
|
+
# ambiguously to multiple coordinates in the genome. By convention, each read
|
|
2251
|
+
# has one and only one alignment where both `secondaryAlignment`
|
|
2252
|
+
# and `supplementaryAlignment` are false.
|
|
2253
|
+
# Corresponds to the JSON property `secondaryAlignment`
|
|
2254
|
+
# @return [Boolean]
|
|
2255
|
+
attr_accessor :secondary_alignment
|
|
2256
|
+
alias_method :secondary_alignment?, :secondary_alignment
|
|
2257
|
+
|
|
2258
|
+
# The fragment name. Equivalent to QNAME (query template name) in SAM.
|
|
2259
|
+
# Corresponds to the JSON property `fragmentName`
|
|
2260
|
+
# @return [String]
|
|
2261
|
+
attr_accessor :fragment_name
|
|
2262
|
+
|
|
2494
2263
|
# The ID of the read group set this read belongs to. A read belongs to
|
|
2495
2264
|
# exactly one read group set.
|
|
2496
2265
|
# Corresponds to the JSON property `readGroupSetId`
|
|
@@ -2509,6 +2278,14 @@ module Google
|
|
|
2509
2278
|
# @return [Fixnum]
|
|
2510
2279
|
attr_accessor :read_number
|
|
2511
2280
|
|
|
2281
|
+
# The ID of the read group this read belongs to. A read belongs to exactly
|
|
2282
|
+
# one read group. This is a server-generated ID which is distinct from SAM's
|
|
2283
|
+
# RG tag (for that value, see
|
|
2284
|
+
# ReadGroup.name).
|
|
2285
|
+
# Corresponds to the JSON property `readGroupId`
|
|
2286
|
+
# @return [String]
|
|
2287
|
+
attr_accessor :read_group_id
|
|
2288
|
+
|
|
2512
2289
|
# The bases of the read sequence contained in this alignment record,
|
|
2513
2290
|
# **without CIGAR operations applied** (equivalent to SEQ in SAM).
|
|
2514
2291
|
# `alignedSequence` and `alignedQuality` may be
|
|
@@ -2520,14 +2297,6 @@ module Google
|
|
|
2520
2297
|
# @return [String]
|
|
2521
2298
|
attr_accessor :aligned_sequence
|
|
2522
2299
|
|
|
2523
|
-
# The ID of the read group this read belongs to. A read belongs to exactly
|
|
2524
|
-
# one read group. This is a server-generated ID which is distinct from SAM's
|
|
2525
|
-
# RG tag (for that value, see
|
|
2526
|
-
# ReadGroup.name).
|
|
2527
|
-
# Corresponds to the JSON property `readGroupId`
|
|
2528
|
-
# @return [String]
|
|
2529
|
-
attr_accessor :read_group_id
|
|
2530
|
-
|
|
2531
2300
|
# An abstraction for referring to a genomic position, in relation to some
|
|
2532
2301
|
# already known reference. For now, represents a genomic position as a
|
|
2533
2302
|
# reference name, a base number on that reference (0-based), and a
|
|
@@ -2588,50 +2357,22 @@ module Google
|
|
|
2588
2357
|
# @return [Array<Fixnum>]
|
|
2589
2358
|
attr_accessor :aligned_quality
|
|
2590
2359
|
|
|
2591
|
-
# A linear alignment can be represented by one CIGAR string. Describes the
|
|
2592
|
-
# mapped position and local alignment of the read to the reference.
|
|
2593
|
-
# Corresponds to the JSON property `alignment`
|
|
2594
|
-
# @return [Google::Apis::GenomicsV1::LinearAlignment]
|
|
2595
|
-
attr_accessor :alignment
|
|
2596
|
-
|
|
2597
|
-
# The number of reads in the fragment (extension to SAM flag 0x1).
|
|
2598
|
-
# Corresponds to the JSON property `numberReads`
|
|
2599
|
-
# @return [Fixnum]
|
|
2600
|
-
attr_accessor :number_reads
|
|
2601
|
-
|
|
2602
|
-
# The server-generated read ID, unique across all reads. This is different
|
|
2603
|
-
# from the `fragmentName`.
|
|
2604
|
-
# Corresponds to the JSON property `id`
|
|
2605
|
-
# @return [String]
|
|
2606
|
-
attr_accessor :id
|
|
2607
|
-
|
|
2608
|
-
# Whether this alignment is secondary. Equivalent to SAM flag 0x100.
|
|
2609
|
-
# A secondary alignment represents an alternative to the primary alignment
|
|
2610
|
-
# for this read. Aligners may return secondary alignments if a read can map
|
|
2611
|
-
# ambiguously to multiple coordinates in the genome. By convention, each read
|
|
2612
|
-
# has one and only one alignment where both `secondaryAlignment`
|
|
2613
|
-
# and `supplementaryAlignment` are false.
|
|
2614
|
-
# Corresponds to the JSON property `secondaryAlignment`
|
|
2615
|
-
# @return [Boolean]
|
|
2616
|
-
attr_accessor :secondary_alignment
|
|
2617
|
-
alias_method :secondary_alignment?, :secondary_alignment
|
|
2618
|
-
|
|
2619
|
-
# The fragment name. Equivalent to QNAME (query template name) in SAM.
|
|
2620
|
-
# Corresponds to the JSON property `fragmentName`
|
|
2621
|
-
# @return [String]
|
|
2622
|
-
attr_accessor :fragment_name
|
|
2623
|
-
|
|
2624
2360
|
def initialize(**args)
|
|
2625
2361
|
update!(**args)
|
|
2626
2362
|
end
|
|
2627
2363
|
|
|
2628
2364
|
# Update properties of this object
|
|
2629
2365
|
def update!(**args)
|
|
2366
|
+
@alignment = args[:alignment] if args.key?(:alignment)
|
|
2367
|
+
@id = args[:id] if args.key?(:id)
|
|
2368
|
+
@number_reads = args[:number_reads] if args.key?(:number_reads)
|
|
2369
|
+
@secondary_alignment = args[:secondary_alignment] if args.key?(:secondary_alignment)
|
|
2370
|
+
@fragment_name = args[:fragment_name] if args.key?(:fragment_name)
|
|
2630
2371
|
@read_group_set_id = args[:read_group_set_id] if args.key?(:read_group_set_id)
|
|
2631
2372
|
@duplicate_fragment = args[:duplicate_fragment] if args.key?(:duplicate_fragment)
|
|
2632
2373
|
@read_number = args[:read_number] if args.key?(:read_number)
|
|
2633
|
-
@aligned_sequence = args[:aligned_sequence] if args.key?(:aligned_sequence)
|
|
2634
2374
|
@read_group_id = args[:read_group_id] if args.key?(:read_group_id)
|
|
2375
|
+
@aligned_sequence = args[:aligned_sequence] if args.key?(:aligned_sequence)
|
|
2635
2376
|
@next_mate_position = args[:next_mate_position] if args.key?(:next_mate_position)
|
|
2636
2377
|
@info = args[:info] if args.key?(:info)
|
|
2637
2378
|
@proper_placement = args[:proper_placement] if args.key?(:proper_placement)
|
|
@@ -2639,73 +2380,29 @@ module Google
|
|
|
2639
2380
|
@fragment_length = args[:fragment_length] if args.key?(:fragment_length)
|
|
2640
2381
|
@failed_vendor_quality_checks = args[:failed_vendor_quality_checks] if args.key?(:failed_vendor_quality_checks)
|
|
2641
2382
|
@aligned_quality = args[:aligned_quality] if args.key?(:aligned_quality)
|
|
2642
|
-
@alignment = args[:alignment] if args.key?(:alignment)
|
|
2643
|
-
@number_reads = args[:number_reads] if args.key?(:number_reads)
|
|
2644
|
-
@id = args[:id] if args.key?(:id)
|
|
2645
|
-
@secondary_alignment = args[:secondary_alignment] if args.key?(:secondary_alignment)
|
|
2646
|
-
@fragment_name = args[:fragment_name] if args.key?(:fragment_name)
|
|
2647
2383
|
end
|
|
2648
2384
|
end
|
|
2649
2385
|
|
|
2650
|
-
#
|
|
2651
|
-
|
|
2652
|
-
# of the human genome. A reference set defines a common coordinate space for
|
|
2653
|
-
# comparing reference-aligned experimental data. A reference set contains 1 or
|
|
2654
|
-
# more references.
|
|
2655
|
-
# For more genomics resource definitions, see [Fundamentals of Google
|
|
2656
|
-
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
2657
|
-
class ReferenceSet
|
|
2386
|
+
#
|
|
2387
|
+
class BatchCreateAnnotationsRequest
|
|
2658
2388
|
include Google::Apis::Core::Hashable
|
|
2659
2389
|
|
|
2660
|
-
#
|
|
2661
|
-
#
|
|
2662
|
-
#
|
|
2663
|
-
#
|
|
2664
|
-
|
|
2665
|
-
|
|
2666
|
-
#
|
|
2667
|
-
#
|
|
2668
|
-
# `reference.md5checksum` (for all reference in this set) in
|
|
2669
|
-
# ascending lexicographic order, concatenating, and taking the MD5 of that
|
|
2670
|
-
# value. The resulting value is represented in lower case hexadecimal format.
|
|
2671
|
-
# Corresponds to the JSON property `md5checksum`
|
|
2672
|
-
# @return [String]
|
|
2673
|
-
attr_accessor :md5checksum
|
|
2674
|
-
|
|
2675
|
-
# Public id of this reference set, such as `GRCh37`.
|
|
2676
|
-
# Corresponds to the JSON property `assemblyId`
|
|
2677
|
-
# @return [String]
|
|
2678
|
-
attr_accessor :assembly_id
|
|
2679
|
-
|
|
2680
|
-
# The server-generated reference set ID, unique across all reference sets.
|
|
2681
|
-
# Corresponds to the JSON property `id`
|
|
2682
|
-
# @return [String]
|
|
2683
|
-
attr_accessor :id
|
|
2684
|
-
|
|
2685
|
-
# Free text description of this reference set.
|
|
2686
|
-
# Corresponds to the JSON property `description`
|
|
2687
|
-
# @return [String]
|
|
2688
|
-
attr_accessor :description
|
|
2689
|
-
|
|
2690
|
-
# All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
|
2691
|
-
# with a version number, for example `NC_000001.11`.
|
|
2692
|
-
# Corresponds to the JSON property `sourceAccessions`
|
|
2693
|
-
# @return [Array<String>]
|
|
2694
|
-
attr_accessor :source_accessions
|
|
2695
|
-
|
|
2696
|
-
# The URI from which the references were obtained.
|
|
2697
|
-
# Corresponds to the JSON property `sourceUri`
|
|
2390
|
+
# A unique request ID which enables the server to detect duplicated requests.
|
|
2391
|
+
# If provided, duplicated requests will result in the same response; if not
|
|
2392
|
+
# provided, duplicated requests may result in duplicated data. For a given
|
|
2393
|
+
# annotation set, callers should not reuse `request_id`s when writing
|
|
2394
|
+
# different batches of annotations - behavior in this case is undefined.
|
|
2395
|
+
# A common approach is to use a UUID. For batch jobs where worker crashes are
|
|
2396
|
+
# a possibility, consider using some unique variant of a worker or run ID.
|
|
2397
|
+
# Corresponds to the JSON property `requestId`
|
|
2698
2398
|
# @return [String]
|
|
2699
|
-
attr_accessor :
|
|
2399
|
+
attr_accessor :request_id
|
|
2700
2400
|
|
|
2701
|
-
#
|
|
2702
|
-
#
|
|
2703
|
-
#
|
|
2704
|
-
#
|
|
2705
|
-
|
|
2706
|
-
# Corresponds to the JSON property `ncbiTaxonId`
|
|
2707
|
-
# @return [Fixnum]
|
|
2708
|
-
attr_accessor :ncbi_taxon_id
|
|
2401
|
+
# The annotations to be created. At most 4096 can be specified in a single
|
|
2402
|
+
# request.
|
|
2403
|
+
# Corresponds to the JSON property `annotations`
|
|
2404
|
+
# @return [Array<Google::Apis::GenomicsV1::Annotation>]
|
|
2405
|
+
attr_accessor :annotations
|
|
2709
2406
|
|
|
2710
2407
|
def initialize(**args)
|
|
2711
2408
|
update!(**args)
|
|
@@ -2713,14 +2410,8 @@ module Google
|
|
|
2713
2410
|
|
|
2714
2411
|
# Update properties of this object
|
|
2715
2412
|
def update!(**args)
|
|
2716
|
-
@
|
|
2717
|
-
@
|
|
2718
|
-
@assembly_id = args[:assembly_id] if args.key?(:assembly_id)
|
|
2719
|
-
@id = args[:id] if args.key?(:id)
|
|
2720
|
-
@description = args[:description] if args.key?(:description)
|
|
2721
|
-
@source_accessions = args[:source_accessions] if args.key?(:source_accessions)
|
|
2722
|
-
@source_uri = args[:source_uri] if args.key?(:source_uri)
|
|
2723
|
-
@ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
|
|
2413
|
+
@request_id = args[:request_id] if args.key?(:request_id)
|
|
2414
|
+
@annotations = args[:annotations] if args.key?(:annotations)
|
|
2724
2415
|
end
|
|
2725
2416
|
end
|
|
2726
2417
|
|
|
@@ -2758,49 +2449,65 @@ module Google
|
|
|
2758
2449
|
end
|
|
2759
2450
|
end
|
|
2760
2451
|
|
|
2761
|
-
#
|
|
2762
|
-
#
|
|
2763
|
-
#
|
|
2764
|
-
|
|
2765
|
-
|
|
2766
|
-
|
|
2767
|
-
|
|
2768
|
-
|
|
2769
|
-
|
|
2770
|
-
attr_accessor :id
|
|
2771
|
-
|
|
2772
|
-
# The dataset to which this annotation set belongs.
|
|
2773
|
-
# Corresponds to the JSON property `datasetId`
|
|
2774
|
-
# @return [String]
|
|
2775
|
-
attr_accessor :dataset_id
|
|
2452
|
+
# A reference set is a set of references which typically comprise a reference
|
|
2453
|
+
# assembly for a species, such as `GRCh38` which is representative
|
|
2454
|
+
# of the human genome. A reference set defines a common coordinate space for
|
|
2455
|
+
# comparing reference-aligned experimental data. A reference set contains 1 or
|
|
2456
|
+
# more references.
|
|
2457
|
+
# For more genomics resource definitions, see [Fundamentals of Google
|
|
2458
|
+
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
2459
|
+
class ReferenceSet
|
|
2460
|
+
include Google::Apis::Core::Hashable
|
|
2776
2461
|
|
|
2777
|
-
#
|
|
2778
|
-
#
|
|
2462
|
+
# ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
|
|
2463
|
+
# indicating the species which this reference set is intended to model. Note
|
|
2464
|
+
# that contained references may specify a different `ncbiTaxonId`, as
|
|
2465
|
+
# assemblies may contain reference sequences which do not belong to the
|
|
2466
|
+
# modeled species, for example EBV in a human reference genome.
|
|
2467
|
+
# Corresponds to the JSON property `ncbiTaxonId`
|
|
2468
|
+
# @return [Fixnum]
|
|
2469
|
+
attr_accessor :ncbi_taxon_id
|
|
2470
|
+
|
|
2471
|
+
# The URI from which the references were obtained.
|
|
2779
2472
|
# Corresponds to the JSON property `sourceUri`
|
|
2780
2473
|
# @return [String]
|
|
2781
2474
|
attr_accessor :source_uri
|
|
2782
2475
|
|
|
2783
|
-
# The
|
|
2784
|
-
#
|
|
2476
|
+
# The IDs of the reference objects that are part of this set.
|
|
2477
|
+
# `Reference.md5checksum` must be unique within this set.
|
|
2478
|
+
# Corresponds to the JSON property `referenceIds`
|
|
2479
|
+
# @return [Array<String>]
|
|
2480
|
+
attr_accessor :reference_ids
|
|
2481
|
+
|
|
2482
|
+
# Order-independent MD5 checksum which identifies this reference set. The
|
|
2483
|
+
# checksum is computed by sorting all lower case hexidecimal string
|
|
2484
|
+
# `reference.md5checksum` (for all reference in this set) in
|
|
2485
|
+
# ascending lexicographic order, concatenating, and taking the MD5 of that
|
|
2486
|
+
# value. The resulting value is represented in lower case hexadecimal format.
|
|
2487
|
+
# Corresponds to the JSON property `md5checksum`
|
|
2785
2488
|
# @return [String]
|
|
2786
|
-
attr_accessor :
|
|
2489
|
+
attr_accessor :md5checksum
|
|
2787
2490
|
|
|
2788
|
-
#
|
|
2789
|
-
#
|
|
2790
|
-
# Corresponds to the JSON property `referenceSetId`
|
|
2491
|
+
# Public id of this reference set, such as `GRCh37`.
|
|
2492
|
+
# Corresponds to the JSON property `assemblyId`
|
|
2791
2493
|
# @return [String]
|
|
2792
|
-
attr_accessor :
|
|
2494
|
+
attr_accessor :assembly_id
|
|
2793
2495
|
|
|
2794
|
-
#
|
|
2795
|
-
#
|
|
2796
|
-
#
|
|
2797
|
-
|
|
2798
|
-
attr_accessor :info
|
|
2496
|
+
# The server-generated reference set ID, unique across all reference sets.
|
|
2497
|
+
# Corresponds to the JSON property `id`
|
|
2498
|
+
# @return [String]
|
|
2499
|
+
attr_accessor :id
|
|
2799
2500
|
|
|
2800
|
-
#
|
|
2801
|
-
#
|
|
2501
|
+
# All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
|
2502
|
+
# with a version number, for example `NC_000001.11`.
|
|
2503
|
+
# Corresponds to the JSON property `sourceAccessions`
|
|
2504
|
+
# @return [Array<String>]
|
|
2505
|
+
attr_accessor :source_accessions
|
|
2506
|
+
|
|
2507
|
+
# Free text description of this reference set.
|
|
2508
|
+
# Corresponds to the JSON property `description`
|
|
2802
2509
|
# @return [String]
|
|
2803
|
-
attr_accessor :
|
|
2510
|
+
attr_accessor :description
|
|
2804
2511
|
|
|
2805
2512
|
def initialize(**args)
|
|
2806
2513
|
update!(**args)
|
|
@@ -2808,13 +2515,14 @@ module Google
|
|
|
2808
2515
|
|
|
2809
2516
|
# Update properties of this object
|
|
2810
2517
|
def update!(**args)
|
|
2811
|
-
@
|
|
2812
|
-
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
2518
|
+
@ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
|
|
2813
2519
|
@source_uri = args[:source_uri] if args.key?(:source_uri)
|
|
2814
|
-
@
|
|
2815
|
-
@
|
|
2816
|
-
@
|
|
2817
|
-
@
|
|
2520
|
+
@reference_ids = args[:reference_ids] if args.key?(:reference_ids)
|
|
2521
|
+
@md5checksum = args[:md5checksum] if args.key?(:md5checksum)
|
|
2522
|
+
@assembly_id = args[:assembly_id] if args.key?(:assembly_id)
|
|
2523
|
+
@id = args[:id] if args.key?(:id)
|
|
2524
|
+
@source_accessions = args[:source_accessions] if args.key?(:source_accessions)
|
|
2525
|
+
@description = args[:description] if args.key?(:description)
|
|
2818
2526
|
end
|
|
2819
2527
|
end
|
|
2820
2528
|
|
|
@@ -2823,6 +2531,22 @@ module Google
|
|
|
2823
2531
|
class Transcript
|
|
2824
2532
|
include Google::Apis::Core::Hashable
|
|
2825
2533
|
|
|
2534
|
+
# The range of the coding sequence for this transcript, if any. To determine
|
|
2535
|
+
# the exact ranges of coding sequence, intersect this range with those of the
|
|
2536
|
+
# exons, if any. If there are any
|
|
2537
|
+
# exons, the
|
|
2538
|
+
# codingSequence must start
|
|
2539
|
+
# and end within them.
|
|
2540
|
+
# Note that in some cases, the reference genome will not exactly match the
|
|
2541
|
+
# observed mRNA transcript e.g. due to variance in the source genome from
|
|
2542
|
+
# reference. In these cases,
|
|
2543
|
+
# exon.frame will not necessarily
|
|
2544
|
+
# match the expected reference reading frame and coding exon reference bases
|
|
2545
|
+
# cannot necessarily be concatenated to produce the original transcript mRNA.
|
|
2546
|
+
# Corresponds to the JSON property `codingSequence`
|
|
2547
|
+
# @return [Google::Apis::GenomicsV1::CodingSequence]
|
|
2548
|
+
attr_accessor :coding_sequence
|
|
2549
|
+
|
|
2826
2550
|
# The annotation ID of the gene from which this transcript is transcribed.
|
|
2827
2551
|
# Corresponds to the JSON property `geneId`
|
|
2828
2552
|
# @return [String]
|
|
@@ -2843,49 +2567,81 @@ module Google
|
|
|
2843
2567
|
# @return [Array<Google::Apis::GenomicsV1::Exon>]
|
|
2844
2568
|
attr_accessor :exons
|
|
2845
2569
|
|
|
2846
|
-
# The range of the coding sequence for this transcript, if any. To determine
|
|
2847
|
-
# the exact ranges of coding sequence, intersect this range with those of the
|
|
2848
|
-
# exons, if any. If there are any
|
|
2849
|
-
# exons, the
|
|
2850
|
-
# codingSequence must start
|
|
2851
|
-
# and end within them.
|
|
2852
|
-
# Note that in some cases, the reference genome will not exactly match the
|
|
2853
|
-
# observed mRNA transcript e.g. due to variance in the source genome from
|
|
2854
|
-
# reference. In these cases,
|
|
2855
|
-
# exon.frame will not necessarily
|
|
2856
|
-
# match the expected reference reading frame and coding exon reference bases
|
|
2857
|
-
# cannot necessarily be concatenated to produce the original transcript mRNA.
|
|
2858
|
-
# Corresponds to the JSON property `codingSequence`
|
|
2859
|
-
# @return [Google::Apis::GenomicsV1::CodingSequence]
|
|
2860
|
-
attr_accessor :coding_sequence
|
|
2861
|
-
|
|
2862
2570
|
def initialize(**args)
|
|
2863
2571
|
update!(**args)
|
|
2864
2572
|
end
|
|
2865
2573
|
|
|
2866
2574
|
# Update properties of this object
|
|
2867
2575
|
def update!(**args)
|
|
2576
|
+
@coding_sequence = args[:coding_sequence] if args.key?(:coding_sequence)
|
|
2868
2577
|
@gene_id = args[:gene_id] if args.key?(:gene_id)
|
|
2869
2578
|
@exons = args[:exons] if args.key?(:exons)
|
|
2870
|
-
@coding_sequence = args[:coding_sequence] if args.key?(:coding_sequence)
|
|
2871
2579
|
end
|
|
2872
2580
|
end
|
|
2873
2581
|
|
|
2874
|
-
#
|
|
2875
|
-
|
|
2582
|
+
# An annotation set is a logical grouping of annotations that share consistent
|
|
2583
|
+
# type information and provenance. Examples of annotation sets include 'all
|
|
2584
|
+
# genes from refseq', and 'all variant annotations from ClinVar'.
|
|
2585
|
+
class AnnotationSet
|
|
2876
2586
|
include Google::Apis::Core::Hashable
|
|
2877
2587
|
|
|
2878
|
-
# The
|
|
2879
|
-
#
|
|
2588
|
+
# The source URI describing the file from which this annotation set was
|
|
2589
|
+
# generated, if any.
|
|
2590
|
+
# Corresponds to the JSON property `sourceUri`
|
|
2880
2591
|
# @return [String]
|
|
2881
|
-
attr_accessor :
|
|
2592
|
+
attr_accessor :source_uri
|
|
2882
2593
|
|
|
2883
|
-
# The
|
|
2884
|
-
#
|
|
2885
|
-
# @RG PU field in the SAM spec.
|
|
2886
|
-
# Corresponds to the JSON property `platformUnit`
|
|
2594
|
+
# The dataset to which this annotation set belongs.
|
|
2595
|
+
# Corresponds to the JSON property `datasetId`
|
|
2887
2596
|
# @return [String]
|
|
2888
|
-
attr_accessor :
|
|
2597
|
+
attr_accessor :dataset_id
|
|
2598
|
+
|
|
2599
|
+
# The display name for this annotation set.
|
|
2600
|
+
# Corresponds to the JSON property `name`
|
|
2601
|
+
# @return [String]
|
|
2602
|
+
attr_accessor :name
|
|
2603
|
+
|
|
2604
|
+
# The ID of the reference set that defines the coordinate space for this
|
|
2605
|
+
# set's annotations.
|
|
2606
|
+
# Corresponds to the JSON property `referenceSetId`
|
|
2607
|
+
# @return [String]
|
|
2608
|
+
attr_accessor :reference_set_id
|
|
2609
|
+
|
|
2610
|
+
# A map of additional read alignment information. This must be of the form
|
|
2611
|
+
# map<string, string[]> (string key mapping to a list of string values).
|
|
2612
|
+
# Corresponds to the JSON property `info`
|
|
2613
|
+
# @return [Hash<String,Array<Object>>]
|
|
2614
|
+
attr_accessor :info
|
|
2615
|
+
|
|
2616
|
+
# The type of annotations contained within this set.
|
|
2617
|
+
# Corresponds to the JSON property `type`
|
|
2618
|
+
# @return [String]
|
|
2619
|
+
attr_accessor :type
|
|
2620
|
+
|
|
2621
|
+
# The server-generated annotation set ID, unique across all annotation sets.
|
|
2622
|
+
# Corresponds to the JSON property `id`
|
|
2623
|
+
# @return [String]
|
|
2624
|
+
attr_accessor :id
|
|
2625
|
+
|
|
2626
|
+
def initialize(**args)
|
|
2627
|
+
update!(**args)
|
|
2628
|
+
end
|
|
2629
|
+
|
|
2630
|
+
# Update properties of this object
|
|
2631
|
+
def update!(**args)
|
|
2632
|
+
@source_uri = args[:source_uri] if args.key?(:source_uri)
|
|
2633
|
+
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
2634
|
+
@name = args[:name] if args.key?(:name)
|
|
2635
|
+
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
2636
|
+
@info = args[:info] if args.key?(:info)
|
|
2637
|
+
@type = args[:type] if args.key?(:type)
|
|
2638
|
+
@id = args[:id] if args.key?(:id)
|
|
2639
|
+
end
|
|
2640
|
+
end
|
|
2641
|
+
|
|
2642
|
+
#
|
|
2643
|
+
class Experiment
|
|
2644
|
+
include Google::Apis::Core::Hashable
|
|
2889
2645
|
|
|
2890
2646
|
# A client-supplied library identifier; a library is a collection of DNA
|
|
2891
2647
|
# fragments which have been prepared for sequencing from a sample. This
|
|
@@ -2901,16 +2657,28 @@ module Google
|
|
|
2901
2657
|
# @return [String]
|
|
2902
2658
|
attr_accessor :instrument_model
|
|
2903
2659
|
|
|
2660
|
+
# The sequencing center used as part of this experiment.
|
|
2661
|
+
# Corresponds to the JSON property `sequencingCenter`
|
|
2662
|
+
# @return [String]
|
|
2663
|
+
attr_accessor :sequencing_center
|
|
2664
|
+
|
|
2665
|
+
# The platform unit used as part of this experiment, for example
|
|
2666
|
+
# flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
|
|
2667
|
+
# @RG PU field in the SAM spec.
|
|
2668
|
+
# Corresponds to the JSON property `platformUnit`
|
|
2669
|
+
# @return [String]
|
|
2670
|
+
attr_accessor :platform_unit
|
|
2671
|
+
|
|
2904
2672
|
def initialize(**args)
|
|
2905
2673
|
update!(**args)
|
|
2906
2674
|
end
|
|
2907
2675
|
|
|
2908
2676
|
# Update properties of this object
|
|
2909
2677
|
def update!(**args)
|
|
2910
|
-
@sequencing_center = args[:sequencing_center] if args.key?(:sequencing_center)
|
|
2911
|
-
@platform_unit = args[:platform_unit] if args.key?(:platform_unit)
|
|
2912
2678
|
@library_id = args[:library_id] if args.key?(:library_id)
|
|
2913
2679
|
@instrument_model = args[:instrument_model] if args.key?(:instrument_model)
|
|
2680
|
+
@sequencing_center = args[:sequencing_center] if args.key?(:sequencing_center)
|
|
2681
|
+
@platform_unit = args[:platform_unit] if args.key?(:platform_unit)
|
|
2914
2682
|
end
|
|
2915
2683
|
end
|
|
2916
2684
|
|
|
@@ -3058,6 +2826,16 @@ module Google
|
|
|
3058
2826
|
class CallSet
|
|
3059
2827
|
include Google::Apis::Core::Hashable
|
|
3060
2828
|
|
|
2829
|
+
# The date this call set was created in milliseconds from the epoch.
|
|
2830
|
+
# Corresponds to the JSON property `created`
|
|
2831
|
+
# @return [String]
|
|
2832
|
+
attr_accessor :created
|
|
2833
|
+
|
|
2834
|
+
# The sample ID this call set corresponds to.
|
|
2835
|
+
# Corresponds to the JSON property `sampleId`
|
|
2836
|
+
# @return [String]
|
|
2837
|
+
attr_accessor :sample_id
|
|
2838
|
+
|
|
3061
2839
|
# The call set name.
|
|
3062
2840
|
# Corresponds to the JSON property `name`
|
|
3063
2841
|
# @return [String]
|
|
@@ -3084,28 +2862,18 @@ module Google
|
|
|
3084
2862
|
# @return [String]
|
|
3085
2863
|
attr_accessor :id
|
|
3086
2864
|
|
|
3087
|
-
# The date this call set was created in milliseconds from the epoch.
|
|
3088
|
-
# Corresponds to the JSON property `created`
|
|
3089
|
-
# @return [String]
|
|
3090
|
-
attr_accessor :created
|
|
3091
|
-
|
|
3092
|
-
# The sample ID this call set corresponds to.
|
|
3093
|
-
# Corresponds to the JSON property `sampleId`
|
|
3094
|
-
# @return [String]
|
|
3095
|
-
attr_accessor :sample_id
|
|
3096
|
-
|
|
3097
2865
|
def initialize(**args)
|
|
3098
2866
|
update!(**args)
|
|
3099
2867
|
end
|
|
3100
2868
|
|
|
3101
2869
|
# Update properties of this object
|
|
3102
2870
|
def update!(**args)
|
|
2871
|
+
@created = args[:created] if args.key?(:created)
|
|
2872
|
+
@sample_id = args[:sample_id] if args.key?(:sample_id)
|
|
3103
2873
|
@name = args[:name] if args.key?(:name)
|
|
3104
2874
|
@info = args[:info] if args.key?(:info)
|
|
3105
2875
|
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
|
3106
2876
|
@id = args[:id] if args.key?(:id)
|
|
3107
|
-
@created = args[:created] if args.key?(:created)
|
|
3108
|
-
@sample_id = args[:sample_id] if args.key?(:sample_id)
|
|
3109
2877
|
end
|
|
3110
2878
|
end
|
|
3111
2879
|
|
|
@@ -3113,11 +2881,6 @@ module Google
|
|
|
3113
2881
|
class SearchAnnotationSetsResponse
|
|
3114
2882
|
include Google::Apis::Core::Hashable
|
|
3115
2883
|
|
|
3116
|
-
# The matching annotation sets.
|
|
3117
|
-
# Corresponds to the JSON property `annotationSets`
|
|
3118
|
-
# @return [Array<Google::Apis::GenomicsV1::AnnotationSet>]
|
|
3119
|
-
attr_accessor :annotation_sets
|
|
3120
|
-
|
|
3121
2884
|
# The continuation token, which is used to page through large result sets.
|
|
3122
2885
|
# Provide this value in a subsequent request to return the next page of
|
|
3123
2886
|
# results. This field will be empty if there aren't any additional results.
|
|
@@ -3125,14 +2888,19 @@ module Google
|
|
|
3125
2888
|
# @return [String]
|
|
3126
2889
|
attr_accessor :next_page_token
|
|
3127
2890
|
|
|
2891
|
+
# The matching annotation sets.
|
|
2892
|
+
# Corresponds to the JSON property `annotationSets`
|
|
2893
|
+
# @return [Array<Google::Apis::GenomicsV1::AnnotationSet>]
|
|
2894
|
+
attr_accessor :annotation_sets
|
|
2895
|
+
|
|
3128
2896
|
def initialize(**args)
|
|
3129
2897
|
update!(**args)
|
|
3130
2898
|
end
|
|
3131
2899
|
|
|
3132
2900
|
# Update properties of this object
|
|
3133
2901
|
def update!(**args)
|
|
3134
|
-
@annotation_sets = args[:annotation_sets] if args.key?(:annotation_sets)
|
|
3135
2902
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
2903
|
+
@annotation_sets = args[:annotation_sets] if args.key?(:annotation_sets)
|
|
3136
2904
|
end
|
|
3137
2905
|
end
|
|
3138
2906
|
|
|
@@ -3140,6 +2908,19 @@ module Google
|
|
|
3140
2908
|
class ImportVariantsRequest
|
|
3141
2909
|
include Google::Apis::Core::Hashable
|
|
3142
2910
|
|
|
2911
|
+
# Convert reference names to the canonical representation.
|
|
2912
|
+
# hg19 haploytypes (those reference names containing "_hap")
|
|
2913
|
+
# are not modified in any way.
|
|
2914
|
+
# All other reference names are modified according to the following rules:
|
|
2915
|
+
# The reference name is capitalized.
|
|
2916
|
+
# The "chr" prefix is dropped for all autosomes and sex chromsomes.
|
|
2917
|
+
# For example "chr17" becomes "17" and "chrX" becomes "X".
|
|
2918
|
+
# All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
|
|
2919
|
+
# Corresponds to the JSON property `normalizeReferenceNames`
|
|
2920
|
+
# @return [Boolean]
|
|
2921
|
+
attr_accessor :normalize_reference_names
|
|
2922
|
+
alias_method :normalize_reference_names?, :normalize_reference_names
|
|
2923
|
+
|
|
3143
2924
|
# The format of the variant data being imported. If unspecified, defaults to
|
|
3144
2925
|
# to `VCF`.
|
|
3145
2926
|
# Corresponds to the JSON property `format`
|
|
@@ -3166,30 +2947,56 @@ module Google
|
|
|
3166
2947
|
# @return [Array<String>]
|
|
3167
2948
|
attr_accessor :source_uris
|
|
3168
2949
|
|
|
3169
|
-
# Convert reference names to the canonical representation.
|
|
3170
|
-
# hg19 haploytypes (those reference names containing "_hap")
|
|
3171
|
-
# are not modified in any way.
|
|
3172
|
-
# All other reference names are modified according to the following rules:
|
|
3173
|
-
# The reference name is capitalized.
|
|
3174
|
-
# The "chr" prefix is dropped for all autosomes and sex chromsomes.
|
|
3175
|
-
# For example "chr17" becomes "17" and "chrX" becomes "X".
|
|
3176
|
-
# All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
|
|
3177
|
-
# Corresponds to the JSON property `normalizeReferenceNames`
|
|
3178
|
-
# @return [Boolean]
|
|
3179
|
-
attr_accessor :normalize_reference_names
|
|
3180
|
-
alias_method :normalize_reference_names?, :normalize_reference_names
|
|
3181
|
-
|
|
3182
2950
|
def initialize(**args)
|
|
3183
2951
|
update!(**args)
|
|
3184
2952
|
end
|
|
3185
2953
|
|
|
3186
2954
|
# Update properties of this object
|
|
3187
2955
|
def update!(**args)
|
|
2956
|
+
@normalize_reference_names = args[:normalize_reference_names] if args.key?(:normalize_reference_names)
|
|
3188
2957
|
@format = args[:format] if args.key?(:format)
|
|
3189
2958
|
@info_merge_config = args[:info_merge_config] if args.key?(:info_merge_config)
|
|
3190
2959
|
@variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
|
|
3191
2960
|
@source_uris = args[:source_uris] if args.key?(:source_uris)
|
|
3192
|
-
|
|
2961
|
+
end
|
|
2962
|
+
end
|
|
2963
|
+
|
|
2964
|
+
#
|
|
2965
|
+
class ListCoverageBucketsResponse
|
|
2966
|
+
include Google::Apis::Core::Hashable
|
|
2967
|
+
|
|
2968
|
+
# The continuation token, which is used to page through large result sets.
|
|
2969
|
+
# Provide this value in a subsequent request to return the next page of
|
|
2970
|
+
# results. This field will be empty if there aren't any additional results.
|
|
2971
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
2972
|
+
# @return [String]
|
|
2973
|
+
attr_accessor :next_page_token
|
|
2974
|
+
|
|
2975
|
+
# The length of each coverage bucket in base pairs. Note that buckets at the
|
|
2976
|
+
# end of a reference sequence may be shorter. This value is omitted if the
|
|
2977
|
+
# bucket width is infinity (the default behaviour, with no range or
|
|
2978
|
+
# `targetBucketWidth`).
|
|
2979
|
+
# Corresponds to the JSON property `bucketWidth`
|
|
2980
|
+
# @return [String]
|
|
2981
|
+
attr_accessor :bucket_width
|
|
2982
|
+
|
|
2983
|
+
# The coverage buckets. The list of buckets is sparse; a bucket with 0
|
|
2984
|
+
# overlapping reads is not returned. A bucket never crosses more than one
|
|
2985
|
+
# reference sequence. Each bucket has width `bucketWidth`, unless
|
|
2986
|
+
# its end is the end of the reference sequence.
|
|
2987
|
+
# Corresponds to the JSON property `coverageBuckets`
|
|
2988
|
+
# @return [Array<Google::Apis::GenomicsV1::CoverageBucket>]
|
|
2989
|
+
attr_accessor :coverage_buckets
|
|
2990
|
+
|
|
2991
|
+
def initialize(**args)
|
|
2992
|
+
update!(**args)
|
|
2993
|
+
end
|
|
2994
|
+
|
|
2995
|
+
# Update properties of this object
|
|
2996
|
+
def update!(**args)
|
|
2997
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
2998
|
+
@bucket_width = args[:bucket_width] if args.key?(:bucket_width)
|
|
2999
|
+
@coverage_buckets = args[:coverage_buckets] if args.key?(:coverage_buckets)
|
|
3193
3000
|
end
|
|
3194
3001
|
end
|
|
3195
3002
|
|
|
@@ -3256,45 +3063,6 @@ module Google
|
|
|
3256
3063
|
end
|
|
3257
3064
|
end
|
|
3258
3065
|
|
|
3259
|
-
#
|
|
3260
|
-
class ListCoverageBucketsResponse
|
|
3261
|
-
include Google::Apis::Core::Hashable
|
|
3262
|
-
|
|
3263
|
-
# The continuation token, which is used to page through large result sets.
|
|
3264
|
-
# Provide this value in a subsequent request to return the next page of
|
|
3265
|
-
# results. This field will be empty if there aren't any additional results.
|
|
3266
|
-
# Corresponds to the JSON property `nextPageToken`
|
|
3267
|
-
# @return [String]
|
|
3268
|
-
attr_accessor :next_page_token
|
|
3269
|
-
|
|
3270
|
-
# The length of each coverage bucket in base pairs. Note that buckets at the
|
|
3271
|
-
# end of a reference sequence may be shorter. This value is omitted if the
|
|
3272
|
-
# bucket width is infinity (the default behaviour, with no range or
|
|
3273
|
-
# `targetBucketWidth`).
|
|
3274
|
-
# Corresponds to the JSON property `bucketWidth`
|
|
3275
|
-
# @return [String]
|
|
3276
|
-
attr_accessor :bucket_width
|
|
3277
|
-
|
|
3278
|
-
# The coverage buckets. The list of buckets is sparse; a bucket with 0
|
|
3279
|
-
# overlapping reads is not returned. A bucket never crosses more than one
|
|
3280
|
-
# reference sequence. Each bucket has width `bucketWidth`, unless
|
|
3281
|
-
# its end is the end of the reference sequence.
|
|
3282
|
-
# Corresponds to the JSON property `coverageBuckets`
|
|
3283
|
-
# @return [Array<Google::Apis::GenomicsV1::CoverageBucket>]
|
|
3284
|
-
attr_accessor :coverage_buckets
|
|
3285
|
-
|
|
3286
|
-
def initialize(**args)
|
|
3287
|
-
update!(**args)
|
|
3288
|
-
end
|
|
3289
|
-
|
|
3290
|
-
# Update properties of this object
|
|
3291
|
-
def update!(**args)
|
|
3292
|
-
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
3293
|
-
@bucket_width = args[:bucket_width] if args.key?(:bucket_width)
|
|
3294
|
-
@coverage_buckets = args[:coverage_buckets] if args.key?(:coverage_buckets)
|
|
3295
|
-
end
|
|
3296
|
-
end
|
|
3297
|
-
|
|
3298
3066
|
# The variant data export request.
|
|
3299
3067
|
class ExportVariantSetRequest
|
|
3300
3068
|
include Google::Apis::Core::Hashable
|
|
@@ -3348,6 +3116,28 @@ module Google
|
|
|
3348
3116
|
class SearchAnnotationsRequest
|
|
3349
3117
|
include Google::Apis::Core::Hashable
|
|
3350
3118
|
|
|
3119
|
+
# The start position of the range on the reference, 0-based inclusive. If
|
|
3120
|
+
# specified,
|
|
3121
|
+
# referenceId or
|
|
3122
|
+
# referenceName
|
|
3123
|
+
# must be specified. Defaults to 0.
|
|
3124
|
+
# Corresponds to the JSON property `start`
|
|
3125
|
+
# @return [String]
|
|
3126
|
+
attr_accessor :start
|
|
3127
|
+
|
|
3128
|
+
# Required. The annotation sets to search within. The caller must have
|
|
3129
|
+
# `READ` access to these annotation sets.
|
|
3130
|
+
# All queried annotation sets must have the same type.
|
|
3131
|
+
# Corresponds to the JSON property `annotationSetIds`
|
|
3132
|
+
# @return [Array<String>]
|
|
3133
|
+
attr_accessor :annotation_set_ids
|
|
3134
|
+
|
|
3135
|
+
# The name of the reference to query, within the reference set associated
|
|
3136
|
+
# with this query.
|
|
3137
|
+
# Corresponds to the JSON property `referenceName`
|
|
3138
|
+
# @return [String]
|
|
3139
|
+
attr_accessor :reference_name
|
|
3140
|
+
|
|
3351
3141
|
# The ID of the reference to query.
|
|
3352
3142
|
# Corresponds to the JSON property `referenceId`
|
|
3353
3143
|
# @return [String]
|
|
@@ -3374,41 +3164,19 @@ module Google
|
|
|
3374
3164
|
# @return [Fixnum]
|
|
3375
3165
|
attr_accessor :page_size
|
|
3376
3166
|
|
|
3377
|
-
# The start position of the range on the reference, 0-based inclusive. If
|
|
3378
|
-
# specified,
|
|
3379
|
-
# referenceId or
|
|
3380
|
-
# referenceName
|
|
3381
|
-
# must be specified. Defaults to 0.
|
|
3382
|
-
# Corresponds to the JSON property `start`
|
|
3383
|
-
# @return [String]
|
|
3384
|
-
attr_accessor :start
|
|
3385
|
-
|
|
3386
|
-
# Required. The annotation sets to search within. The caller must have
|
|
3387
|
-
# `READ` access to these annotation sets.
|
|
3388
|
-
# All queried annotation sets must have the same type.
|
|
3389
|
-
# Corresponds to the JSON property `annotationSetIds`
|
|
3390
|
-
# @return [Array<String>]
|
|
3391
|
-
attr_accessor :annotation_set_ids
|
|
3392
|
-
|
|
3393
|
-
# The name of the reference to query, within the reference set associated
|
|
3394
|
-
# with this query.
|
|
3395
|
-
# Corresponds to the JSON property `referenceName`
|
|
3396
|
-
# @return [String]
|
|
3397
|
-
attr_accessor :reference_name
|
|
3398
|
-
|
|
3399
3167
|
def initialize(**args)
|
|
3400
3168
|
update!(**args)
|
|
3401
3169
|
end
|
|
3402
3170
|
|
|
3403
3171
|
# Update properties of this object
|
|
3404
3172
|
def update!(**args)
|
|
3173
|
+
@start = args[:start] if args.key?(:start)
|
|
3174
|
+
@annotation_set_ids = args[:annotation_set_ids] if args.key?(:annotation_set_ids)
|
|
3175
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
3405
3176
|
@reference_id = args[:reference_id] if args.key?(:reference_id)
|
|
3406
3177
|
@end = args[:end] if args.key?(:end)
|
|
3407
3178
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
3408
3179
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
3409
|
-
@start = args[:start] if args.key?(:start)
|
|
3410
|
-
@annotation_set_ids = args[:annotation_set_ids] if args.key?(:annotation_set_ids)
|
|
3411
|
-
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
3412
3180
|
end
|
|
3413
3181
|
end
|
|
3414
3182
|
|
|
@@ -3416,6 +3184,12 @@ module Google
|
|
|
3416
3184
|
class OperationEvent
|
|
3417
3185
|
include Google::Apis::Core::Hashable
|
|
3418
3186
|
|
|
3187
|
+
# Optional time of when event finished. An event can have a start time and no
|
|
3188
|
+
# finish time. If an event has a finish time, there must be a start time.
|
|
3189
|
+
# Corresponds to the JSON property `endTime`
|
|
3190
|
+
# @return [String]
|
|
3191
|
+
attr_accessor :end_time
|
|
3192
|
+
|
|
3419
3193
|
# Optional time of when event started.
|
|
3420
3194
|
# Corresponds to the JSON property `startTime`
|
|
3421
3195
|
# @return [String]
|
|
@@ -3426,21 +3200,15 @@ module Google
|
|
|
3426
3200
|
# @return [String]
|
|
3427
3201
|
attr_accessor :description
|
|
3428
3202
|
|
|
3429
|
-
# Optional time of when event finished. An event can have a start time and no
|
|
3430
|
-
# finish time. If an event has a finish time, there must be a start time.
|
|
3431
|
-
# Corresponds to the JSON property `endTime`
|
|
3432
|
-
# @return [String]
|
|
3433
|
-
attr_accessor :end_time
|
|
3434
|
-
|
|
3435
3203
|
def initialize(**args)
|
|
3436
3204
|
update!(**args)
|
|
3437
3205
|
end
|
|
3438
3206
|
|
|
3439
3207
|
# Update properties of this object
|
|
3440
3208
|
def update!(**args)
|
|
3209
|
+
@end_time = args[:end_time] if args.key?(:end_time)
|
|
3441
3210
|
@start_time = args[:start_time] if args.key?(:start_time)
|
|
3442
3211
|
@description = args[:description] if args.key?(:description)
|
|
3443
|
-
@end_time = args[:end_time] if args.key?(:end_time)
|
|
3444
3212
|
end
|
|
3445
3213
|
end
|
|
3446
3214
|
|
|
@@ -3472,6 +3240,238 @@ module Google
|
|
|
3472
3240
|
@end = args[:end] if args.key?(:end)
|
|
3473
3241
|
end
|
|
3474
3242
|
end
|
|
3243
|
+
|
|
3244
|
+
# Request message for `GetIamPolicy` method.
|
|
3245
|
+
class GetIamPolicyRequest
|
|
3246
|
+
include Google::Apis::Core::Hashable
|
|
3247
|
+
|
|
3248
|
+
def initialize(**args)
|
|
3249
|
+
update!(**args)
|
|
3250
|
+
end
|
|
3251
|
+
|
|
3252
|
+
# Update properties of this object
|
|
3253
|
+
def update!(**args)
|
|
3254
|
+
end
|
|
3255
|
+
end
|
|
3256
|
+
|
|
3257
|
+
# Response message for `TestIamPermissions` method.
|
|
3258
|
+
class TestIamPermissionsResponse
|
|
3259
|
+
include Google::Apis::Core::Hashable
|
|
3260
|
+
|
|
3261
|
+
# A subset of `TestPermissionsRequest.permissions` that the caller is
|
|
3262
|
+
# allowed.
|
|
3263
|
+
# Corresponds to the JSON property `permissions`
|
|
3264
|
+
# @return [Array<String>]
|
|
3265
|
+
attr_accessor :permissions
|
|
3266
|
+
|
|
3267
|
+
def initialize(**args)
|
|
3268
|
+
update!(**args)
|
|
3269
|
+
end
|
|
3270
|
+
|
|
3271
|
+
# Update properties of this object
|
|
3272
|
+
def update!(**args)
|
|
3273
|
+
@permissions = args[:permissions] if args.key?(:permissions)
|
|
3274
|
+
end
|
|
3275
|
+
end
|
|
3276
|
+
|
|
3277
|
+
#
|
|
3278
|
+
class SearchReferencesResponse
|
|
3279
|
+
include Google::Apis::Core::Hashable
|
|
3280
|
+
|
|
3281
|
+
# The matching references.
|
|
3282
|
+
# Corresponds to the JSON property `references`
|
|
3283
|
+
# @return [Array<Google::Apis::GenomicsV1::Reference>]
|
|
3284
|
+
attr_accessor :references
|
|
3285
|
+
|
|
3286
|
+
# The continuation token, which is used to page through large result sets.
|
|
3287
|
+
# Provide this value in a subsequent request to return the next page of
|
|
3288
|
+
# results. This field will be empty if there aren't any additional results.
|
|
3289
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
3290
|
+
# @return [String]
|
|
3291
|
+
attr_accessor :next_page_token
|
|
3292
|
+
|
|
3293
|
+
def initialize(**args)
|
|
3294
|
+
update!(**args)
|
|
3295
|
+
end
|
|
3296
|
+
|
|
3297
|
+
# Update properties of this object
|
|
3298
|
+
def update!(**args)
|
|
3299
|
+
@references = args[:references] if args.key?(:references)
|
|
3300
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
3301
|
+
end
|
|
3302
|
+
end
|
|
3303
|
+
|
|
3304
|
+
#
|
|
3305
|
+
class SearchAnnotationSetsRequest
|
|
3306
|
+
include Google::Apis::Core::Hashable
|
|
3307
|
+
|
|
3308
|
+
# The continuation token, which is used to page through large result sets.
|
|
3309
|
+
# To get the next page of results, set this parameter to the value of
|
|
3310
|
+
# `nextPageToken` from the previous response.
|
|
3311
|
+
# Corresponds to the JSON property `pageToken`
|
|
3312
|
+
# @return [String]
|
|
3313
|
+
attr_accessor :page_token
|
|
3314
|
+
|
|
3315
|
+
# The maximum number of results to return in a single page. If unspecified,
|
|
3316
|
+
# defaults to 128. The maximum value is 1024.
|
|
3317
|
+
# Corresponds to the JSON property `pageSize`
|
|
3318
|
+
# @return [Fixnum]
|
|
3319
|
+
attr_accessor :page_size
|
|
3320
|
+
|
|
3321
|
+
# Required. The dataset IDs to search within. Caller must have `READ` access
|
|
3322
|
+
# to these datasets.
|
|
3323
|
+
# Corresponds to the JSON property `datasetIds`
|
|
3324
|
+
# @return [Array<String>]
|
|
3325
|
+
attr_accessor :dataset_ids
|
|
3326
|
+
|
|
3327
|
+
# If specified, only annotation sets that have any of these types are
|
|
3328
|
+
# returned.
|
|
3329
|
+
# Corresponds to the JSON property `types`
|
|
3330
|
+
# @return [Array<String>]
|
|
3331
|
+
attr_accessor :types
|
|
3332
|
+
|
|
3333
|
+
# Only return annotations sets for which a substring of the name matches this
|
|
3334
|
+
# string (case insensitive).
|
|
3335
|
+
# Corresponds to the JSON property `name`
|
|
3336
|
+
# @return [String]
|
|
3337
|
+
attr_accessor :name
|
|
3338
|
+
|
|
3339
|
+
# If specified, only annotation sets associated with the given reference set
|
|
3340
|
+
# are returned.
|
|
3341
|
+
# Corresponds to the JSON property `referenceSetId`
|
|
3342
|
+
# @return [String]
|
|
3343
|
+
attr_accessor :reference_set_id
|
|
3344
|
+
|
|
3345
|
+
def initialize(**args)
|
|
3346
|
+
update!(**args)
|
|
3347
|
+
end
|
|
3348
|
+
|
|
3349
|
+
# Update properties of this object
|
|
3350
|
+
def update!(**args)
|
|
3351
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
|
3352
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
|
3353
|
+
@dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
|
|
3354
|
+
@types = args[:types] if args.key?(:types)
|
|
3355
|
+
@name = args[:name] if args.key?(:name)
|
|
3356
|
+
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
3357
|
+
end
|
|
3358
|
+
end
|
|
3359
|
+
|
|
3360
|
+
# The read group set search response.
|
|
3361
|
+
class SearchReadGroupSetsResponse
|
|
3362
|
+
include Google::Apis::Core::Hashable
|
|
3363
|
+
|
|
3364
|
+
# The continuation token, which is used to page through large result sets.
|
|
3365
|
+
# Provide this value in a subsequent request to return the next page of
|
|
3366
|
+
# results. This field will be empty if there aren't any additional results.
|
|
3367
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
3368
|
+
# @return [String]
|
|
3369
|
+
attr_accessor :next_page_token
|
|
3370
|
+
|
|
3371
|
+
# The list of matching read group sets.
|
|
3372
|
+
# Corresponds to the JSON property `readGroupSets`
|
|
3373
|
+
# @return [Array<Google::Apis::GenomicsV1::ReadGroupSet>]
|
|
3374
|
+
attr_accessor :read_group_sets
|
|
3375
|
+
|
|
3376
|
+
def initialize(**args)
|
|
3377
|
+
update!(**args)
|
|
3378
|
+
end
|
|
3379
|
+
|
|
3380
|
+
# Update properties of this object
|
|
3381
|
+
def update!(**args)
|
|
3382
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
|
3383
|
+
@read_group_sets = args[:read_group_sets] if args.key?(:read_group_sets)
|
|
3384
|
+
end
|
|
3385
|
+
end
|
|
3386
|
+
|
|
3387
|
+
# A linear alignment can be represented by one CIGAR string. Describes the
|
|
3388
|
+
# mapped position and local alignment of the read to the reference.
|
|
3389
|
+
class LinearAlignment
|
|
3390
|
+
include Google::Apis::Core::Hashable
|
|
3391
|
+
|
|
3392
|
+
# An abstraction for referring to a genomic position, in relation to some
|
|
3393
|
+
# already known reference. For now, represents a genomic position as a
|
|
3394
|
+
# reference name, a base number on that reference (0-based), and a
|
|
3395
|
+
# determination of forward or reverse strand.
|
|
3396
|
+
# Corresponds to the JSON property `position`
|
|
3397
|
+
# @return [Google::Apis::GenomicsV1::Position]
|
|
3398
|
+
attr_accessor :position
|
|
3399
|
+
|
|
3400
|
+
# Represents the local alignment of this sequence (alignment matches, indels,
|
|
3401
|
+
# etc) against the reference.
|
|
3402
|
+
# Corresponds to the JSON property `cigar`
|
|
3403
|
+
# @return [Array<Google::Apis::GenomicsV1::CigarUnit>]
|
|
3404
|
+
attr_accessor :cigar
|
|
3405
|
+
|
|
3406
|
+
# The mapping quality of this alignment. Represents how likely
|
|
3407
|
+
# the read maps to this position as opposed to other locations.
|
|
3408
|
+
# Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
|
|
3409
|
+
# the nearest integer.
|
|
3410
|
+
# Corresponds to the JSON property `mappingQuality`
|
|
3411
|
+
# @return [Fixnum]
|
|
3412
|
+
attr_accessor :mapping_quality
|
|
3413
|
+
|
|
3414
|
+
def initialize(**args)
|
|
3415
|
+
update!(**args)
|
|
3416
|
+
end
|
|
3417
|
+
|
|
3418
|
+
# Update properties of this object
|
|
3419
|
+
def update!(**args)
|
|
3420
|
+
@position = args[:position] if args.key?(:position)
|
|
3421
|
+
@cigar = args[:cigar] if args.key?(:cigar)
|
|
3422
|
+
@mapping_quality = args[:mapping_quality] if args.key?(:mapping_quality)
|
|
3423
|
+
end
|
|
3424
|
+
end
|
|
3425
|
+
|
|
3426
|
+
#
|
|
3427
|
+
class SearchReferencesRequest
|
|
3428
|
+
include Google::Apis::Core::Hashable
|
|
3429
|
+
|
|
3430
|
+
# If present, return references for which a prefix of any of
|
|
3431
|
+
# sourceAccessions match
|
|
3432
|
+
# any of these strings. Accession numbers typically have a main number and a
|
|
3433
|
+
# version, for example `GCF_000001405.26`.
|
|
3434
|
+
# Corresponds to the JSON property `accessions`
|
|
3435
|
+
# @return [Array<String>]
|
|
3436
|
+
attr_accessor :accessions
|
|
3437
|
+
|
|
3438
|
+
# The continuation token, which is used to page through large result sets.
|
|
3439
|
+
# To get the next page of results, set this parameter to the value of
|
|
3440
|
+
# `nextPageToken` from the previous response.
|
|
3441
|
+
# Corresponds to the JSON property `pageToken`
|
|
3442
|
+
# @return [String]
|
|
3443
|
+
attr_accessor :page_token
|
|
3444
|
+
|
|
3445
|
+
# If present, return only references which belong to this reference set.
|
|
3446
|
+
# Corresponds to the JSON property `referenceSetId`
|
|
3447
|
+
# @return [String]
|
|
3448
|
+
attr_accessor :reference_set_id
|
|
3449
|
+
|
|
3450
|
+
# The maximum number of results to return in a single page. If unspecified,
|
|
3451
|
+
# defaults to 1024. The maximum value is 4096.
|
|
3452
|
+
# Corresponds to the JSON property `pageSize`
|
|
3453
|
+
# @return [Fixnum]
|
|
3454
|
+
attr_accessor :page_size
|
|
3455
|
+
|
|
3456
|
+
# If present, return references for which the
|
|
3457
|
+
# md5checksum matches exactly.
|
|
3458
|
+
# Corresponds to the JSON property `md5checksums`
|
|
3459
|
+
# @return [Array<String>]
|
|
3460
|
+
attr_accessor :md5checksums
|
|
3461
|
+
|
|
3462
|
+
def initialize(**args)
|
|
3463
|
+
update!(**args)
|
|
3464
|
+
end
|
|
3465
|
+
|
|
3466
|
+
# Update properties of this object
|
|
3467
|
+
def update!(**args)
|
|
3468
|
+
@accessions = args[:accessions] if args.key?(:accessions)
|
|
3469
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
|
3470
|
+
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
3471
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
|
3472
|
+
@md5checksums = args[:md5checksums] if args.key?(:md5checksums)
|
|
3473
|
+
end
|
|
3474
|
+
end
|
|
3475
3475
|
end
|
|
3476
3476
|
end
|
|
3477
3477
|
end
|