lemboy-google-api-client 0.9.26
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +7 -0
- data/.gitignore +20 -0
- data/.rspec +2 -0
- data/.rubocop.yml +7 -0
- data/.rubocop_todo.yml +63 -0
- data/.travis.yml +27 -0
- data/.yardopts +12 -0
- data/CHANGELOG.md +309 -0
- data/CONTRIBUTING.md +31 -0
- data/Gemfile +53 -0
- data/LICENSE +202 -0
- data/MIGRATING.md +171 -0
- data/README.md +327 -0
- data/Rakefile +2 -0
- data/api_names.yaml +36215 -0
- data/bin/generate-api +109 -0
- data/generated/google/apis/adexchangebuyer2_v2beta1.rb +35 -0
- data/generated/google/apis/adexchangebuyer2_v2beta1/classes.rb +298 -0
- data/generated/google/apis/adexchangebuyer2_v2beta1/representations.rb +122 -0
- data/generated/google/apis/adexchangebuyer2_v2beta1/service.rb +458 -0
- data/generated/google/apis/adexchangebuyer_v1_3.rb +35 -0
- data/generated/google/apis/adexchangebuyer_v1_3/classes.rb +1335 -0
- data/generated/google/apis/adexchangebuyer_v1_3/representations.rb +446 -0
- data/generated/google/apis/adexchangebuyer_v1_3/service.rb +872 -0
- data/generated/google/apis/adexchangebuyer_v1_4.rb +35 -0
- data/generated/google/apis/adexchangebuyer_v1_4/classes.rb +3550 -0
- data/generated/google/apis/adexchangebuyer_v1_4/representations.rb +1421 -0
- data/generated/google/apis/adexchangebuyer_v1_4/service.rb +1538 -0
- data/generated/google/apis/adexchangeseller_v2_0.rb +37 -0
- data/generated/google/apis/adexchangeseller_v2_0/classes.rb +792 -0
- data/generated/google/apis/adexchangeseller_v2_0/representations.rb +347 -0
- data/generated/google/apis/adexchangeseller_v2_0/service.rb +667 -0
- data/generated/google/apis/admin_datatransfer_v1.rb +37 -0
- data/generated/google/apis/admin_datatransfer_v1/classes.rb +267 -0
- data/generated/google/apis/admin_datatransfer_v1/representations.rb +130 -0
- data/generated/google/apis/admin_datatransfer_v1/service.rb +262 -0
- data/generated/google/apis/admin_directory_v1.rb +113 -0
- data/generated/google/apis/admin_directory_v1/classes.rb +3241 -0
- data/generated/google/apis/admin_directory_v1/representations.rb +1172 -0
- data/generated/google/apis/admin_directory_v1/service.rb +3857 -0
- data/generated/google/apis/admin_reports_v1.rb +38 -0
- data/generated/google/apis/admin_reports_v1/classes.rb +582 -0
- data/generated/google/apis/admin_reports_v1/representations.rb +257 -0
- data/generated/google/apis/admin_reports_v1/service.rb +336 -0
- data/generated/google/apis/adsense_v1_4.rb +37 -0
- data/generated/google/apis/adsense_v1_4/classes.rb +1280 -0
- data/generated/google/apis/adsense_v1_4/representations.rb +555 -0
- data/generated/google/apis/adsense_v1_4/service.rb +1713 -0
- data/generated/google/apis/adsensehost_v4_1.rb +35 -0
- data/generated/google/apis/adsensehost_v4_1/classes.rb +836 -0
- data/generated/google/apis/adsensehost_v4_1/representations.rb +367 -0
- data/generated/google/apis/adsensehost_v4_1/service.rb +1164 -0
- data/generated/google/apis/analytics_v3.rb +49 -0
- data/generated/google/apis/analytics_v3/classes.rb +5536 -0
- data/generated/google/apis/analytics_v3/representations.rb +1992 -0
- data/generated/google/apis/analytics_v3/service.rb +3785 -0
- data/generated/google/apis/analyticsreporting_v4.rb +37 -0
- data/generated/google/apis/analyticsreporting_v4/classes.rb +1420 -0
- data/generated/google/apis/analyticsreporting_v4/representations.rb +598 -0
- data/generated/google/apis/analyticsreporting_v4/service.rb +88 -0
- data/generated/google/apis/androidenterprise_v1.rb +34 -0
- data/generated/google/apis/androidenterprise_v1/classes.rb +2250 -0
- data/generated/google/apis/androidenterprise_v1/representations.rb +970 -0
- data/generated/google/apis/androidenterprise_v1/service.rb +3267 -0
- data/generated/google/apis/androidpublisher_v2.rb +34 -0
- data/generated/google/apis/androidpublisher_v2/classes.rb +1941 -0
- data/generated/google/apis/androidpublisher_v2/representations.rb +975 -0
- data/generated/google/apis/androidpublisher_v2/service.rb +2572 -0
- data/generated/google/apis/appengine_v1beta4.rb +35 -0
- data/generated/google/apis/appengine_v1beta4/classes.rb +1585 -0
- data/generated/google/apis/appengine_v1beta4/representations.rb +542 -0
- data/generated/google/apis/appengine_v1beta4/service.rb +477 -0
- data/generated/google/apis/appengine_v1beta5.rb +40 -0
- data/generated/google/apis/appengine_v1beta5/classes.rb +1984 -0
- data/generated/google/apis/appengine_v1beta5/representations.rb +765 -0
- data/generated/google/apis/appengine_v1beta5/service.rb +864 -0
- data/generated/google/apis/appsactivity_v1.rb +46 -0
- data/generated/google/apis/appsactivity_v1/classes.rb +415 -0
- data/generated/google/apis/appsactivity_v1/representations.rb +209 -0
- data/generated/google/apis/appsactivity_v1/service.rb +128 -0
- data/generated/google/apis/appstate_v1.rb +34 -0
- data/generated/google/apis/appstate_v1/classes.rb +154 -0
- data/generated/google/apis/appstate_v1/representations.rb +87 -0
- data/generated/google/apis/appstate_v1/service.rb +260 -0
- data/generated/google/apis/autoscaler_v1beta2.rb +38 -0
- data/generated/google/apis/autoscaler_v1beta2/classes.rb +710 -0
- data/generated/google/apis/autoscaler_v1beta2/representations.rb +296 -0
- data/generated/google/apis/autoscaler_v1beta2/service.rb +478 -0
- data/generated/google/apis/bigquery_v2.rb +52 -0
- data/generated/google/apis/bigquery_v2/classes.rb +3081 -0
- data/generated/google/apis/bigquery_v2/representations.rb +1094 -0
- data/generated/google/apis/bigquery_v2/service.rb +988 -0
- data/generated/google/apis/blogger_v3.rb +37 -0
- data/generated/google/apis/blogger_v3/classes.rb +1354 -0
- data/generated/google/apis/blogger_v3/representations.rb +632 -0
- data/generated/google/apis/blogger_v3/service.rb +1587 -0
- data/generated/google/apis/books_v1.rb +34 -0
- data/generated/google/apis/books_v1/classes.rb +4160 -0
- data/generated/google/apis/books_v1/representations.rb +1799 -0
- data/generated/google/apis/books_v1/service.rb +2300 -0
- data/generated/google/apis/calendar_v3.rb +37 -0
- data/generated/google/apis/calendar_v3/classes.rb +1742 -0
- data/generated/google/apis/calendar_v3/representations.rb +631 -0
- data/generated/google/apis/calendar_v3/service.rb +1968 -0
- data/generated/google/apis/civicinfo_v2.rb +32 -0
- data/generated/google/apis/civicinfo_v2/classes.rb +1499 -0
- data/generated/google/apis/civicinfo_v2/representations.rb +572 -0
- data/generated/google/apis/civicinfo_v2/service.rb +300 -0
- data/generated/google/apis/classroom_v1.rb +70 -0
- data/generated/google/apis/classroom_v1/classes.rb +1572 -0
- data/generated/google/apis/classroom_v1/representations.rb +729 -0
- data/generated/google/apis/classroom_v1/service.rb +1945 -0
- data/generated/google/apis/classroom_v1beta1.rb +49 -0
- data/generated/google/apis/classroom_v1beta1/classes.rb +447 -0
- data/generated/google/apis/classroom_v1beta1/representations.rb +190 -0
- data/generated/google/apis/classroom_v1beta1/service.rb +791 -0
- data/generated/google/apis/cloudbilling_v1.rb +35 -0
- data/generated/google/apis/cloudbilling_v1/classes.rb +169 -0
- data/generated/google/apis/cloudbilling_v1/representations.rb +87 -0
- data/generated/google/apis/cloudbilling_v1/service.rb +258 -0
- data/generated/google/apis/cloudbuild_v1.rb +34 -0
- data/generated/google/apis/cloudbuild_v1/classes.rb +919 -0
- data/generated/google/apis/cloudbuild_v1/representations.rb +364 -0
- data/generated/google/apis/cloudbuild_v1/service.rb +492 -0
- data/generated/google/apis/clouddebugger_v2.rb +38 -0
- data/generated/google/apis/clouddebugger_v2/classes.rb +1081 -0
- data/generated/google/apis/clouddebugger_v2/representations.rb +465 -0
- data/generated/google/apis/clouddebugger_v2/service.rb +396 -0
- data/generated/google/apis/cloudkms_v1beta1.rb +34 -0
- data/generated/google/apis/cloudkms_v1beta1/classes.rb +999 -0
- data/generated/google/apis/cloudkms_v1beta1/representations.rb +448 -0
- data/generated/google/apis/cloudkms_v1beta1/service.rb +932 -0
- data/generated/google/apis/cloudlatencytest_v2.rb +34 -0
- data/generated/google/apis/cloudlatencytest_v2/classes.rb +195 -0
- data/generated/google/apis/cloudlatencytest_v2/representations.rb +127 -0
- data/generated/google/apis/cloudlatencytest_v2/service.rb +135 -0
- data/generated/google/apis/cloudmonitoring_v2beta2.rb +37 -0
- data/generated/google/apis/cloudmonitoring_v2beta2/classes.rb +679 -0
- data/generated/google/apis/cloudmonitoring_v2beta2/representations.rb +353 -0
- data/generated/google/apis/cloudmonitoring_v2beta2/service.rb +452 -0
- data/generated/google/apis/cloudresourcemanager_v1.rb +38 -0
- data/generated/google/apis/cloudresourcemanager_v1/classes.rb +886 -0
- data/generated/google/apis/cloudresourcemanager_v1/representations.rb +359 -0
- data/generated/google/apis/cloudresourcemanager_v1/service.rb +686 -0
- data/generated/google/apis/cloudresourcemanager_v1beta1.rb +38 -0
- data/generated/google/apis/cloudresourcemanager_v1beta1/classes.rb +682 -0
- data/generated/google/apis/cloudresourcemanager_v1beta1/representations.rb +312 -0
- data/generated/google/apis/cloudresourcemanager_v1beta1/service.rb +710 -0
- data/generated/google/apis/cloudtrace_v1.rb +43 -0
- data/generated/google/apis/cloudtrace_v1/classes.rb +188 -0
- data/generated/google/apis/cloudtrace_v1/representations.rb +102 -0
- data/generated/google/apis/cloudtrace_v1/service.rb +192 -0
- data/generated/google/apis/clouduseraccounts_beta.rb +44 -0
- data/generated/google/apis/clouduseraccounts_beta/classes.rb +845 -0
- data/generated/google/apis/clouduseraccounts_beta/representations.rb +352 -0
- data/generated/google/apis/clouduseraccounts_beta/service.rb +907 -0
- data/generated/google/apis/compute_beta.rb +49 -0
- data/generated/google/apis/compute_beta/classes.rb +12261 -0
- data/generated/google/apis/compute_beta/representations.rb +4615 -0
- data/generated/google/apis/compute_beta/service.rb +15330 -0
- data/generated/google/apis/compute_v1.rb +49 -0
- data/generated/google/apis/compute_v1/classes.rb +11179 -0
- data/generated/google/apis/compute_v1/representations.rb +4203 -0
- data/generated/google/apis/compute_v1/service.rb +12937 -0
- data/generated/google/apis/container_v1.rb +35 -0
- data/generated/google/apis/container_v1/classes.rb +1040 -0
- data/generated/google/apis/container_v1/representations.rb +415 -0
- data/generated/google/apis/container_v1/service.rb +659 -0
- data/generated/google/apis/container_v1beta1.rb +35 -0
- data/generated/google/apis/container_v1beta1/classes.rb +466 -0
- data/generated/google/apis/container_v1beta1/representations.rb +177 -0
- data/generated/google/apis/container_v1beta1/service.rb +394 -0
- data/generated/google/apis/content_v2.rb +35 -0
- data/generated/google/apis/content_v2/classes.rb +6887 -0
- data/generated/google/apis/content_v2/representations.rb +2963 -0
- data/generated/google/apis/content_v2/service.rb +2653 -0
- data/generated/google/apis/coordinate_v1.rb +37 -0
- data/generated/google/apis/coordinate_v1/classes.rb +669 -0
- data/generated/google/apis/coordinate_v1/representations.rb +321 -0
- data/generated/google/apis/coordinate_v1/service.rb +678 -0
- data/generated/google/apis/customsearch_v1.rb +31 -0
- data/generated/google/apis/customsearch_v1/classes.rb +771 -0
- data/generated/google/apis/customsearch_v1/representations.rb +302 -0
- data/generated/google/apis/customsearch_v1/service.rb +207 -0
- data/generated/google/apis/dataflow_v1b3.rb +37 -0
- data/generated/google/apis/dataflow_v1b3/classes.rb +4225 -0
- data/generated/google/apis/dataflow_v1b3/representations.rb +1809 -0
- data/generated/google/apis/dataflow_v1b3/service.rb +874 -0
- data/generated/google/apis/dataproc_v1.rb +34 -0
- data/generated/google/apis/dataproc_v1/classes.rb +1716 -0
- data/generated/google/apis/dataproc_v1/representations.rb +678 -0
- data/generated/google/apis/dataproc_v1/service.rb +670 -0
- data/generated/google/apis/datastore_v1.rb +38 -0
- data/generated/google/apis/datastore_v1/classes.rb +1289 -0
- data/generated/google/apis/datastore_v1/representations.rb +572 -0
- data/generated/google/apis/datastore_v1/service.rb +259 -0
- data/generated/google/apis/datastore_v1beta2.rb +40 -0
- data/generated/google/apis/datastore_v1beta2/classes.rb +1186 -0
- data/generated/google/apis/datastore_v1beta2/representations.rb +594 -0
- data/generated/google/apis/datastore_v1beta2/service.rb +294 -0
- data/generated/google/apis/datastore_v1beta3.rb +38 -0
- data/generated/google/apis/datastore_v1beta3/classes.rb +1284 -0
- data/generated/google/apis/datastore_v1beta3/representations.rb +572 -0
- data/generated/google/apis/datastore_v1beta3/service.rb +259 -0
- data/generated/google/apis/deploymentmanager_v2.rb +43 -0
- data/generated/google/apis/deploymentmanager_v2/classes.rb +1582 -0
- data/generated/google/apis/deploymentmanager_v2/representations.rb +686 -0
- data/generated/google/apis/deploymentmanager_v2/service.rb +1026 -0
- data/generated/google/apis/deploymentmanager_v2beta2.rb +44 -0
- data/generated/google/apis/deploymentmanager_v2beta2/classes.rb +843 -0
- data/generated/google/apis/deploymentmanager_v2beta2/representations.rb +306 -0
- data/generated/google/apis/deploymentmanager_v2beta2/service.rb +689 -0
- data/generated/google/apis/dfareporting_v2_1.rb +37 -0
- data/generated/google/apis/dfareporting_v2_1/classes.rb +10770 -0
- data/generated/google/apis/dfareporting_v2_1/representations.rb +3438 -0
- data/generated/google/apis/dfareporting_v2_1/service.rb +8585 -0
- data/generated/google/apis/dfareporting_v2_3.rb +37 -0
- data/generated/google/apis/dfareporting_v2_3/classes.rb +10839 -0
- data/generated/google/apis/dfareporting_v2_3/representations.rb +3829 -0
- data/generated/google/apis/dfareporting_v2_3/service.rb +8581 -0
- data/generated/google/apis/dfareporting_v2_5.rb +40 -0
- data/generated/google/apis/dfareporting_v2_5/classes.rb +11225 -0
- data/generated/google/apis/dfareporting_v2_5/representations.rb +3982 -0
- data/generated/google/apis/dfareporting_v2_5/service.rb +8755 -0
- data/generated/google/apis/dfareporting_v2_6.rb +40 -0
- data/generated/google/apis/dfareporting_v2_6/classes.rb +11586 -0
- data/generated/google/apis/dfareporting_v2_6/representations.rb +4119 -0
- data/generated/google/apis/dfareporting_v2_6/service.rb +9025 -0
- data/generated/google/apis/dfareporting_v2_7.rb +40 -0
- data/generated/google/apis/dfareporting_v2_7/classes.rb +11876 -0
- data/generated/google/apis/dfareporting_v2_7/representations.rb +4243 -0
- data/generated/google/apis/dfareporting_v2_7/service.rb +9095 -0
- data/generated/google/apis/discovery_v1.rb +32 -0
- data/generated/google/apis/discovery_v1/classes.rb +961 -0
- data/generated/google/apis/discovery_v1/representations.rb +397 -0
- data/generated/google/apis/discovery_v1/service.rb +142 -0
- data/generated/google/apis/dns_v1.rb +43 -0
- data/generated/google/apis/dns_v1/classes.rb +406 -0
- data/generated/google/apis/dns_v1/representations.rb +167 -0
- data/generated/google/apis/dns_v1/service.rb +453 -0
- data/generated/google/apis/dns_v2beta1.rb +43 -0
- data/generated/google/apis/dns_v2beta1/classes.rb +915 -0
- data/generated/google/apis/dns_v2beta1/representations.rb +368 -0
- data/generated/google/apis/dns_v2beta1/service.rb +768 -0
- data/generated/google/apis/doubleclickbidmanager_v1.rb +31 -0
- data/generated/google/apis/doubleclickbidmanager_v1/classes.rb +795 -0
- data/generated/google/apis/doubleclickbidmanager_v1/representations.rb +368 -0
- data/generated/google/apis/doubleclickbidmanager_v1/service.rb +376 -0
- data/generated/google/apis/doubleclicksearch_v2.rb +35 -0
- data/generated/google/apis/doubleclicksearch_v2/classes.rb +960 -0
- data/generated/google/apis/doubleclicksearch_v2/representations.rb +350 -0
- data/generated/google/apis/doubleclicksearch_v2/service.rb +480 -0
- data/generated/google/apis/drive_v2.rb +59 -0
- data/generated/google/apis/drive_v2/classes.rb +2633 -0
- data/generated/google/apis/drive_v2/representations.rb +885 -0
- data/generated/google/apis/drive_v2/service.rb +2754 -0
- data/generated/google/apis/drive_v3.rb +56 -0
- data/generated/google/apis/drive_v3/classes.rb +1611 -0
- data/generated/google/apis/drive_v3/representations.rb +555 -0
- data/generated/google/apis/drive_v3/service.rb +1553 -0
- data/generated/google/apis/fitness_v1.rb +85 -0
- data/generated/google/apis/fitness_v1/classes.rb +943 -0
- data/generated/google/apis/fitness_v1/representations.rb +380 -0
- data/generated/google/apis/fitness_v1/service.rb +674 -0
- data/generated/google/apis/fusiontables_v2.rb +37 -0
- data/generated/google/apis/fusiontables_v2/classes.rb +1049 -0
- data/generated/google/apis/fusiontables_v2/representations.rb +457 -0
- data/generated/google/apis/fusiontables_v2/service.rb +1463 -0
- data/generated/google/apis/games_configuration_v1configuration.rb +34 -0
- data/generated/google/apis/games_configuration_v1configuration/classes.rb +506 -0
- data/generated/google/apis/games_configuration_v1configuration/representations.rb +228 -0
- data/generated/google/apis/games_configuration_v1configuration/service.rb +565 -0
- data/generated/google/apis/games_management_v1management.rb +37 -0
- data/generated/google/apis/games_management_v1management/classes.rb +567 -0
- data/generated/google/apis/games_management_v1management/representations.rb +278 -0
- data/generated/google/apis/games_management_v1management/service.rb +994 -0
- data/generated/google/apis/games_v1.rb +40 -0
- data/generated/google/apis/games_v1/classes.rb +4667 -0
- data/generated/google/apis/games_v1/representations.rb +1800 -0
- data/generated/google/apis/games_v1/service.rb +2449 -0
- data/generated/google/apis/gan_v1beta1.rb +31 -0
- data/generated/google/apis/gan_v1beta1/classes.rb +1428 -0
- data/generated/google/apis/gan_v1beta1/representations.rb +462 -0
- data/generated/google/apis/gan_v1beta1/service.rb +682 -0
- data/generated/google/apis/genomics_v1.rb +46 -0
- data/generated/google/apis/genomics_v1/classes.rb +3477 -0
- data/generated/google/apis/genomics_v1/representations.rb +1284 -0
- data/generated/google/apis/genomics_v1/service.rb +2207 -0
- data/generated/google/apis/genomics_v1beta2.rb +46 -0
- data/generated/google/apis/genomics_v1beta2/classes.rb +3288 -0
- data/generated/google/apis/genomics_v1beta2/representations.rb +1194 -0
- data/generated/google/apis/genomics_v1beta2/service.rb +2392 -0
- data/generated/google/apis/gmail_v1.rb +61 -0
- data/generated/google/apis/gmail_v1/classes.rb +1382 -0
- data/generated/google/apis/gmail_v1/representations.rb +624 -0
- data/generated/google/apis/gmail_v1/service.rb +2447 -0
- data/generated/google/apis/groupsmigration_v1.rb +34 -0
- data/generated/google/apis/groupsmigration_v1/classes.rb +51 -0
- data/generated/google/apis/groupsmigration_v1/representations.rb +40 -0
- data/generated/google/apis/groupsmigration_v1/service.rb +110 -0
- data/generated/google/apis/groupssettings_v1.rb +34 -0
- data/generated/google/apis/groupssettings_v1/classes.rb +240 -0
- data/generated/google/apis/groupssettings_v1/representations.rb +69 -0
- data/generated/google/apis/groupssettings_v1/service.rb +179 -0
- data/generated/google/apis/iam_v1.rb +36 -0
- data/generated/google/apis/iam_v1/classes.rb +640 -0
- data/generated/google/apis/iam_v1/representations.rb +316 -0
- data/generated/google/apis/iam_v1/service.rb +554 -0
- data/generated/google/apis/identitytoolkit_v3.rb +37 -0
- data/generated/google/apis/identitytoolkit_v3/classes.rb +2182 -0
- data/generated/google/apis/identitytoolkit_v3/representations.rb +742 -0
- data/generated/google/apis/identitytoolkit_v3/service.rb +657 -0
- data/generated/google/apis/kgsearch_v1.rb +31 -0
- data/generated/google/apis/kgsearch_v1/classes.rb +59 -0
- data/generated/google/apis/kgsearch_v1/representations.rb +41 -0
- data/generated/google/apis/kgsearch_v1/service.rb +113 -0
- data/generated/google/apis/language_v1beta1.rb +36 -0
- data/generated/google/apis/language_v1beta1/classes.rb +757 -0
- data/generated/google/apis/language_v1beta1/representations.rb +339 -0
- data/generated/google/apis/language_v1beta1/service.rb +184 -0
- data/generated/google/apis/licensing_v1.rb +34 -0
- data/generated/google/apis/licensing_v1/classes.rb +132 -0
- data/generated/google/apis/licensing_v1/representations.rb +74 -0
- data/generated/google/apis/licensing_v1/service.rb +369 -0
- data/generated/google/apis/logging_v1beta3.rb +47 -0
- data/generated/google/apis/logging_v1beta3/classes.rb +1079 -0
- data/generated/google/apis/logging_v1beta3/representations.rb +366 -0
- data/generated/google/apis/logging_v1beta3/service.rb +1001 -0
- data/generated/google/apis/logging_v2beta1.rb +46 -0
- data/generated/google/apis/logging_v2beta1/classes.rb +1254 -0
- data/generated/google/apis/logging_v2beta1/representations.rb +421 -0
- data/generated/google/apis/logging_v2beta1/service.rb +788 -0
- data/generated/google/apis/manager_v1beta2.rb +53 -0
- data/generated/google/apis/manager_v1beta2/classes.rb +1287 -0
- data/generated/google/apis/manager_v1beta2/representations.rb +606 -0
- data/generated/google/apis/manager_v1beta2/service.rb +372 -0
- data/generated/google/apis/manufacturers_v1.rb +34 -0
- data/generated/google/apis/manufacturers_v1/classes.rb +258 -0
- data/generated/google/apis/manufacturers_v1/representations.rb +103 -0
- data/generated/google/apis/manufacturers_v1/service.rb +138 -0
- data/generated/google/apis/mirror_v1.rb +37 -0
- data/generated/google/apis/mirror_v1/classes.rb +1072 -0
- data/generated/google/apis/mirror_v1/representations.rb +390 -0
- data/generated/google/apis/mirror_v1/service.rb +977 -0
- data/generated/google/apis/monitoring_v3.rb +45 -0
- data/generated/google/apis/monitoring_v3/classes.rb +1335 -0
- data/generated/google/apis/monitoring_v3/representations.rb +516 -0
- data/generated/google/apis/monitoring_v3/service.rb +706 -0
- data/generated/google/apis/mybusiness_v3.rb +32 -0
- data/generated/google/apis/mybusiness_v3/classes.rb +1864 -0
- data/generated/google/apis/mybusiness_v3/representations.rb +741 -0
- data/generated/google/apis/mybusiness_v3/service.rb +960 -0
- data/generated/google/apis/oauth2_v2.rb +43 -0
- data/generated/google/apis/oauth2_v2/classes.rb +245 -0
- data/generated/google/apis/oauth2_v2/representations.rb +102 -0
- data/generated/google/apis/oauth2_v2/service.rb +199 -0
- data/generated/google/apis/pagespeedonline_v2.rb +32 -0
- data/generated/google/apis/pagespeedonline_v2/classes.rb +614 -0
- data/generated/google/apis/pagespeedonline_v2/representations.rb +272 -0
- data/generated/google/apis/pagespeedonline_v2/service.rb +119 -0
- data/generated/google/apis/partners_v2.rb +32 -0
- data/generated/google/apis/partners_v2/classes.rb +942 -0
- data/generated/google/apis/partners_v2/representations.rb +454 -0
- data/generated/google/apis/partners_v2/service.rb +400 -0
- data/generated/google/apis/people_v1.rb +59 -0
- data/generated/google/apis/people_v1/classes.rb +1521 -0
- data/generated/google/apis/people_v1/representations.rb +663 -0
- data/generated/google/apis/people_v1/service.rb +189 -0
- data/generated/google/apis/plus_domains_v1.rb +61 -0
- data/generated/google/apis/plus_domains_v1/classes.rb +2609 -0
- data/generated/google/apis/plus_domains_v1/representations.rb +1111 -0
- data/generated/google/apis/plus_domains_v1/service.rb +904 -0
- data/generated/google/apis/plus_v1.rb +43 -0
- data/generated/google/apis/plus_v1/classes.rb +2094 -0
- data/generated/google/apis/plus_v1/representations.rb +907 -0
- data/generated/google/apis/plus_v1/service.rb +470 -0
- data/generated/google/apis/prediction_v1_6.rb +47 -0
- data/generated/google/apis/prediction_v1_6/classes.rb +751 -0
- data/generated/google/apis/prediction_v1_6/representations.rb +369 -0
- data/generated/google/apis/prediction_v1_6/service.rb +380 -0
- data/generated/google/apis/proximitybeacon_v1beta1.rb +34 -0
- data/generated/google/apis/proximitybeacon_v1beta1/classes.rb +786 -0
- data/generated/google/apis/proximitybeacon_v1beta1/representations.rb +347 -0
- data/generated/google/apis/proximitybeacon_v1beta1/service.rb +806 -0
- data/generated/google/apis/pubsub_v1.rb +37 -0
- data/generated/google/apis/pubsub_v1/classes.rb +676 -0
- data/generated/google/apis/pubsub_v1/representations.rb +323 -0
- data/generated/google/apis/pubsub_v1/service.rb +900 -0
- data/generated/google/apis/pubsub_v1beta2.rb +37 -0
- data/generated/google/apis/pubsub_v1beta2/classes.rb +620 -0
- data/generated/google/apis/pubsub_v1beta2/representations.rb +282 -0
- data/generated/google/apis/pubsub_v1beta2/service.rb +774 -0
- data/generated/google/apis/qpx_express_v1.rb +31 -0
- data/generated/google/apis/qpx_express_v1/classes.rb +1274 -0
- data/generated/google/apis/qpx_express_v1/representations.rb +473 -0
- data/generated/google/apis/qpx_express_v1/service.rb +100 -0
- data/generated/google/apis/replicapool_v1beta2.rb +44 -0
- data/generated/google/apis/replicapool_v1beta2/classes.rb +631 -0
- data/generated/google/apis/replicapool_v1beta2/representations.rb +264 -0
- data/generated/google/apis/replicapool_v1beta2/service.rb +608 -0
- data/generated/google/apis/replicapoolupdater_v1beta1.rb +45 -0
- data/generated/google/apis/replicapoolupdater_v1beta1/classes.rb +733 -0
- data/generated/google/apis/replicapoolupdater_v1beta1/representations.rb +294 -0
- data/generated/google/apis/replicapoolupdater_v1beta1/service.rb +509 -0
- data/generated/google/apis/reseller_v1.rb +37 -0
- data/generated/google/apis/reseller_v1/classes.rb +540 -0
- data/generated/google/apis/reseller_v1/representations.rb +225 -0
- data/generated/google/apis/reseller_v1/service.rb +623 -0
- data/generated/google/apis/resourceviews_v1beta2.rb +50 -0
- data/generated/google/apis/resourceviews_v1beta2/classes.rb +660 -0
- data/generated/google/apis/resourceviews_v1beta2/representations.rb +301 -0
- data/generated/google/apis/resourceviews_v1beta2/service.rb +563 -0
- data/generated/google/apis/script_v1.rb +64 -0
- data/generated/google/apis/script_v1/classes.rb +265 -0
- data/generated/google/apis/script_v1/representations.rb +119 -0
- data/generated/google/apis/script_v1/service.rb +98 -0
- data/generated/google/apis/sheets_v4.rb +43 -0
- data/generated/google/apis/sheets_v4/classes.rb +6368 -0
- data/generated/google/apis/sheets_v4/representations.rb +2289 -0
- data/generated/google/apis/sheets_v4/service.rb +569 -0
- data/generated/google/apis/site_verification_v1.rb +37 -0
- data/generated/google/apis/site_verification_v1/classes.rb +185 -0
- data/generated/google/apis/site_verification_v1/representations.rb +113 -0
- data/generated/google/apis/site_verification_v1/service.rb +315 -0
- data/generated/google/apis/slides_v1.rb +49 -0
- data/generated/google/apis/slides_v1/classes.rb +4044 -0
- data/generated/google/apis/slides_v1/representations.rb +1765 -0
- data/generated/google/apis/slides_v1/service.rb +202 -0
- data/generated/google/apis/speech_v1beta1.rb +34 -0
- data/generated/google/apis/speech_v1beta1/classes.rb +513 -0
- data/generated/google/apis/speech_v1beta1/representations.rb +218 -0
- data/generated/google/apis/speech_v1beta1/service.rb +273 -0
- data/generated/google/apis/sqladmin_v1beta4.rb +38 -0
- data/generated/google/apis/sqladmin_v1beta4/classes.rb +2142 -0
- data/generated/google/apis/sqladmin_v1beta4/representations.rb +893 -0
- data/generated/google/apis/sqladmin_v1beta4/service.rb +1709 -0
- data/generated/google/apis/storage_v1.rb +46 -0
- data/generated/google/apis/storage_v1/classes.rb +1255 -0
- data/generated/google/apis/storage_v1/representations.rb +502 -0
- data/generated/google/apis/storage_v1/service.rb +1906 -0
- data/generated/google/apis/storagetransfer_v1.rb +35 -0
- data/generated/google/apis/storagetransfer_v1/classes.rb +1046 -0
- data/generated/google/apis/storagetransfer_v1/representations.rb +418 -0
- data/generated/google/apis/storagetransfer_v1/service.rb +473 -0
- data/generated/google/apis/tagmanager_v1.rb +52 -0
- data/generated/google/apis/tagmanager_v1/classes.rb +1494 -0
- data/generated/google/apis/tagmanager_v1/representations.rb +611 -0
- data/generated/google/apis/tagmanager_v1/service.rb +2119 -0
- data/generated/google/apis/taskqueue_v1beta2.rb +37 -0
- data/generated/google/apis/taskqueue_v1beta2/classes.rb +254 -0
- data/generated/google/apis/taskqueue_v1beta2/representations.rb +126 -0
- data/generated/google/apis/taskqueue_v1beta2/service.rb +408 -0
- data/generated/google/apis/tasks_v1.rb +37 -0
- data/generated/google/apis/tasks_v1/classes.rb +296 -0
- data/generated/google/apis/tasks_v1/representations.rb +125 -0
- data/generated/google/apis/tasks_v1/service.rb +643 -0
- data/generated/google/apis/translate_v2.rb +31 -0
- data/generated/google/apis/translate_v2/classes.rb +168 -0
- data/generated/google/apis/translate_v2/representations.rb +121 -0
- data/generated/google/apis/translate_v2/service.rb +182 -0
- data/generated/google/apis/urlshortener_v1.rb +34 -0
- data/generated/google/apis/urlshortener_v1/classes.rb +246 -0
- data/generated/google/apis/urlshortener_v1/representations.rb +121 -0
- data/generated/google/apis/urlshortener_v1/service.rb +176 -0
- data/generated/google/apis/vision_v1.rb +36 -0
- data/generated/google/apis/vision_v1/classes.rb +1267 -0
- data/generated/google/apis/vision_v1/representations.rb +418 -0
- data/generated/google/apis/vision_v1/service.rb +90 -0
- data/generated/google/apis/webmasters_v3.rb +37 -0
- data/generated/google/apis/webmasters_v3/classes.rb +570 -0
- data/generated/google/apis/webmasters_v3/representations.rb +283 -0
- data/generated/google/apis/webmasters_v3/service.rb +573 -0
- data/generated/google/apis/youtube_analytics_v1.rb +46 -0
- data/generated/google/apis/youtube_analytics_v1/classes.rb +337 -0
- data/generated/google/apis/youtube_analytics_v1/representations.rb +174 -0
- data/generated/google/apis/youtube_analytics_v1/service.rb +486 -0
- data/generated/google/apis/youtube_partner_v1.rb +37 -0
- data/generated/google/apis/youtube_partner_v1/classes.rb +3854 -0
- data/generated/google/apis/youtube_partner_v1/representations.rb +1537 -0
- data/generated/google/apis/youtube_partner_v1/service.rb +3269 -0
- data/generated/google/apis/youtube_v3.rb +50 -0
- data/generated/google/apis/youtube_v3/classes.rb +8375 -0
- data/generated/google/apis/youtube_v3/representations.rb +3273 -0
- data/generated/google/apis/youtube_v3/service.rb +4440 -0
- data/generated/google/apis/youtubereporting_v1.rb +38 -0
- data/generated/google/apis/youtubereporting_v1/classes.rb +302 -0
- data/generated/google/apis/youtubereporting_v1/representations.rb +149 -0
- data/generated/google/apis/youtubereporting_v1/service.rb +385 -0
- data/google-api-client.gemspec +33 -0
- data/lib/cacerts.pem +2183 -0
- data/lib/google/api_client/auth/installed_app.rb +128 -0
- data/lib/google/api_client/auth/key_utils.rb +94 -0
- data/lib/google/api_client/auth/storage.rb +104 -0
- data/lib/google/api_client/auth/storages/file_store.rb +57 -0
- data/lib/google/api_client/auth/storages/redis_store.rb +59 -0
- data/lib/google/api_client/client_secrets.rb +177 -0
- data/lib/google/apis.rb +58 -0
- data/lib/google/apis/core/api_command.rb +146 -0
- data/lib/google/apis/core/base_service.rb +401 -0
- data/lib/google/apis/core/batch.rb +239 -0
- data/lib/google/apis/core/download.rb +108 -0
- data/lib/google/apis/core/hashable.rb +44 -0
- data/lib/google/apis/core/http_client_adapter.rb +82 -0
- data/lib/google/apis/core/http_command.rb +332 -0
- data/lib/google/apis/core/json_representation.rb +145 -0
- data/lib/google/apis/core/logging.rb +30 -0
- data/lib/google/apis/core/multipart.rb +187 -0
- data/lib/google/apis/core/upload.rb +295 -0
- data/lib/google/apis/errors.rb +80 -0
- data/lib/google/apis/generator.rb +70 -0
- data/lib/google/apis/generator/annotator.rb +301 -0
- data/lib/google/apis/generator/helpers.rb +74 -0
- data/lib/google/apis/generator/model.rb +143 -0
- data/lib/google/apis/generator/template.rb +124 -0
- data/lib/google/apis/generator/templates/_class.tmpl +40 -0
- data/lib/google/apis/generator/templates/_method.tmpl +92 -0
- data/lib/google/apis/generator/templates/_representation.tmpl +51 -0
- data/lib/google/apis/generator/templates/_representation_stub.tmpl +17 -0
- data/lib/google/apis/generator/templates/_representation_type.tmpl +10 -0
- data/lib/google/apis/generator/templates/classes.rb.tmpl +29 -0
- data/lib/google/apis/generator/templates/module.rb.tmpl +40 -0
- data/lib/google/apis/generator/templates/representations.rb.tmpl +32 -0
- data/lib/google/apis/generator/templates/service.rb.tmpl +60 -0
- data/lib/google/apis/options.rb +85 -0
- data/lib/google/apis/version.rb +39 -0
- data/rakelib/metrics.rake +22 -0
- data/rakelib/rubocop.rake +10 -0
- data/rakelib/spec.rake +11 -0
- data/rakelib/yard.rake +11 -0
- data/samples/cli/.env +4 -0
- data/samples/cli/Gemfile +7 -0
- data/samples/cli/README.md +51 -0
- data/samples/cli/google-api-samples +32 -0
- data/samples/cli/lib/base_cli.rb +95 -0
- data/samples/cli/lib/samples/analytics.rb +62 -0
- data/samples/cli/lib/samples/androidpublisher.rb +47 -0
- data/samples/cli/lib/samples/bigquery.rb +101 -0
- data/samples/cli/lib/samples/calendar.rb +83 -0
- data/samples/cli/lib/samples/drive.rb +82 -0
- data/samples/cli/lib/samples/gmail.rb +124 -0
- data/samples/cli/lib/samples/pubsub.rb +114 -0
- data/samples/cli/lib/samples/sheets.rb +61 -0
- data/samples/cli/lib/samples/translate.rb +44 -0
- data/samples/cli/lib/samples/you_tube.rb +44 -0
- data/samples/web/.env +2 -0
- data/samples/web/Gemfile +7 -0
- data/samples/web/README.md +44 -0
- data/samples/web/app.rb +120 -0
- data/samples/web/views/calendar.erb +34 -0
- data/samples/web/views/drive.erb +33 -0
- data/samples/web/views/home.erb +34 -0
- data/samples/web/views/layout.erb +40 -0
- data/sync.rb +71 -0
- data/third_party/hurley_patches.rb +103 -0
- metadata +735 -0
@@ -0,0 +1,46 @@
|
|
1
|
+
# Copyright 2015 Google Inc.
|
2
|
+
#
|
3
|
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4
|
+
# you may not use this file except in compliance with the License.
|
5
|
+
# You may obtain a copy of the License at
|
6
|
+
#
|
7
|
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8
|
+
#
|
9
|
+
# Unless required by applicable law or agreed to in writing, software
|
10
|
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11
|
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12
|
+
# See the License for the specific language governing permissions and
|
13
|
+
# limitations under the License.
|
14
|
+
|
15
|
+
require 'google/apis/genomics_v1/service.rb'
|
16
|
+
require 'google/apis/genomics_v1/classes.rb'
|
17
|
+
require 'google/apis/genomics_v1/representations.rb'
|
18
|
+
|
19
|
+
module Google
|
20
|
+
module Apis
|
21
|
+
# Genomics API
|
22
|
+
#
|
23
|
+
# Upload, process, query, and search Genomics data in the cloud.
|
24
|
+
#
|
25
|
+
# @see https://cloud.google.com/genomics
|
26
|
+
module GenomicsV1
|
27
|
+
VERSION = 'V1'
|
28
|
+
REVISION = '20170126'
|
29
|
+
|
30
|
+
# View and manage your data in Google BigQuery
|
31
|
+
AUTH_BIGQUERY = 'https://www.googleapis.com/auth/bigquery'
|
32
|
+
|
33
|
+
# Manage your data in Google Cloud Storage
|
34
|
+
AUTH_DEVSTORAGE_READ_WRITE = 'https://www.googleapis.com/auth/devstorage.read_write'
|
35
|
+
|
36
|
+
# View and manage your data across Google Cloud Platform services
|
37
|
+
AUTH_CLOUD_PLATFORM = 'https://www.googleapis.com/auth/cloud-platform'
|
38
|
+
|
39
|
+
# View Genomics data
|
40
|
+
AUTH_GENOMICS_READONLY = 'https://www.googleapis.com/auth/genomics.readonly'
|
41
|
+
|
42
|
+
# View and manage Genomics data
|
43
|
+
AUTH_GENOMICS = 'https://www.googleapis.com/auth/genomics'
|
44
|
+
end
|
45
|
+
end
|
46
|
+
end
|
@@ -0,0 +1,3477 @@
|
|
1
|
+
# Copyright 2015 Google Inc.
|
2
|
+
#
|
3
|
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4
|
+
# you may not use this file except in compliance with the License.
|
5
|
+
# You may obtain a copy of the License at
|
6
|
+
#
|
7
|
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8
|
+
#
|
9
|
+
# Unless required by applicable law or agreed to in writing, software
|
10
|
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11
|
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12
|
+
# See the License for the specific language governing permissions and
|
13
|
+
# limitations under the License.
|
14
|
+
|
15
|
+
require 'date'
|
16
|
+
require 'google/apis/core/base_service'
|
17
|
+
require 'google/apis/core/json_representation'
|
18
|
+
require 'google/apis/core/hashable'
|
19
|
+
require 'google/apis/errors'
|
20
|
+
|
21
|
+
module Google
|
22
|
+
module Apis
|
23
|
+
module GenomicsV1
|
24
|
+
|
25
|
+
# A bucket over which read coverage has been precomputed. A bucket corresponds
|
26
|
+
# to a specific range of the reference sequence.
|
27
|
+
class CoverageBucket
|
28
|
+
include Google::Apis::Core::Hashable
|
29
|
+
|
30
|
+
# The average number of reads which are aligned to each individual
|
31
|
+
# reference base in this bucket.
|
32
|
+
# Corresponds to the JSON property `meanCoverage`
|
33
|
+
# @return [Float]
|
34
|
+
attr_accessor :mean_coverage
|
35
|
+
|
36
|
+
# A 0-based half-open genomic coordinate range for search requests.
|
37
|
+
# Corresponds to the JSON property `range`
|
38
|
+
# @return [Google::Apis::GenomicsV1::Range]
|
39
|
+
attr_accessor :range
|
40
|
+
|
41
|
+
def initialize(**args)
|
42
|
+
update!(**args)
|
43
|
+
end
|
44
|
+
|
45
|
+
# Update properties of this object
|
46
|
+
def update!(**args)
|
47
|
+
@mean_coverage = args[:mean_coverage] if args.key?(:mean_coverage)
|
48
|
+
@range = args[:range] if args.key?(:range)
|
49
|
+
end
|
50
|
+
end
|
51
|
+
|
52
|
+
# Describes a Compute Engine resource that is being managed by a running
|
53
|
+
# pipeline.
|
54
|
+
class ComputeEngine
|
55
|
+
include Google::Apis::Core::Hashable
|
56
|
+
|
57
|
+
# The instance on which the operation is running.
|
58
|
+
# Corresponds to the JSON property `instanceName`
|
59
|
+
# @return [String]
|
60
|
+
attr_accessor :instance_name
|
61
|
+
|
62
|
+
# The availability zone in which the instance resides.
|
63
|
+
# Corresponds to the JSON property `zone`
|
64
|
+
# @return [String]
|
65
|
+
attr_accessor :zone
|
66
|
+
|
67
|
+
# The machine type of the instance.
|
68
|
+
# Corresponds to the JSON property `machineType`
|
69
|
+
# @return [String]
|
70
|
+
attr_accessor :machine_type
|
71
|
+
|
72
|
+
# The names of the disks that were created for this pipeline.
|
73
|
+
# Corresponds to the JSON property `diskNames`
|
74
|
+
# @return [Array<String>]
|
75
|
+
attr_accessor :disk_names
|
76
|
+
|
77
|
+
def initialize(**args)
|
78
|
+
update!(**args)
|
79
|
+
end
|
80
|
+
|
81
|
+
# Update properties of this object
|
82
|
+
def update!(**args)
|
83
|
+
@instance_name = args[:instance_name] if args.key?(:instance_name)
|
84
|
+
@zone = args[:zone] if args.key?(:zone)
|
85
|
+
@machine_type = args[:machine_type] if args.key?(:machine_type)
|
86
|
+
@disk_names = args[:disk_names] if args.key?(:disk_names)
|
87
|
+
end
|
88
|
+
end
|
89
|
+
|
90
|
+
#
|
91
|
+
class ExternalId
|
92
|
+
include Google::Apis::Core::Hashable
|
93
|
+
|
94
|
+
# The name of the source of this data.
|
95
|
+
# Corresponds to the JSON property `sourceName`
|
96
|
+
# @return [String]
|
97
|
+
attr_accessor :source_name
|
98
|
+
|
99
|
+
# The id used by the source of this data.
|
100
|
+
# Corresponds to the JSON property `id`
|
101
|
+
# @return [String]
|
102
|
+
attr_accessor :id
|
103
|
+
|
104
|
+
def initialize(**args)
|
105
|
+
update!(**args)
|
106
|
+
end
|
107
|
+
|
108
|
+
# Update properties of this object
|
109
|
+
def update!(**args)
|
110
|
+
@source_name = args[:source_name] if args.key?(:source_name)
|
111
|
+
@id = args[:id] if args.key?(:id)
|
112
|
+
end
|
113
|
+
end
|
114
|
+
|
115
|
+
# A reference is a canonical assembled DNA sequence, intended to act as a
|
116
|
+
# reference coordinate space for other genomic annotations. A single reference
|
117
|
+
# might represent the human chromosome 1 or mitochandrial DNA, for instance. A
|
118
|
+
# reference belongs to one or more reference sets.
|
119
|
+
# For more genomics resource definitions, see [Fundamentals of Google
|
120
|
+
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
121
|
+
class Reference
|
122
|
+
include Google::Apis::Core::Hashable
|
123
|
+
|
124
|
+
# ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
|
125
|
+
# Corresponds to the JSON property `ncbiTaxonId`
|
126
|
+
# @return [Fixnum]
|
127
|
+
attr_accessor :ncbi_taxon_id
|
128
|
+
|
129
|
+
# The URI from which the sequence was obtained. Typically specifies a FASTA
|
130
|
+
# format file.
|
131
|
+
# Corresponds to the JSON property `sourceUri`
|
132
|
+
# @return [String]
|
133
|
+
attr_accessor :source_uri
|
134
|
+
|
135
|
+
# The name of this reference, for example `22`.
|
136
|
+
# Corresponds to the JSON property `name`
|
137
|
+
# @return [String]
|
138
|
+
attr_accessor :name
|
139
|
+
|
140
|
+
# MD5 of the upper-case sequence excluding all whitespace characters (this
|
141
|
+
# is equivalent to SQ:M5 in SAM). This value is represented in lower case
|
142
|
+
# hexadecimal format.
|
143
|
+
# Corresponds to the JSON property `md5checksum`
|
144
|
+
# @return [String]
|
145
|
+
attr_accessor :md5checksum
|
146
|
+
|
147
|
+
# The server-generated reference ID, unique across all references.
|
148
|
+
# Corresponds to the JSON property `id`
|
149
|
+
# @return [String]
|
150
|
+
attr_accessor :id
|
151
|
+
|
152
|
+
# The length of this reference's sequence.
|
153
|
+
# Corresponds to the JSON property `length`
|
154
|
+
# @return [String]
|
155
|
+
attr_accessor :length
|
156
|
+
|
157
|
+
# All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
158
|
+
# with a version number, for example `GCF_000001405.26`.
|
159
|
+
# Corresponds to the JSON property `sourceAccessions`
|
160
|
+
# @return [Array<String>]
|
161
|
+
attr_accessor :source_accessions
|
162
|
+
|
163
|
+
def initialize(**args)
|
164
|
+
update!(**args)
|
165
|
+
end
|
166
|
+
|
167
|
+
# Update properties of this object
|
168
|
+
def update!(**args)
|
169
|
+
@ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
|
170
|
+
@source_uri = args[:source_uri] if args.key?(:source_uri)
|
171
|
+
@name = args[:name] if args.key?(:name)
|
172
|
+
@md5checksum = args[:md5checksum] if args.key?(:md5checksum)
|
173
|
+
@id = args[:id] if args.key?(:id)
|
174
|
+
@length = args[:length] if args.key?(:length)
|
175
|
+
@source_accessions = args[:source_accessions] if args.key?(:source_accessions)
|
176
|
+
end
|
177
|
+
end
|
178
|
+
|
179
|
+
# Metadata describes a single piece of variant call metadata.
|
180
|
+
# These data include a top level key and either a single value string (value)
|
181
|
+
# or a list of key-value pairs (info.)
|
182
|
+
# Value and info are mutually exclusive.
|
183
|
+
class VariantSetMetadata
|
184
|
+
include Google::Apis::Core::Hashable
|
185
|
+
|
186
|
+
# The number of values that can be included in a field described by this
|
187
|
+
# metadata.
|
188
|
+
# Corresponds to the JSON property `number`
|
189
|
+
# @return [String]
|
190
|
+
attr_accessor :number
|
191
|
+
|
192
|
+
# User-provided ID field, not enforced by this API.
|
193
|
+
# Two or more pieces of structured metadata with identical
|
194
|
+
# id and key fields are considered equivalent.
|
195
|
+
# Corresponds to the JSON property `id`
|
196
|
+
# @return [String]
|
197
|
+
attr_accessor :id
|
198
|
+
|
199
|
+
# The value field for simple metadata
|
200
|
+
# Corresponds to the JSON property `value`
|
201
|
+
# @return [String]
|
202
|
+
attr_accessor :value
|
203
|
+
|
204
|
+
# The top-level key.
|
205
|
+
# Corresponds to the JSON property `key`
|
206
|
+
# @return [String]
|
207
|
+
attr_accessor :key
|
208
|
+
|
209
|
+
# A textual description of this metadata.
|
210
|
+
# Corresponds to the JSON property `description`
|
211
|
+
# @return [String]
|
212
|
+
attr_accessor :description
|
213
|
+
|
214
|
+
# Remaining structured metadata key-value pairs. This must be of the form
|
215
|
+
# map<string, string[]> (string key mapping to a list of string values).
|
216
|
+
# Corresponds to the JSON property `info`
|
217
|
+
# @return [Hash<String,Array<Object>>]
|
218
|
+
attr_accessor :info
|
219
|
+
|
220
|
+
# The type of data. Possible types include: Integer, Float,
|
221
|
+
# Flag, Character, and String.
|
222
|
+
# Corresponds to the JSON property `type`
|
223
|
+
# @return [String]
|
224
|
+
attr_accessor :type
|
225
|
+
|
226
|
+
def initialize(**args)
|
227
|
+
update!(**args)
|
228
|
+
end
|
229
|
+
|
230
|
+
# Update properties of this object
|
231
|
+
def update!(**args)
|
232
|
+
@number = args[:number] if args.key?(:number)
|
233
|
+
@id = args[:id] if args.key?(:id)
|
234
|
+
@value = args[:value] if args.key?(:value)
|
235
|
+
@key = args[:key] if args.key?(:key)
|
236
|
+
@description = args[:description] if args.key?(:description)
|
237
|
+
@info = args[:info] if args.key?(:info)
|
238
|
+
@type = args[:type] if args.key?(:type)
|
239
|
+
end
|
240
|
+
end
|
241
|
+
|
242
|
+
# The search variant sets request.
|
243
|
+
class SearchVariantSetsRequest
|
244
|
+
include Google::Apis::Core::Hashable
|
245
|
+
|
246
|
+
# Exactly one dataset ID must be provided here. Only variant sets which
|
247
|
+
# belong to this dataset will be returned.
|
248
|
+
# Corresponds to the JSON property `datasetIds`
|
249
|
+
# @return [Array<String>]
|
250
|
+
attr_accessor :dataset_ids
|
251
|
+
|
252
|
+
# The continuation token, which is used to page through large result sets.
|
253
|
+
# To get the next page of results, set this parameter to the value of
|
254
|
+
# `nextPageToken` from the previous response.
|
255
|
+
# Corresponds to the JSON property `pageToken`
|
256
|
+
# @return [String]
|
257
|
+
attr_accessor :page_token
|
258
|
+
|
259
|
+
# The maximum number of results to return in a single page. If unspecified,
|
260
|
+
# defaults to 1024.
|
261
|
+
# Corresponds to the JSON property `pageSize`
|
262
|
+
# @return [Fixnum]
|
263
|
+
attr_accessor :page_size
|
264
|
+
|
265
|
+
def initialize(**args)
|
266
|
+
update!(**args)
|
267
|
+
end
|
268
|
+
|
269
|
+
# Update properties of this object
|
270
|
+
def update!(**args)
|
271
|
+
@dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
|
272
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
273
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
274
|
+
end
|
275
|
+
end
|
276
|
+
|
277
|
+
#
|
278
|
+
class SearchReferenceSetsRequest
|
279
|
+
include Google::Apis::Core::Hashable
|
280
|
+
|
281
|
+
# If present, return reference sets for which a substring of their
|
282
|
+
# `assemblyId` matches this string (case insensitive).
|
283
|
+
# Corresponds to the JSON property `assemblyId`
|
284
|
+
# @return [String]
|
285
|
+
attr_accessor :assembly_id
|
286
|
+
|
287
|
+
# If present, return reference sets for which the
|
288
|
+
# md5checksum matches exactly.
|
289
|
+
# Corresponds to the JSON property `md5checksums`
|
290
|
+
# @return [Array<String>]
|
291
|
+
attr_accessor :md5checksums
|
292
|
+
|
293
|
+
# If present, return reference sets for which a prefix of any of
|
294
|
+
# sourceAccessions
|
295
|
+
# match any of these strings. Accession numbers typically have a main number
|
296
|
+
# and a version, for example `NC_000001.11`.
|
297
|
+
# Corresponds to the JSON property `accessions`
|
298
|
+
# @return [Array<String>]
|
299
|
+
attr_accessor :accessions
|
300
|
+
|
301
|
+
# The continuation token, which is used to page through large result sets.
|
302
|
+
# To get the next page of results, set this parameter to the value of
|
303
|
+
# `nextPageToken` from the previous response.
|
304
|
+
# Corresponds to the JSON property `pageToken`
|
305
|
+
# @return [String]
|
306
|
+
attr_accessor :page_token
|
307
|
+
|
308
|
+
# The maximum number of results to return in a single page. If unspecified,
|
309
|
+
# defaults to 1024. The maximum value is 4096.
|
310
|
+
# Corresponds to the JSON property `pageSize`
|
311
|
+
# @return [Fixnum]
|
312
|
+
attr_accessor :page_size
|
313
|
+
|
314
|
+
def initialize(**args)
|
315
|
+
update!(**args)
|
316
|
+
end
|
317
|
+
|
318
|
+
# Update properties of this object
|
319
|
+
def update!(**args)
|
320
|
+
@assembly_id = args[:assembly_id] if args.key?(:assembly_id)
|
321
|
+
@md5checksums = args[:md5checksums] if args.key?(:md5checksums)
|
322
|
+
@accessions = args[:accessions] if args.key?(:accessions)
|
323
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
324
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
325
|
+
end
|
326
|
+
end
|
327
|
+
|
328
|
+
# Request message for `SetIamPolicy` method.
|
329
|
+
class SetIamPolicyRequest
|
330
|
+
include Google::Apis::Core::Hashable
|
331
|
+
|
332
|
+
# Defines an Identity and Access Management (IAM) policy. It is used to
|
333
|
+
# specify access control policies for Cloud Platform resources.
|
334
|
+
# A `Policy` consists of a list of `bindings`. A `Binding` binds a list of
|
335
|
+
# `members` to a `role`, where the members can be user accounts, Google groups,
|
336
|
+
# Google domains, and service accounts. A `role` is a named list of permissions
|
337
|
+
# defined by IAM.
|
338
|
+
# **Example**
|
339
|
+
# `
|
340
|
+
# "bindings": [
|
341
|
+
# `
|
342
|
+
# "role": "roles/owner",
|
343
|
+
# "members": [
|
344
|
+
# "user:mike@example.com",
|
345
|
+
# "group:admins@example.com",
|
346
|
+
# "domain:google.com",
|
347
|
+
# "serviceAccount:my-other-app@appspot.gserviceaccount.com",
|
348
|
+
# ]
|
349
|
+
# `,
|
350
|
+
# `
|
351
|
+
# "role": "roles/viewer",
|
352
|
+
# "members": ["user:sean@example.com"]
|
353
|
+
# `
|
354
|
+
# ]
|
355
|
+
# `
|
356
|
+
# For a description of IAM and its features, see the
|
357
|
+
# [IAM developer's guide](https://cloud.google.com/iam).
|
358
|
+
# Corresponds to the JSON property `policy`
|
359
|
+
# @return [Google::Apis::GenomicsV1::Policy]
|
360
|
+
attr_accessor :policy
|
361
|
+
|
362
|
+
def initialize(**args)
|
363
|
+
update!(**args)
|
364
|
+
end
|
365
|
+
|
366
|
+
# Update properties of this object
|
367
|
+
def update!(**args)
|
368
|
+
@policy = args[:policy] if args.key?(:policy)
|
369
|
+
end
|
370
|
+
end
|
371
|
+
|
372
|
+
#
|
373
|
+
class MergeVariantsRequest
|
374
|
+
include Google::Apis::Core::Hashable
|
375
|
+
|
376
|
+
# A mapping between info field keys and the InfoMergeOperations to
|
377
|
+
# be performed on them.
|
378
|
+
# Corresponds to the JSON property `infoMergeConfig`
|
379
|
+
# @return [Hash<String,String>]
|
380
|
+
attr_accessor :info_merge_config
|
381
|
+
|
382
|
+
# The destination variant set.
|
383
|
+
# Corresponds to the JSON property `variantSetId`
|
384
|
+
# @return [String]
|
385
|
+
attr_accessor :variant_set_id
|
386
|
+
|
387
|
+
# The variants to be merged with existing variants.
|
388
|
+
# Corresponds to the JSON property `variants`
|
389
|
+
# @return [Array<Google::Apis::GenomicsV1::Variant>]
|
390
|
+
attr_accessor :variants
|
391
|
+
|
392
|
+
def initialize(**args)
|
393
|
+
update!(**args)
|
394
|
+
end
|
395
|
+
|
396
|
+
# Update properties of this object
|
397
|
+
def update!(**args)
|
398
|
+
@info_merge_config = args[:info_merge_config] if args.key?(:info_merge_config)
|
399
|
+
@variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
|
400
|
+
@variants = args[:variants] if args.key?(:variants)
|
401
|
+
end
|
402
|
+
end
|
403
|
+
|
404
|
+
#
|
405
|
+
class BatchCreateAnnotationsRequest
|
406
|
+
include Google::Apis::Core::Hashable
|
407
|
+
|
408
|
+
# The annotations to be created. At most 4096 can be specified in a single
|
409
|
+
# request.
|
410
|
+
# Corresponds to the JSON property `annotations`
|
411
|
+
# @return [Array<Google::Apis::GenomicsV1::Annotation>]
|
412
|
+
attr_accessor :annotations
|
413
|
+
|
414
|
+
# A unique request ID which enables the server to detect duplicated requests.
|
415
|
+
# If provided, duplicated requests will result in the same response; if not
|
416
|
+
# provided, duplicated requests may result in duplicated data. For a given
|
417
|
+
# annotation set, callers should not reuse `request_id`s when writing
|
418
|
+
# different batches of annotations - behavior in this case is undefined.
|
419
|
+
# A common approach is to use a UUID. For batch jobs where worker crashes are
|
420
|
+
# a possibility, consider using some unique variant of a worker or run ID.
|
421
|
+
# Corresponds to the JSON property `requestId`
|
422
|
+
# @return [String]
|
423
|
+
attr_accessor :request_id
|
424
|
+
|
425
|
+
def initialize(**args)
|
426
|
+
update!(**args)
|
427
|
+
end
|
428
|
+
|
429
|
+
# Update properties of this object
|
430
|
+
def update!(**args)
|
431
|
+
@annotations = args[:annotations] if args.key?(:annotations)
|
432
|
+
@request_id = args[:request_id] if args.key?(:request_id)
|
433
|
+
end
|
434
|
+
end
|
435
|
+
|
436
|
+
# A read alignment describes a linear alignment of a string of DNA to a
|
437
|
+
# reference sequence, in addition to metadata
|
438
|
+
# about the fragment (the molecule of DNA sequenced) and the read (the bases
|
439
|
+
# which were read by the sequencer). A read is equivalent to a line in a SAM
|
440
|
+
# file. A read belongs to exactly one read group and exactly one
|
441
|
+
# read group set.
|
442
|
+
# For more genomics resource definitions, see [Fundamentals of Google
|
443
|
+
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
444
|
+
# ### Reverse-stranded reads
|
445
|
+
# Mapped reads (reads having a non-null `alignment`) can be aligned to either
|
446
|
+
# the forward or the reverse strand of their associated reference. Strandedness
|
447
|
+
# of a mapped read is encoded by `alignment.position.reverseStrand`.
|
448
|
+
# If we consider the reference to be a forward-stranded coordinate space of
|
449
|
+
# `[0, reference.length)` with `0` as the left-most position and
|
450
|
+
# `reference.length` as the right-most position, reads are always aligned left
|
451
|
+
# to right. That is, `alignment.position.position` always refers to the
|
452
|
+
# left-most reference coordinate and `alignment.cigar` describes the alignment
|
453
|
+
# of this read to the reference from left to right. All per-base fields such as
|
454
|
+
# `alignedSequence` and `alignedQuality` share this same left-to-right
|
455
|
+
# orientation; this is true of reads which are aligned to either strand. For
|
456
|
+
# reverse-stranded reads, this means that `alignedSequence` is the reverse
|
457
|
+
# complement of the bases that were originally reported by the sequencing
|
458
|
+
# machine.
|
459
|
+
# ### Generating a reference-aligned sequence string
|
460
|
+
# When interacting with mapped reads, it's often useful to produce a string
|
461
|
+
# representing the local alignment of the read to reference. The following
|
462
|
+
# pseudocode demonstrates one way of doing this:
|
463
|
+
# out = ""
|
464
|
+
# offset = 0
|
465
|
+
# for c in read.alignment.cigar `
|
466
|
+
# switch c.operation `
|
467
|
+
# case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH":
|
468
|
+
# out += read.alignedSequence[offset:offset+c.operationLength]
|
469
|
+
# offset += c.operationLength
|
470
|
+
# break
|
471
|
+
# case "CLIP_SOFT", "INSERT":
|
472
|
+
# offset += c.operationLength
|
473
|
+
# break
|
474
|
+
# case "PAD":
|
475
|
+
# out += repeat("*", c.operationLength)
|
476
|
+
# break
|
477
|
+
# case "DELETE":
|
478
|
+
# out += repeat("-", c.operationLength)
|
479
|
+
# break
|
480
|
+
# case "SKIP":
|
481
|
+
# out += repeat(" ", c.operationLength)
|
482
|
+
# break
|
483
|
+
# case "CLIP_HARD":
|
484
|
+
# break
|
485
|
+
# `
|
486
|
+
# `
|
487
|
+
# return out
|
488
|
+
# ### Converting to SAM's CIGAR string
|
489
|
+
# The following pseudocode generates a SAM CIGAR string from the
|
490
|
+
# `cigar` field. Note that this is a lossy conversion
|
491
|
+
# (`cigar.referenceSequence` is lost).
|
492
|
+
# cigarMap = `
|
493
|
+
# "ALIGNMENT_MATCH": "M",
|
494
|
+
# "INSERT": "I",
|
495
|
+
# "DELETE": "D",
|
496
|
+
# "SKIP": "N",
|
497
|
+
# "CLIP_SOFT": "S",
|
498
|
+
# "CLIP_HARD": "H",
|
499
|
+
# "PAD": "P",
|
500
|
+
# "SEQUENCE_MATCH": "=",
|
501
|
+
# "SEQUENCE_MISMATCH": "X",
|
502
|
+
# `
|
503
|
+
# cigarStr = ""
|
504
|
+
# for c in read.alignment.cigar `
|
505
|
+
# cigarStr += c.operationLength + cigarMap[c.operation]
|
506
|
+
# `
|
507
|
+
# return cigarStr
|
508
|
+
class Read
|
509
|
+
include Google::Apis::Core::Hashable
|
510
|
+
|
511
|
+
# The fragment is a PCR or optical duplicate (SAM flag 0x400).
|
512
|
+
# Corresponds to the JSON property `duplicateFragment`
|
513
|
+
# @return [Boolean]
|
514
|
+
attr_accessor :duplicate_fragment
|
515
|
+
alias_method :duplicate_fragment?, :duplicate_fragment
|
516
|
+
|
517
|
+
# The read number in sequencing. 0-based and less than numberReads. This
|
518
|
+
# field replaces SAM flag 0x40 and 0x80.
|
519
|
+
# Corresponds to the JSON property `readNumber`
|
520
|
+
# @return [Fixnum]
|
521
|
+
attr_accessor :read_number
|
522
|
+
|
523
|
+
# The ID of the read group this read belongs to. A read belongs to exactly
|
524
|
+
# one read group. This is a server-generated ID which is distinct from SAM's
|
525
|
+
# RG tag (for that value, see
|
526
|
+
# ReadGroup.name).
|
527
|
+
# Corresponds to the JSON property `readGroupId`
|
528
|
+
# @return [String]
|
529
|
+
attr_accessor :read_group_id
|
530
|
+
|
531
|
+
# The bases of the read sequence contained in this alignment record,
|
532
|
+
# **without CIGAR operations applied** (equivalent to SEQ in SAM).
|
533
|
+
# `alignedSequence` and `alignedQuality` may be
|
534
|
+
# shorter than the full read sequence and quality. This will occur if the
|
535
|
+
# alignment is part of a chimeric alignment, or if the read was trimmed. When
|
536
|
+
# this occurs, the CIGAR for this read will begin/end with a hard clip
|
537
|
+
# operator that will indicate the length of the excised sequence.
|
538
|
+
# Corresponds to the JSON property `alignedSequence`
|
539
|
+
# @return [String]
|
540
|
+
attr_accessor :aligned_sequence
|
541
|
+
|
542
|
+
# A map of additional read alignment information. This must be of the form
|
543
|
+
# map<string, string[]> (string key mapping to a list of string values).
|
544
|
+
# Corresponds to the JSON property `info`
|
545
|
+
# @return [Hash<String,Array<Object>>]
|
546
|
+
attr_accessor :info
|
547
|
+
|
548
|
+
# An abstraction for referring to a genomic position, in relation to some
|
549
|
+
# already known reference. For now, represents a genomic position as a
|
550
|
+
# reference name, a base number on that reference (0-based), and a
|
551
|
+
# determination of forward or reverse strand.
|
552
|
+
# Corresponds to the JSON property `nextMatePosition`
|
553
|
+
# @return [Google::Apis::GenomicsV1::Position]
|
554
|
+
attr_accessor :next_mate_position
|
555
|
+
|
556
|
+
# Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
|
557
|
+
# Supplementary alignments are used in the representation of a chimeric
|
558
|
+
# alignment. In a chimeric alignment, a read is split into multiple
|
559
|
+
# linear alignments that map to different reference contigs. The first
|
560
|
+
# linear alignment in the read will be designated as the representative
|
561
|
+
# alignment; the remaining linear alignments will be designated as
|
562
|
+
# supplementary alignments. These alignments may have different mapping
|
563
|
+
# quality scores. In each linear alignment in a chimeric alignment, the read
|
564
|
+
# will be hard clipped. The `alignedSequence` and
|
565
|
+
# `alignedQuality` fields in the alignment record will only
|
566
|
+
# represent the bases for its respective linear alignment.
|
567
|
+
# Corresponds to the JSON property `supplementaryAlignment`
|
568
|
+
# @return [Boolean]
|
569
|
+
attr_accessor :supplementary_alignment
|
570
|
+
alias_method :supplementary_alignment?, :supplementary_alignment
|
571
|
+
|
572
|
+
# The orientation and the distance between reads from the fragment are
|
573
|
+
# consistent with the sequencing protocol (SAM flag 0x2).
|
574
|
+
# Corresponds to the JSON property `properPlacement`
|
575
|
+
# @return [Boolean]
|
576
|
+
attr_accessor :proper_placement
|
577
|
+
alias_method :proper_placement?, :proper_placement
|
578
|
+
|
579
|
+
# The observed length of the fragment, equivalent to TLEN in SAM.
|
580
|
+
# Corresponds to the JSON property `fragmentLength`
|
581
|
+
# @return [Fixnum]
|
582
|
+
attr_accessor :fragment_length
|
583
|
+
|
584
|
+
# Whether this read did not pass filters, such as platform or vendor quality
|
585
|
+
# controls (SAM flag 0x200).
|
586
|
+
# Corresponds to the JSON property `failedVendorQualityChecks`
|
587
|
+
# @return [Boolean]
|
588
|
+
attr_accessor :failed_vendor_quality_checks
|
589
|
+
alias_method :failed_vendor_quality_checks?, :failed_vendor_quality_checks
|
590
|
+
|
591
|
+
# The quality of the read sequence contained in this alignment record
|
592
|
+
# (equivalent to QUAL in SAM).
|
593
|
+
# `alignedSequence` and `alignedQuality` may be shorter than the full read
|
594
|
+
# sequence and quality. This will occur if the alignment is part of a
|
595
|
+
# chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
|
596
|
+
# for this read will begin/end with a hard clip operator that will indicate
|
597
|
+
# the length of the excised sequence.
|
598
|
+
# Corresponds to the JSON property `alignedQuality`
|
599
|
+
# @return [Array<Fixnum>]
|
600
|
+
attr_accessor :aligned_quality
|
601
|
+
|
602
|
+
# A linear alignment can be represented by one CIGAR string. Describes the
|
603
|
+
# mapped position and local alignment of the read to the reference.
|
604
|
+
# Corresponds to the JSON property `alignment`
|
605
|
+
# @return [Google::Apis::GenomicsV1::LinearAlignment]
|
606
|
+
attr_accessor :alignment
|
607
|
+
|
608
|
+
# The number of reads in the fragment (extension to SAM flag 0x1).
|
609
|
+
# Corresponds to the JSON property `numberReads`
|
610
|
+
# @return [Fixnum]
|
611
|
+
attr_accessor :number_reads
|
612
|
+
|
613
|
+
# The server-generated read ID, unique across all reads. This is different
|
614
|
+
# from the `fragmentName`.
|
615
|
+
# Corresponds to the JSON property `id`
|
616
|
+
# @return [String]
|
617
|
+
attr_accessor :id
|
618
|
+
|
619
|
+
# Whether this alignment is secondary. Equivalent to SAM flag 0x100.
|
620
|
+
# A secondary alignment represents an alternative to the primary alignment
|
621
|
+
# for this read. Aligners may return secondary alignments if a read can map
|
622
|
+
# ambiguously to multiple coordinates in the genome. By convention, each read
|
623
|
+
# has one and only one alignment where both `secondaryAlignment`
|
624
|
+
# and `supplementaryAlignment` are false.
|
625
|
+
# Corresponds to the JSON property `secondaryAlignment`
|
626
|
+
# @return [Boolean]
|
627
|
+
attr_accessor :secondary_alignment
|
628
|
+
alias_method :secondary_alignment?, :secondary_alignment
|
629
|
+
|
630
|
+
# The fragment name. Equivalent to QNAME (query template name) in SAM.
|
631
|
+
# Corresponds to the JSON property `fragmentName`
|
632
|
+
# @return [String]
|
633
|
+
attr_accessor :fragment_name
|
634
|
+
|
635
|
+
# The ID of the read group set this read belongs to. A read belongs to
|
636
|
+
# exactly one read group set.
|
637
|
+
# Corresponds to the JSON property `readGroupSetId`
|
638
|
+
# @return [String]
|
639
|
+
attr_accessor :read_group_set_id
|
640
|
+
|
641
|
+
def initialize(**args)
|
642
|
+
update!(**args)
|
643
|
+
end
|
644
|
+
|
645
|
+
# Update properties of this object
|
646
|
+
def update!(**args)
|
647
|
+
@duplicate_fragment = args[:duplicate_fragment] if args.key?(:duplicate_fragment)
|
648
|
+
@read_number = args[:read_number] if args.key?(:read_number)
|
649
|
+
@read_group_id = args[:read_group_id] if args.key?(:read_group_id)
|
650
|
+
@aligned_sequence = args[:aligned_sequence] if args.key?(:aligned_sequence)
|
651
|
+
@info = args[:info] if args.key?(:info)
|
652
|
+
@next_mate_position = args[:next_mate_position] if args.key?(:next_mate_position)
|
653
|
+
@supplementary_alignment = args[:supplementary_alignment] if args.key?(:supplementary_alignment)
|
654
|
+
@proper_placement = args[:proper_placement] if args.key?(:proper_placement)
|
655
|
+
@fragment_length = args[:fragment_length] if args.key?(:fragment_length)
|
656
|
+
@failed_vendor_quality_checks = args[:failed_vendor_quality_checks] if args.key?(:failed_vendor_quality_checks)
|
657
|
+
@aligned_quality = args[:aligned_quality] if args.key?(:aligned_quality)
|
658
|
+
@alignment = args[:alignment] if args.key?(:alignment)
|
659
|
+
@number_reads = args[:number_reads] if args.key?(:number_reads)
|
660
|
+
@id = args[:id] if args.key?(:id)
|
661
|
+
@secondary_alignment = args[:secondary_alignment] if args.key?(:secondary_alignment)
|
662
|
+
@fragment_name = args[:fragment_name] if args.key?(:fragment_name)
|
663
|
+
@read_group_set_id = args[:read_group_set_id] if args.key?(:read_group_set_id)
|
664
|
+
end
|
665
|
+
end
|
666
|
+
|
667
|
+
# A reference set is a set of references which typically comprise a reference
|
668
|
+
# assembly for a species, such as `GRCh38` which is representative
|
669
|
+
# of the human genome. A reference set defines a common coordinate space for
|
670
|
+
# comparing reference-aligned experimental data. A reference set contains 1 or
|
671
|
+
# more references.
|
672
|
+
# For more genomics resource definitions, see [Fundamentals of Google
|
673
|
+
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
674
|
+
class ReferenceSet
|
675
|
+
include Google::Apis::Core::Hashable
|
676
|
+
|
677
|
+
# All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
678
|
+
# with a version number, for example `NC_000001.11`.
|
679
|
+
# Corresponds to the JSON property `sourceAccessions`
|
680
|
+
# @return [Array<String>]
|
681
|
+
attr_accessor :source_accessions
|
682
|
+
|
683
|
+
# Free text description of this reference set.
|
684
|
+
# Corresponds to the JSON property `description`
|
685
|
+
# @return [String]
|
686
|
+
attr_accessor :description
|
687
|
+
|
688
|
+
# The URI from which the references were obtained.
|
689
|
+
# Corresponds to the JSON property `sourceUri`
|
690
|
+
# @return [String]
|
691
|
+
attr_accessor :source_uri
|
692
|
+
|
693
|
+
# ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
|
694
|
+
# indicating the species which this reference set is intended to model. Note
|
695
|
+
# that contained references may specify a different `ncbiTaxonId`, as
|
696
|
+
# assemblies may contain reference sequences which do not belong to the
|
697
|
+
# modeled species, for example EBV in a human reference genome.
|
698
|
+
# Corresponds to the JSON property `ncbiTaxonId`
|
699
|
+
# @return [Fixnum]
|
700
|
+
attr_accessor :ncbi_taxon_id
|
701
|
+
|
702
|
+
# The IDs of the reference objects that are part of this set.
|
703
|
+
# `Reference.md5checksum` must be unique within this set.
|
704
|
+
# Corresponds to the JSON property `referenceIds`
|
705
|
+
# @return [Array<String>]
|
706
|
+
attr_accessor :reference_ids
|
707
|
+
|
708
|
+
# Public id of this reference set, such as `GRCh37`.
|
709
|
+
# Corresponds to the JSON property `assemblyId`
|
710
|
+
# @return [String]
|
711
|
+
attr_accessor :assembly_id
|
712
|
+
|
713
|
+
# Order-independent MD5 checksum which identifies this reference set. The
|
714
|
+
# checksum is computed by sorting all lower case hexidecimal string
|
715
|
+
# `reference.md5checksum` (for all reference in this set) in
|
716
|
+
# ascending lexicographic order, concatenating, and taking the MD5 of that
|
717
|
+
# value. The resulting value is represented in lower case hexadecimal format.
|
718
|
+
# Corresponds to the JSON property `md5checksum`
|
719
|
+
# @return [String]
|
720
|
+
attr_accessor :md5checksum
|
721
|
+
|
722
|
+
# The server-generated reference set ID, unique across all reference sets.
|
723
|
+
# Corresponds to the JSON property `id`
|
724
|
+
# @return [String]
|
725
|
+
attr_accessor :id
|
726
|
+
|
727
|
+
def initialize(**args)
|
728
|
+
update!(**args)
|
729
|
+
end
|
730
|
+
|
731
|
+
# Update properties of this object
|
732
|
+
def update!(**args)
|
733
|
+
@source_accessions = args[:source_accessions] if args.key?(:source_accessions)
|
734
|
+
@description = args[:description] if args.key?(:description)
|
735
|
+
@source_uri = args[:source_uri] if args.key?(:source_uri)
|
736
|
+
@ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
|
737
|
+
@reference_ids = args[:reference_ids] if args.key?(:reference_ids)
|
738
|
+
@assembly_id = args[:assembly_id] if args.key?(:assembly_id)
|
739
|
+
@md5checksum = args[:md5checksum] if args.key?(:md5checksum)
|
740
|
+
@id = args[:id] if args.key?(:id)
|
741
|
+
end
|
742
|
+
end
|
743
|
+
|
744
|
+
# A single CIGAR operation.
|
745
|
+
class CigarUnit
|
746
|
+
include Google::Apis::Core::Hashable
|
747
|
+
|
748
|
+
# `referenceSequence` is only used at mismatches
|
749
|
+
# (`SEQUENCE_MISMATCH`) and deletions (`DELETE`).
|
750
|
+
# Filling this field replaces SAM's MD tag. If the relevant information is
|
751
|
+
# not available, this field is unset.
|
752
|
+
# Corresponds to the JSON property `referenceSequence`
|
753
|
+
# @return [String]
|
754
|
+
attr_accessor :reference_sequence
|
755
|
+
|
756
|
+
# The number of genomic bases that the operation runs for. Required.
|
757
|
+
# Corresponds to the JSON property `operationLength`
|
758
|
+
# @return [String]
|
759
|
+
attr_accessor :operation_length
|
760
|
+
|
761
|
+
#
|
762
|
+
# Corresponds to the JSON property `operation`
|
763
|
+
# @return [String]
|
764
|
+
attr_accessor :operation
|
765
|
+
|
766
|
+
def initialize(**args)
|
767
|
+
update!(**args)
|
768
|
+
end
|
769
|
+
|
770
|
+
# Update properties of this object
|
771
|
+
def update!(**args)
|
772
|
+
@reference_sequence = args[:reference_sequence] if args.key?(:reference_sequence)
|
773
|
+
@operation_length = args[:operation_length] if args.key?(:operation_length)
|
774
|
+
@operation = args[:operation] if args.key?(:operation)
|
775
|
+
end
|
776
|
+
end
|
777
|
+
|
778
|
+
# An annotation set is a logical grouping of annotations that share consistent
|
779
|
+
# type information and provenance. Examples of annotation sets include 'all
|
780
|
+
# genes from refseq', and 'all variant annotations from ClinVar'.
|
781
|
+
class AnnotationSet
|
782
|
+
include Google::Apis::Core::Hashable
|
783
|
+
|
784
|
+
# The dataset to which this annotation set belongs.
|
785
|
+
# Corresponds to the JSON property `datasetId`
|
786
|
+
# @return [String]
|
787
|
+
attr_accessor :dataset_id
|
788
|
+
|
789
|
+
# The source URI describing the file from which this annotation set was
|
790
|
+
# generated, if any.
|
791
|
+
# Corresponds to the JSON property `sourceUri`
|
792
|
+
# @return [String]
|
793
|
+
attr_accessor :source_uri
|
794
|
+
|
795
|
+
# The display name for this annotation set.
|
796
|
+
# Corresponds to the JSON property `name`
|
797
|
+
# @return [String]
|
798
|
+
attr_accessor :name
|
799
|
+
|
800
|
+
# The ID of the reference set that defines the coordinate space for this
|
801
|
+
# set's annotations.
|
802
|
+
# Corresponds to the JSON property `referenceSetId`
|
803
|
+
# @return [String]
|
804
|
+
attr_accessor :reference_set_id
|
805
|
+
|
806
|
+
# A map of additional read alignment information. This must be of the form
|
807
|
+
# map<string, string[]> (string key mapping to a list of string values).
|
808
|
+
# Corresponds to the JSON property `info`
|
809
|
+
# @return [Hash<String,Array<Object>>]
|
810
|
+
attr_accessor :info
|
811
|
+
|
812
|
+
# The type of annotations contained within this set.
|
813
|
+
# Corresponds to the JSON property `type`
|
814
|
+
# @return [String]
|
815
|
+
attr_accessor :type
|
816
|
+
|
817
|
+
# The server-generated annotation set ID, unique across all annotation sets.
|
818
|
+
# Corresponds to the JSON property `id`
|
819
|
+
# @return [String]
|
820
|
+
attr_accessor :id
|
821
|
+
|
822
|
+
def initialize(**args)
|
823
|
+
update!(**args)
|
824
|
+
end
|
825
|
+
|
826
|
+
# Update properties of this object
|
827
|
+
def update!(**args)
|
828
|
+
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
829
|
+
@source_uri = args[:source_uri] if args.key?(:source_uri)
|
830
|
+
@name = args[:name] if args.key?(:name)
|
831
|
+
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
832
|
+
@info = args[:info] if args.key?(:info)
|
833
|
+
@type = args[:type] if args.key?(:type)
|
834
|
+
@id = args[:id] if args.key?(:id)
|
835
|
+
end
|
836
|
+
end
|
837
|
+
|
838
|
+
# A transcript represents the assertion that a particular region of the
|
839
|
+
# reference genome may be transcribed as RNA.
|
840
|
+
class Transcript
|
841
|
+
include Google::Apis::Core::Hashable
|
842
|
+
|
843
|
+
# The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose
|
844
|
+
# this transcript. This field should be unset for genomes where transcript
|
845
|
+
# splicing does not occur, for example prokaryotes.
|
846
|
+
# Introns are regions of the transcript that are not included in the
|
847
|
+
# spliced RNA product. Though not explicitly modeled here, intron ranges can
|
848
|
+
# be deduced; all regions of this transcript that are not exons are introns.
|
849
|
+
# Exonic sequences do not necessarily code for a translational product
|
850
|
+
# (amino acids). Only the regions of exons bounded by the
|
851
|
+
# codingSequence correspond
|
852
|
+
# to coding DNA sequence.
|
853
|
+
# Exons are ordered by start position and may not overlap.
|
854
|
+
# Corresponds to the JSON property `exons`
|
855
|
+
# @return [Array<Google::Apis::GenomicsV1::Exon>]
|
856
|
+
attr_accessor :exons
|
857
|
+
|
858
|
+
# The range of the coding sequence for this transcript, if any. To determine
|
859
|
+
# the exact ranges of coding sequence, intersect this range with those of the
|
860
|
+
# exons, if any. If there are any
|
861
|
+
# exons, the
|
862
|
+
# codingSequence must start
|
863
|
+
# and end within them.
|
864
|
+
# Note that in some cases, the reference genome will not exactly match the
|
865
|
+
# observed mRNA transcript e.g. due to variance in the source genome from
|
866
|
+
# reference. In these cases,
|
867
|
+
# exon.frame will not necessarily
|
868
|
+
# match the expected reference reading frame and coding exon reference bases
|
869
|
+
# cannot necessarily be concatenated to produce the original transcript mRNA.
|
870
|
+
# Corresponds to the JSON property `codingSequence`
|
871
|
+
# @return [Google::Apis::GenomicsV1::CodingSequence]
|
872
|
+
attr_accessor :coding_sequence
|
873
|
+
|
874
|
+
# The annotation ID of the gene from which this transcript is transcribed.
|
875
|
+
# Corresponds to the JSON property `geneId`
|
876
|
+
# @return [String]
|
877
|
+
attr_accessor :gene_id
|
878
|
+
|
879
|
+
def initialize(**args)
|
880
|
+
update!(**args)
|
881
|
+
end
|
882
|
+
|
883
|
+
# Update properties of this object
|
884
|
+
def update!(**args)
|
885
|
+
@exons = args[:exons] if args.key?(:exons)
|
886
|
+
@coding_sequence = args[:coding_sequence] if args.key?(:coding_sequence)
|
887
|
+
@gene_id = args[:gene_id] if args.key?(:gene_id)
|
888
|
+
end
|
889
|
+
end
|
890
|
+
|
891
|
+
#
|
892
|
+
class Experiment
|
893
|
+
include Google::Apis::Core::Hashable
|
894
|
+
|
895
|
+
# The platform unit used as part of this experiment, for example
|
896
|
+
# flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
|
897
|
+
# @RG PU field in the SAM spec.
|
898
|
+
# Corresponds to the JSON property `platformUnit`
|
899
|
+
# @return [String]
|
900
|
+
attr_accessor :platform_unit
|
901
|
+
|
902
|
+
# A client-supplied library identifier; a library is a collection of DNA
|
903
|
+
# fragments which have been prepared for sequencing from a sample. This
|
904
|
+
# field is important for quality control as error or bias can be introduced
|
905
|
+
# during sample preparation.
|
906
|
+
# Corresponds to the JSON property `libraryId`
|
907
|
+
# @return [String]
|
908
|
+
attr_accessor :library_id
|
909
|
+
|
910
|
+
# The instrument model used as part of this experiment. This maps to
|
911
|
+
# sequencing technology in the SAM spec.
|
912
|
+
# Corresponds to the JSON property `instrumentModel`
|
913
|
+
# @return [String]
|
914
|
+
attr_accessor :instrument_model
|
915
|
+
|
916
|
+
# The sequencing center used as part of this experiment.
|
917
|
+
# Corresponds to the JSON property `sequencingCenter`
|
918
|
+
# @return [String]
|
919
|
+
attr_accessor :sequencing_center
|
920
|
+
|
921
|
+
def initialize(**args)
|
922
|
+
update!(**args)
|
923
|
+
end
|
924
|
+
|
925
|
+
# Update properties of this object
|
926
|
+
def update!(**args)
|
927
|
+
@platform_unit = args[:platform_unit] if args.key?(:platform_unit)
|
928
|
+
@library_id = args[:library_id] if args.key?(:library_id)
|
929
|
+
@instrument_model = args[:instrument_model] if args.key?(:instrument_model)
|
930
|
+
@sequencing_center = args[:sequencing_center] if args.key?(:sequencing_center)
|
931
|
+
end
|
932
|
+
end
|
933
|
+
|
934
|
+
# The dataset list response.
|
935
|
+
class ListDatasetsResponse
|
936
|
+
include Google::Apis::Core::Hashable
|
937
|
+
|
938
|
+
# The list of matching Datasets.
|
939
|
+
# Corresponds to the JSON property `datasets`
|
940
|
+
# @return [Array<Google::Apis::GenomicsV1::Dataset>]
|
941
|
+
attr_accessor :datasets
|
942
|
+
|
943
|
+
# The continuation token, which is used to page through large result sets.
|
944
|
+
# Provide this value in a subsequent request to return the next page of
|
945
|
+
# results. This field will be empty if there aren't any additional results.
|
946
|
+
# Corresponds to the JSON property `nextPageToken`
|
947
|
+
# @return [String]
|
948
|
+
attr_accessor :next_page_token
|
949
|
+
|
950
|
+
def initialize(**args)
|
951
|
+
update!(**args)
|
952
|
+
end
|
953
|
+
|
954
|
+
# Update properties of this object
|
955
|
+
def update!(**args)
|
956
|
+
@datasets = args[:datasets] if args.key?(:datasets)
|
957
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
958
|
+
end
|
959
|
+
end
|
960
|
+
|
961
|
+
# Request message for `TestIamPermissions` method.
|
962
|
+
class TestIamPermissionsRequest
|
963
|
+
include Google::Apis::Core::Hashable
|
964
|
+
|
965
|
+
# REQUIRED: The set of permissions to check for the 'resource'.
|
966
|
+
# Permissions with wildcards (such as '*' or 'storage.*') are not allowed.
|
967
|
+
# Allowed permissions are:
|
968
|
+
# * `genomics.datasets.create`
|
969
|
+
# * `genomics.datasets.delete`
|
970
|
+
# * `genomics.datasets.get`
|
971
|
+
# * `genomics.datasets.list`
|
972
|
+
# * `genomics.datasets.update`
|
973
|
+
# * `genomics.datasets.getIamPolicy`
|
974
|
+
# * `genomics.datasets.setIamPolicy`
|
975
|
+
# Corresponds to the JSON property `permissions`
|
976
|
+
# @return [Array<String>]
|
977
|
+
attr_accessor :permissions
|
978
|
+
|
979
|
+
def initialize(**args)
|
980
|
+
update!(**args)
|
981
|
+
end
|
982
|
+
|
983
|
+
# Update properties of this object
|
984
|
+
def update!(**args)
|
985
|
+
@permissions = args[:permissions] if args.key?(:permissions)
|
986
|
+
end
|
987
|
+
end
|
988
|
+
|
989
|
+
# The read group set export request.
|
990
|
+
class ExportReadGroupSetRequest
|
991
|
+
include Google::Apis::Core::Hashable
|
992
|
+
|
993
|
+
# Required. A Google Cloud Storage URI for the exported BAM file.
|
994
|
+
# The currently authenticated user must have write access to the new file.
|
995
|
+
# An error will be returned if the URI already contains data.
|
996
|
+
# Corresponds to the JSON property `exportUri`
|
997
|
+
# @return [String]
|
998
|
+
attr_accessor :export_uri
|
999
|
+
|
1000
|
+
# The reference names to export. If this is not specified, all reference
|
1001
|
+
# sequences, including unmapped reads, are exported.
|
1002
|
+
# Use `*` to export only unmapped reads.
|
1003
|
+
# Corresponds to the JSON property `referenceNames`
|
1004
|
+
# @return [Array<String>]
|
1005
|
+
attr_accessor :reference_names
|
1006
|
+
|
1007
|
+
# Required. The Google Cloud project ID that owns this
|
1008
|
+
# export. The caller must have WRITE access to this project.
|
1009
|
+
# Corresponds to the JSON property `projectId`
|
1010
|
+
# @return [String]
|
1011
|
+
attr_accessor :project_id
|
1012
|
+
|
1013
|
+
def initialize(**args)
|
1014
|
+
update!(**args)
|
1015
|
+
end
|
1016
|
+
|
1017
|
+
# Update properties of this object
|
1018
|
+
def update!(**args)
|
1019
|
+
@export_uri = args[:export_uri] if args.key?(:export_uri)
|
1020
|
+
@reference_names = args[:reference_names] if args.key?(:reference_names)
|
1021
|
+
@project_id = args[:project_id] if args.key?(:project_id)
|
1022
|
+
end
|
1023
|
+
end
|
1024
|
+
|
1025
|
+
#
|
1026
|
+
class Exon
|
1027
|
+
include Google::Apis::Core::Hashable
|
1028
|
+
|
1029
|
+
# The start position of the exon on this annotation's reference sequence,
|
1030
|
+
# 0-based inclusive. Note that this is relative to the reference start, and
|
1031
|
+
# **not** the containing annotation start.
|
1032
|
+
# Corresponds to the JSON property `start`
|
1033
|
+
# @return [String]
|
1034
|
+
attr_accessor :start
|
1035
|
+
|
1036
|
+
# The end position of the exon on this annotation's reference sequence,
|
1037
|
+
# 0-based exclusive. Note that this is relative to the reference start, and
|
1038
|
+
# *not* the containing annotation start.
|
1039
|
+
# Corresponds to the JSON property `end`
|
1040
|
+
# @return [String]
|
1041
|
+
attr_accessor :end
|
1042
|
+
|
1043
|
+
# The frame of this exon. Contains a value of 0, 1, or 2, which indicates
|
1044
|
+
# the offset of the first coding base of the exon within the reading frame
|
1045
|
+
# of the coding DNA sequence, if any. This field is dependent on the
|
1046
|
+
# strandedness of this annotation (see
|
1047
|
+
# Annotation.reverse_strand).
|
1048
|
+
# For forward stranded annotations, this offset is relative to the
|
1049
|
+
# exon.start. For reverse
|
1050
|
+
# strand annotations, this offset is relative to the
|
1051
|
+
# exon.end `- 1`.
|
1052
|
+
# Unset if this exon does not intersect the coding sequence. Upon creation
|
1053
|
+
# of a transcript, the frame must be populated for all or none of the
|
1054
|
+
# coding exons.
|
1055
|
+
# Corresponds to the JSON property `frame`
|
1056
|
+
# @return [Fixnum]
|
1057
|
+
attr_accessor :frame
|
1058
|
+
|
1059
|
+
def initialize(**args)
|
1060
|
+
update!(**args)
|
1061
|
+
end
|
1062
|
+
|
1063
|
+
# Update properties of this object
|
1064
|
+
def update!(**args)
|
1065
|
+
@start = args[:start] if args.key?(:start)
|
1066
|
+
@end = args[:end] if args.key?(:end)
|
1067
|
+
@frame = args[:frame] if args.key?(:frame)
|
1068
|
+
end
|
1069
|
+
end
|
1070
|
+
|
1071
|
+
# A call set is a collection of variant calls, typically for one sample. It
|
1072
|
+
# belongs to a variant set.
|
1073
|
+
# For more genomics resource definitions, see [Fundamentals of Google
|
1074
|
+
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
1075
|
+
class CallSet
|
1076
|
+
include Google::Apis::Core::Hashable
|
1077
|
+
|
1078
|
+
# The date this call set was created in milliseconds from the epoch.
|
1079
|
+
# Corresponds to the JSON property `created`
|
1080
|
+
# @return [String]
|
1081
|
+
attr_accessor :created
|
1082
|
+
|
1083
|
+
# The sample ID this call set corresponds to.
|
1084
|
+
# Corresponds to the JSON property `sampleId`
|
1085
|
+
# @return [String]
|
1086
|
+
attr_accessor :sample_id
|
1087
|
+
|
1088
|
+
# The call set name.
|
1089
|
+
# Corresponds to the JSON property `name`
|
1090
|
+
# @return [String]
|
1091
|
+
attr_accessor :name
|
1092
|
+
|
1093
|
+
# A map of additional call set information. This must be of the form
|
1094
|
+
# map<string, string[]> (string key mapping to a list of string values).
|
1095
|
+
# Corresponds to the JSON property `info`
|
1096
|
+
# @return [Hash<String,Array<Object>>]
|
1097
|
+
attr_accessor :info
|
1098
|
+
|
1099
|
+
# The IDs of the variant sets this call set belongs to. This field must
|
1100
|
+
# have exactly length one, as a call set belongs to a single variant set.
|
1101
|
+
# This field is repeated for compatibility with the
|
1102
|
+
# [GA4GH 0.5.1
|
1103
|
+
# API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/
|
1104
|
+
# variants.avdl#L76).
|
1105
|
+
# Corresponds to the JSON property `variantSetIds`
|
1106
|
+
# @return [Array<String>]
|
1107
|
+
attr_accessor :variant_set_ids
|
1108
|
+
|
1109
|
+
# The server-generated call set ID, unique across all call sets.
|
1110
|
+
# Corresponds to the JSON property `id`
|
1111
|
+
# @return [String]
|
1112
|
+
attr_accessor :id
|
1113
|
+
|
1114
|
+
def initialize(**args)
|
1115
|
+
update!(**args)
|
1116
|
+
end
|
1117
|
+
|
1118
|
+
# Update properties of this object
|
1119
|
+
def update!(**args)
|
1120
|
+
@created = args[:created] if args.key?(:created)
|
1121
|
+
@sample_id = args[:sample_id] if args.key?(:sample_id)
|
1122
|
+
@name = args[:name] if args.key?(:name)
|
1123
|
+
@info = args[:info] if args.key?(:info)
|
1124
|
+
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
1125
|
+
@id = args[:id] if args.key?(:id)
|
1126
|
+
end
|
1127
|
+
end
|
1128
|
+
|
1129
|
+
#
|
1130
|
+
class SearchAnnotationSetsResponse
|
1131
|
+
include Google::Apis::Core::Hashable
|
1132
|
+
|
1133
|
+
# The matching annotation sets.
|
1134
|
+
# Corresponds to the JSON property `annotationSets`
|
1135
|
+
# @return [Array<Google::Apis::GenomicsV1::AnnotationSet>]
|
1136
|
+
attr_accessor :annotation_sets
|
1137
|
+
|
1138
|
+
# The continuation token, which is used to page through large result sets.
|
1139
|
+
# Provide this value in a subsequent request to return the next page of
|
1140
|
+
# results. This field will be empty if there aren't any additional results.
|
1141
|
+
# Corresponds to the JSON property `nextPageToken`
|
1142
|
+
# @return [String]
|
1143
|
+
attr_accessor :next_page_token
|
1144
|
+
|
1145
|
+
def initialize(**args)
|
1146
|
+
update!(**args)
|
1147
|
+
end
|
1148
|
+
|
1149
|
+
# Update properties of this object
|
1150
|
+
def update!(**args)
|
1151
|
+
@annotation_sets = args[:annotation_sets] if args.key?(:annotation_sets)
|
1152
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
1153
|
+
end
|
1154
|
+
end
|
1155
|
+
|
1156
|
+
# The variant data import request.
|
1157
|
+
class ImportVariantsRequest
|
1158
|
+
include Google::Apis::Core::Hashable
|
1159
|
+
|
1160
|
+
# A mapping between info field keys and the InfoMergeOperations to
|
1161
|
+
# be performed on them. This is plumbed down to the MergeVariantRequests
|
1162
|
+
# generated by the resulting import job.
|
1163
|
+
# Corresponds to the JSON property `infoMergeConfig`
|
1164
|
+
# @return [Hash<String,String>]
|
1165
|
+
attr_accessor :info_merge_config
|
1166
|
+
|
1167
|
+
# Required. The variant set to which variant data should be imported.
|
1168
|
+
# Corresponds to the JSON property `variantSetId`
|
1169
|
+
# @return [String]
|
1170
|
+
attr_accessor :variant_set_id
|
1171
|
+
|
1172
|
+
# A list of URIs referencing variant files in Google Cloud Storage. URIs can
|
1173
|
+
# include wildcards [as described
|
1174
|
+
# here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames).
|
1175
|
+
# Note that recursive wildcards ('**') are not supported.
|
1176
|
+
# Corresponds to the JSON property `sourceUris`
|
1177
|
+
# @return [Array<String>]
|
1178
|
+
attr_accessor :source_uris
|
1179
|
+
|
1180
|
+
# Convert reference names to the canonical representation.
|
1181
|
+
# hg19 haploytypes (those reference names containing "_hap")
|
1182
|
+
# are not modified in any way.
|
1183
|
+
# All other reference names are modified according to the following rules:
|
1184
|
+
# The reference name is capitalized.
|
1185
|
+
# The "chr" prefix is dropped for all autosomes and sex chromsomes.
|
1186
|
+
# For example "chr17" becomes "17" and "chrX" becomes "X".
|
1187
|
+
# All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
|
1188
|
+
# Corresponds to the JSON property `normalizeReferenceNames`
|
1189
|
+
# @return [Boolean]
|
1190
|
+
attr_accessor :normalize_reference_names
|
1191
|
+
alias_method :normalize_reference_names?, :normalize_reference_names
|
1192
|
+
|
1193
|
+
# The format of the variant data being imported. If unspecified, defaults to
|
1194
|
+
# to `VCF`.
|
1195
|
+
# Corresponds to the JSON property `format`
|
1196
|
+
# @return [String]
|
1197
|
+
attr_accessor :format
|
1198
|
+
|
1199
|
+
def initialize(**args)
|
1200
|
+
update!(**args)
|
1201
|
+
end
|
1202
|
+
|
1203
|
+
# Update properties of this object
|
1204
|
+
def update!(**args)
|
1205
|
+
@info_merge_config = args[:info_merge_config] if args.key?(:info_merge_config)
|
1206
|
+
@variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
|
1207
|
+
@source_uris = args[:source_uris] if args.key?(:source_uris)
|
1208
|
+
@normalize_reference_names = args[:normalize_reference_names] if args.key?(:normalize_reference_names)
|
1209
|
+
@format = args[:format] if args.key?(:format)
|
1210
|
+
end
|
1211
|
+
end
|
1212
|
+
|
1213
|
+
#
|
1214
|
+
class VariantAnnotation
|
1215
|
+
include Google::Apis::Core::Hashable
|
1216
|
+
|
1217
|
+
# The set of conditions associated with this variant.
|
1218
|
+
# A condition describes the way a variant influences human health.
|
1219
|
+
# Corresponds to the JSON property `conditions`
|
1220
|
+
# @return [Array<Google::Apis::GenomicsV1::ClinicalCondition>]
|
1221
|
+
attr_accessor :conditions
|
1222
|
+
|
1223
|
+
# Effect of the variant on the coding sequence.
|
1224
|
+
# Corresponds to the JSON property `effect`
|
1225
|
+
# @return [String]
|
1226
|
+
attr_accessor :effect
|
1227
|
+
|
1228
|
+
# Google annotation IDs of the transcripts affected by this variant. These
|
1229
|
+
# should be provided when the variant is created.
|
1230
|
+
# Corresponds to the JSON property `transcriptIds`
|
1231
|
+
# @return [Array<String>]
|
1232
|
+
attr_accessor :transcript_ids
|
1233
|
+
|
1234
|
+
# Type has been adapted from ClinVar's list of variant types.
|
1235
|
+
# Corresponds to the JSON property `type`
|
1236
|
+
# @return [String]
|
1237
|
+
attr_accessor :type
|
1238
|
+
|
1239
|
+
# The alternate allele for this variant. If multiple alternate alleles
|
1240
|
+
# exist at this location, create a separate variant for each one, as they
|
1241
|
+
# may represent distinct conditions.
|
1242
|
+
# Corresponds to the JSON property `alternateBases`
|
1243
|
+
# @return [String]
|
1244
|
+
attr_accessor :alternate_bases
|
1245
|
+
|
1246
|
+
# Google annotation ID of the gene affected by this variant. This should
|
1247
|
+
# be provided when the variant is created.
|
1248
|
+
# Corresponds to the JSON property `geneId`
|
1249
|
+
# @return [String]
|
1250
|
+
attr_accessor :gene_id
|
1251
|
+
|
1252
|
+
# Describes the clinical significance of a variant.
|
1253
|
+
# It is adapted from the ClinVar controlled vocabulary for clinical
|
1254
|
+
# significance described at:
|
1255
|
+
# http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
|
1256
|
+
# Corresponds to the JSON property `clinicalSignificance`
|
1257
|
+
# @return [String]
|
1258
|
+
attr_accessor :clinical_significance
|
1259
|
+
|
1260
|
+
def initialize(**args)
|
1261
|
+
update!(**args)
|
1262
|
+
end
|
1263
|
+
|
1264
|
+
# Update properties of this object
|
1265
|
+
def update!(**args)
|
1266
|
+
@conditions = args[:conditions] if args.key?(:conditions)
|
1267
|
+
@effect = args[:effect] if args.key?(:effect)
|
1268
|
+
@transcript_ids = args[:transcript_ids] if args.key?(:transcript_ids)
|
1269
|
+
@type = args[:type] if args.key?(:type)
|
1270
|
+
@alternate_bases = args[:alternate_bases] if args.key?(:alternate_bases)
|
1271
|
+
@gene_id = args[:gene_id] if args.key?(:gene_id)
|
1272
|
+
@clinical_significance = args[:clinical_significance] if args.key?(:clinical_significance)
|
1273
|
+
end
|
1274
|
+
end
|
1275
|
+
|
1276
|
+
#
|
1277
|
+
class ListCoverageBucketsResponse
|
1278
|
+
include Google::Apis::Core::Hashable
|
1279
|
+
|
1280
|
+
# The length of each coverage bucket in base pairs. Note that buckets at the
|
1281
|
+
# end of a reference sequence may be shorter. This value is omitted if the
|
1282
|
+
# bucket width is infinity (the default behaviour, with no range or
|
1283
|
+
# `targetBucketWidth`).
|
1284
|
+
# Corresponds to the JSON property `bucketWidth`
|
1285
|
+
# @return [String]
|
1286
|
+
attr_accessor :bucket_width
|
1287
|
+
|
1288
|
+
# The coverage buckets. The list of buckets is sparse; a bucket with 0
|
1289
|
+
# overlapping reads is not returned. A bucket never crosses more than one
|
1290
|
+
# reference sequence. Each bucket has width `bucketWidth`, unless
|
1291
|
+
# its end is the end of the reference sequence.
|
1292
|
+
# Corresponds to the JSON property `coverageBuckets`
|
1293
|
+
# @return [Array<Google::Apis::GenomicsV1::CoverageBucket>]
|
1294
|
+
attr_accessor :coverage_buckets
|
1295
|
+
|
1296
|
+
# The continuation token, which is used to page through large result sets.
|
1297
|
+
# Provide this value in a subsequent request to return the next page of
|
1298
|
+
# results. This field will be empty if there aren't any additional results.
|
1299
|
+
# Corresponds to the JSON property `nextPageToken`
|
1300
|
+
# @return [String]
|
1301
|
+
attr_accessor :next_page_token
|
1302
|
+
|
1303
|
+
def initialize(**args)
|
1304
|
+
update!(**args)
|
1305
|
+
end
|
1306
|
+
|
1307
|
+
# Update properties of this object
|
1308
|
+
def update!(**args)
|
1309
|
+
@bucket_width = args[:bucket_width] if args.key?(:bucket_width)
|
1310
|
+
@coverage_buckets = args[:coverage_buckets] if args.key?(:coverage_buckets)
|
1311
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
1312
|
+
end
|
1313
|
+
end
|
1314
|
+
|
1315
|
+
# The variant data export request.
|
1316
|
+
class ExportVariantSetRequest
|
1317
|
+
include Google::Apis::Core::Hashable
|
1318
|
+
|
1319
|
+
# The format for the exported data.
|
1320
|
+
# Corresponds to the JSON property `format`
|
1321
|
+
# @return [String]
|
1322
|
+
attr_accessor :format
|
1323
|
+
|
1324
|
+
# Required. The BigQuery dataset to export data to. This dataset must already
|
1325
|
+
# exist. Note that this is distinct from the Genomics concept of "dataset".
|
1326
|
+
# Corresponds to the JSON property `bigqueryDataset`
|
1327
|
+
# @return [String]
|
1328
|
+
attr_accessor :bigquery_dataset
|
1329
|
+
|
1330
|
+
# Required. The BigQuery table to export data to.
|
1331
|
+
# If the table doesn't exist, it will be created. If it already exists, it
|
1332
|
+
# will be overwritten.
|
1333
|
+
# Corresponds to the JSON property `bigqueryTable`
|
1334
|
+
# @return [String]
|
1335
|
+
attr_accessor :bigquery_table
|
1336
|
+
|
1337
|
+
# If provided, only variant call information from the specified call sets
|
1338
|
+
# will be exported. By default all variant calls are exported.
|
1339
|
+
# Corresponds to the JSON property `callSetIds`
|
1340
|
+
# @return [Array<String>]
|
1341
|
+
attr_accessor :call_set_ids
|
1342
|
+
|
1343
|
+
# Required. The Google Cloud project ID that owns the destination
|
1344
|
+
# BigQuery dataset. The caller must have WRITE access to this project. This
|
1345
|
+
# project will also own the resulting export job.
|
1346
|
+
# Corresponds to the JSON property `projectId`
|
1347
|
+
# @return [String]
|
1348
|
+
attr_accessor :project_id
|
1349
|
+
|
1350
|
+
def initialize(**args)
|
1351
|
+
update!(**args)
|
1352
|
+
end
|
1353
|
+
|
1354
|
+
# Update properties of this object
|
1355
|
+
def update!(**args)
|
1356
|
+
@format = args[:format] if args.key?(:format)
|
1357
|
+
@bigquery_dataset = args[:bigquery_dataset] if args.key?(:bigquery_dataset)
|
1358
|
+
@bigquery_table = args[:bigquery_table] if args.key?(:bigquery_table)
|
1359
|
+
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
1360
|
+
@project_id = args[:project_id] if args.key?(:project_id)
|
1361
|
+
end
|
1362
|
+
end
|
1363
|
+
|
1364
|
+
#
|
1365
|
+
class SearchAnnotationsRequest
|
1366
|
+
include Google::Apis::Core::Hashable
|
1367
|
+
|
1368
|
+
# The continuation token, which is used to page through large result sets.
|
1369
|
+
# To get the next page of results, set this parameter to the value of
|
1370
|
+
# `nextPageToken` from the previous response.
|
1371
|
+
# Corresponds to the JSON property `pageToken`
|
1372
|
+
# @return [String]
|
1373
|
+
attr_accessor :page_token
|
1374
|
+
|
1375
|
+
# The maximum number of results to return in a single page. If unspecified,
|
1376
|
+
# defaults to 256. The maximum value is 2048.
|
1377
|
+
# Corresponds to the JSON property `pageSize`
|
1378
|
+
# @return [Fixnum]
|
1379
|
+
attr_accessor :page_size
|
1380
|
+
|
1381
|
+
# The start position of the range on the reference, 0-based inclusive. If
|
1382
|
+
# specified,
|
1383
|
+
# referenceId or
|
1384
|
+
# referenceName
|
1385
|
+
# must be specified. Defaults to 0.
|
1386
|
+
# Corresponds to the JSON property `start`
|
1387
|
+
# @return [String]
|
1388
|
+
attr_accessor :start
|
1389
|
+
|
1390
|
+
# Required. The annotation sets to search within. The caller must have
|
1391
|
+
# `READ` access to these annotation sets.
|
1392
|
+
# All queried annotation sets must have the same type.
|
1393
|
+
# Corresponds to the JSON property `annotationSetIds`
|
1394
|
+
# @return [Array<String>]
|
1395
|
+
attr_accessor :annotation_set_ids
|
1396
|
+
|
1397
|
+
# The name of the reference to query, within the reference set associated
|
1398
|
+
# with this query.
|
1399
|
+
# Corresponds to the JSON property `referenceName`
|
1400
|
+
# @return [String]
|
1401
|
+
attr_accessor :reference_name
|
1402
|
+
|
1403
|
+
# The ID of the reference to query.
|
1404
|
+
# Corresponds to the JSON property `referenceId`
|
1405
|
+
# @return [String]
|
1406
|
+
attr_accessor :reference_id
|
1407
|
+
|
1408
|
+
# The end position of the range on the reference, 0-based exclusive. If
|
1409
|
+
# referenceId or
|
1410
|
+
# referenceName
|
1411
|
+
# must be specified, Defaults to the length of the reference.
|
1412
|
+
# Corresponds to the JSON property `end`
|
1413
|
+
# @return [String]
|
1414
|
+
attr_accessor :end
|
1415
|
+
|
1416
|
+
def initialize(**args)
|
1417
|
+
update!(**args)
|
1418
|
+
end
|
1419
|
+
|
1420
|
+
# Update properties of this object
|
1421
|
+
def update!(**args)
|
1422
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
1423
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
1424
|
+
@start = args[:start] if args.key?(:start)
|
1425
|
+
@annotation_set_ids = args[:annotation_set_ids] if args.key?(:annotation_set_ids)
|
1426
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
1427
|
+
@reference_id = args[:reference_id] if args.key?(:reference_id)
|
1428
|
+
@end = args[:end] if args.key?(:end)
|
1429
|
+
end
|
1430
|
+
end
|
1431
|
+
|
1432
|
+
# An event that occurred during an Operation.
|
1433
|
+
class OperationEvent
|
1434
|
+
include Google::Apis::Core::Hashable
|
1435
|
+
|
1436
|
+
# Optional time of when event finished. An event can have a start time and no
|
1437
|
+
# finish time. If an event has a finish time, there must be a start time.
|
1438
|
+
# Corresponds to the JSON property `endTime`
|
1439
|
+
# @return [String]
|
1440
|
+
attr_accessor :end_time
|
1441
|
+
|
1442
|
+
# Optional time of when event started.
|
1443
|
+
# Corresponds to the JSON property `startTime`
|
1444
|
+
# @return [String]
|
1445
|
+
attr_accessor :start_time
|
1446
|
+
|
1447
|
+
# Required description of event.
|
1448
|
+
# Corresponds to the JSON property `description`
|
1449
|
+
# @return [String]
|
1450
|
+
attr_accessor :description
|
1451
|
+
|
1452
|
+
def initialize(**args)
|
1453
|
+
update!(**args)
|
1454
|
+
end
|
1455
|
+
|
1456
|
+
# Update properties of this object
|
1457
|
+
def update!(**args)
|
1458
|
+
@end_time = args[:end_time] if args.key?(:end_time)
|
1459
|
+
@start_time = args[:start_time] if args.key?(:start_time)
|
1460
|
+
@description = args[:description] if args.key?(:description)
|
1461
|
+
end
|
1462
|
+
end
|
1463
|
+
|
1464
|
+
#
|
1465
|
+
class CodingSequence
|
1466
|
+
include Google::Apis::Core::Hashable
|
1467
|
+
|
1468
|
+
# The start of the coding sequence on this annotation's reference sequence,
|
1469
|
+
# 0-based inclusive. Note that this position is relative to the reference
|
1470
|
+
# start, and *not* the containing annotation start.
|
1471
|
+
# Corresponds to the JSON property `start`
|
1472
|
+
# @return [String]
|
1473
|
+
attr_accessor :start
|
1474
|
+
|
1475
|
+
# The end of the coding sequence on this annotation's reference sequence,
|
1476
|
+
# 0-based exclusive. Note that this position is relative to the reference
|
1477
|
+
# start, and *not* the containing annotation start.
|
1478
|
+
# Corresponds to the JSON property `end`
|
1479
|
+
# @return [String]
|
1480
|
+
attr_accessor :end
|
1481
|
+
|
1482
|
+
def initialize(**args)
|
1483
|
+
update!(**args)
|
1484
|
+
end
|
1485
|
+
|
1486
|
+
# Update properties of this object
|
1487
|
+
def update!(**args)
|
1488
|
+
@start = args[:start] if args.key?(:start)
|
1489
|
+
@end = args[:end] if args.key?(:end)
|
1490
|
+
end
|
1491
|
+
end
|
1492
|
+
|
1493
|
+
#
|
1494
|
+
class SearchReferencesResponse
|
1495
|
+
include Google::Apis::Core::Hashable
|
1496
|
+
|
1497
|
+
# The matching references.
|
1498
|
+
# Corresponds to the JSON property `references`
|
1499
|
+
# @return [Array<Google::Apis::GenomicsV1::Reference>]
|
1500
|
+
attr_accessor :references
|
1501
|
+
|
1502
|
+
# The continuation token, which is used to page through large result sets.
|
1503
|
+
# Provide this value in a subsequent request to return the next page of
|
1504
|
+
# results. This field will be empty if there aren't any additional results.
|
1505
|
+
# Corresponds to the JSON property `nextPageToken`
|
1506
|
+
# @return [String]
|
1507
|
+
attr_accessor :next_page_token
|
1508
|
+
|
1509
|
+
def initialize(**args)
|
1510
|
+
update!(**args)
|
1511
|
+
end
|
1512
|
+
|
1513
|
+
# Update properties of this object
|
1514
|
+
def update!(**args)
|
1515
|
+
@references = args[:references] if args.key?(:references)
|
1516
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
1517
|
+
end
|
1518
|
+
end
|
1519
|
+
|
1520
|
+
# Request message for `GetIamPolicy` method.
|
1521
|
+
class GetIamPolicyRequest
|
1522
|
+
include Google::Apis::Core::Hashable
|
1523
|
+
|
1524
|
+
def initialize(**args)
|
1525
|
+
update!(**args)
|
1526
|
+
end
|
1527
|
+
|
1528
|
+
# Update properties of this object
|
1529
|
+
def update!(**args)
|
1530
|
+
end
|
1531
|
+
end
|
1532
|
+
|
1533
|
+
# Response message for `TestIamPermissions` method.
|
1534
|
+
class TestIamPermissionsResponse
|
1535
|
+
include Google::Apis::Core::Hashable
|
1536
|
+
|
1537
|
+
# A subset of `TestPermissionsRequest.permissions` that the caller is
|
1538
|
+
# allowed.
|
1539
|
+
# Corresponds to the JSON property `permissions`
|
1540
|
+
# @return [Array<String>]
|
1541
|
+
attr_accessor :permissions
|
1542
|
+
|
1543
|
+
def initialize(**args)
|
1544
|
+
update!(**args)
|
1545
|
+
end
|
1546
|
+
|
1547
|
+
# Update properties of this object
|
1548
|
+
def update!(**args)
|
1549
|
+
@permissions = args[:permissions] if args.key?(:permissions)
|
1550
|
+
end
|
1551
|
+
end
|
1552
|
+
|
1553
|
+
#
|
1554
|
+
class SearchAnnotationSetsRequest
|
1555
|
+
include Google::Apis::Core::Hashable
|
1556
|
+
|
1557
|
+
# The continuation token, which is used to page through large result sets.
|
1558
|
+
# To get the next page of results, set this parameter to the value of
|
1559
|
+
# `nextPageToken` from the previous response.
|
1560
|
+
# Corresponds to the JSON property `pageToken`
|
1561
|
+
# @return [String]
|
1562
|
+
attr_accessor :page_token
|
1563
|
+
|
1564
|
+
# The maximum number of results to return in a single page. If unspecified,
|
1565
|
+
# defaults to 128. The maximum value is 1024.
|
1566
|
+
# Corresponds to the JSON property `pageSize`
|
1567
|
+
# @return [Fixnum]
|
1568
|
+
attr_accessor :page_size
|
1569
|
+
|
1570
|
+
# Required. The dataset IDs to search within. Caller must have `READ` access
|
1571
|
+
# to these datasets.
|
1572
|
+
# Corresponds to the JSON property `datasetIds`
|
1573
|
+
# @return [Array<String>]
|
1574
|
+
attr_accessor :dataset_ids
|
1575
|
+
|
1576
|
+
# If specified, only annotation sets that have any of these types are
|
1577
|
+
# returned.
|
1578
|
+
# Corresponds to the JSON property `types`
|
1579
|
+
# @return [Array<String>]
|
1580
|
+
attr_accessor :types
|
1581
|
+
|
1582
|
+
# Only return annotations sets for which a substring of the name matches this
|
1583
|
+
# string (case insensitive).
|
1584
|
+
# Corresponds to the JSON property `name`
|
1585
|
+
# @return [String]
|
1586
|
+
attr_accessor :name
|
1587
|
+
|
1588
|
+
# If specified, only annotation sets associated with the given reference set
|
1589
|
+
# are returned.
|
1590
|
+
# Corresponds to the JSON property `referenceSetId`
|
1591
|
+
# @return [String]
|
1592
|
+
attr_accessor :reference_set_id
|
1593
|
+
|
1594
|
+
def initialize(**args)
|
1595
|
+
update!(**args)
|
1596
|
+
end
|
1597
|
+
|
1598
|
+
# Update properties of this object
|
1599
|
+
def update!(**args)
|
1600
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
1601
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
1602
|
+
@dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
|
1603
|
+
@types = args[:types] if args.key?(:types)
|
1604
|
+
@name = args[:name] if args.key?(:name)
|
1605
|
+
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
1606
|
+
end
|
1607
|
+
end
|
1608
|
+
|
1609
|
+
# The read group set search response.
|
1610
|
+
class SearchReadGroupSetsResponse
|
1611
|
+
include Google::Apis::Core::Hashable
|
1612
|
+
|
1613
|
+
# The list of matching read group sets.
|
1614
|
+
# Corresponds to the JSON property `readGroupSets`
|
1615
|
+
# @return [Array<Google::Apis::GenomicsV1::ReadGroupSet>]
|
1616
|
+
attr_accessor :read_group_sets
|
1617
|
+
|
1618
|
+
# The continuation token, which is used to page through large result sets.
|
1619
|
+
# Provide this value in a subsequent request to return the next page of
|
1620
|
+
# results. This field will be empty if there aren't any additional results.
|
1621
|
+
# Corresponds to the JSON property `nextPageToken`
|
1622
|
+
# @return [String]
|
1623
|
+
attr_accessor :next_page_token
|
1624
|
+
|
1625
|
+
def initialize(**args)
|
1626
|
+
update!(**args)
|
1627
|
+
end
|
1628
|
+
|
1629
|
+
# Update properties of this object
|
1630
|
+
def update!(**args)
|
1631
|
+
@read_group_sets = args[:read_group_sets] if args.key?(:read_group_sets)
|
1632
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
1633
|
+
end
|
1634
|
+
end
|
1635
|
+
|
1636
|
+
# A linear alignment can be represented by one CIGAR string. Describes the
|
1637
|
+
# mapped position and local alignment of the read to the reference.
|
1638
|
+
class LinearAlignment
|
1639
|
+
include Google::Apis::Core::Hashable
|
1640
|
+
|
1641
|
+
# An abstraction for referring to a genomic position, in relation to some
|
1642
|
+
# already known reference. For now, represents a genomic position as a
|
1643
|
+
# reference name, a base number on that reference (0-based), and a
|
1644
|
+
# determination of forward or reverse strand.
|
1645
|
+
# Corresponds to the JSON property `position`
|
1646
|
+
# @return [Google::Apis::GenomicsV1::Position]
|
1647
|
+
attr_accessor :position
|
1648
|
+
|
1649
|
+
# Represents the local alignment of this sequence (alignment matches, indels,
|
1650
|
+
# etc) against the reference.
|
1651
|
+
# Corresponds to the JSON property `cigar`
|
1652
|
+
# @return [Array<Google::Apis::GenomicsV1::CigarUnit>]
|
1653
|
+
attr_accessor :cigar
|
1654
|
+
|
1655
|
+
# The mapping quality of this alignment. Represents how likely
|
1656
|
+
# the read maps to this position as opposed to other locations.
|
1657
|
+
# Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
|
1658
|
+
# the nearest integer.
|
1659
|
+
# Corresponds to the JSON property `mappingQuality`
|
1660
|
+
# @return [Fixnum]
|
1661
|
+
attr_accessor :mapping_quality
|
1662
|
+
|
1663
|
+
def initialize(**args)
|
1664
|
+
update!(**args)
|
1665
|
+
end
|
1666
|
+
|
1667
|
+
# Update properties of this object
|
1668
|
+
def update!(**args)
|
1669
|
+
@position = args[:position] if args.key?(:position)
|
1670
|
+
@cigar = args[:cigar] if args.key?(:cigar)
|
1671
|
+
@mapping_quality = args[:mapping_quality] if args.key?(:mapping_quality)
|
1672
|
+
end
|
1673
|
+
end
|
1674
|
+
|
1675
|
+
#
|
1676
|
+
class SearchReferencesRequest
|
1677
|
+
include Google::Apis::Core::Hashable
|
1678
|
+
|
1679
|
+
# If present, return references for which the
|
1680
|
+
# md5checksum matches exactly.
|
1681
|
+
# Corresponds to the JSON property `md5checksums`
|
1682
|
+
# @return [Array<String>]
|
1683
|
+
attr_accessor :md5checksums
|
1684
|
+
|
1685
|
+
# If present, return references for which a prefix of any of
|
1686
|
+
# sourceAccessions match
|
1687
|
+
# any of these strings. Accession numbers typically have a main number and a
|
1688
|
+
# version, for example `GCF_000001405.26`.
|
1689
|
+
# Corresponds to the JSON property `accessions`
|
1690
|
+
# @return [Array<String>]
|
1691
|
+
attr_accessor :accessions
|
1692
|
+
|
1693
|
+
# The continuation token, which is used to page through large result sets.
|
1694
|
+
# To get the next page of results, set this parameter to the value of
|
1695
|
+
# `nextPageToken` from the previous response.
|
1696
|
+
# Corresponds to the JSON property `pageToken`
|
1697
|
+
# @return [String]
|
1698
|
+
attr_accessor :page_token
|
1699
|
+
|
1700
|
+
# If present, return only references which belong to this reference set.
|
1701
|
+
# Corresponds to the JSON property `referenceSetId`
|
1702
|
+
# @return [String]
|
1703
|
+
attr_accessor :reference_set_id
|
1704
|
+
|
1705
|
+
# The maximum number of results to return in a single page. If unspecified,
|
1706
|
+
# defaults to 1024. The maximum value is 4096.
|
1707
|
+
# Corresponds to the JSON property `pageSize`
|
1708
|
+
# @return [Fixnum]
|
1709
|
+
attr_accessor :page_size
|
1710
|
+
|
1711
|
+
def initialize(**args)
|
1712
|
+
update!(**args)
|
1713
|
+
end
|
1714
|
+
|
1715
|
+
# Update properties of this object
|
1716
|
+
def update!(**args)
|
1717
|
+
@md5checksums = args[:md5checksums] if args.key?(:md5checksums)
|
1718
|
+
@accessions = args[:accessions] if args.key?(:accessions)
|
1719
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
1720
|
+
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
1721
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
1722
|
+
end
|
1723
|
+
end
|
1724
|
+
|
1725
|
+
# A Dataset is a collection of genomic data.
|
1726
|
+
# For more genomics resource definitions, see [Fundamentals of Google
|
1727
|
+
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
1728
|
+
class Dataset
|
1729
|
+
include Google::Apis::Core::Hashable
|
1730
|
+
|
1731
|
+
# The time this dataset was created, in seconds from the epoch.
|
1732
|
+
# Corresponds to the JSON property `createTime`
|
1733
|
+
# @return [String]
|
1734
|
+
attr_accessor :create_time
|
1735
|
+
|
1736
|
+
# The dataset name.
|
1737
|
+
# Corresponds to the JSON property `name`
|
1738
|
+
# @return [String]
|
1739
|
+
attr_accessor :name
|
1740
|
+
|
1741
|
+
# The Google Cloud project ID that this dataset belongs to.
|
1742
|
+
# Corresponds to the JSON property `projectId`
|
1743
|
+
# @return [String]
|
1744
|
+
attr_accessor :project_id
|
1745
|
+
|
1746
|
+
# The server-generated dataset ID, unique across all datasets.
|
1747
|
+
# Corresponds to the JSON property `id`
|
1748
|
+
# @return [String]
|
1749
|
+
attr_accessor :id
|
1750
|
+
|
1751
|
+
def initialize(**args)
|
1752
|
+
update!(**args)
|
1753
|
+
end
|
1754
|
+
|
1755
|
+
# Update properties of this object
|
1756
|
+
def update!(**args)
|
1757
|
+
@create_time = args[:create_time] if args.key?(:create_time)
|
1758
|
+
@name = args[:name] if args.key?(:name)
|
1759
|
+
@project_id = args[:project_id] if args.key?(:project_id)
|
1760
|
+
@id = args[:id] if args.key?(:id)
|
1761
|
+
end
|
1762
|
+
end
|
1763
|
+
|
1764
|
+
# The variant data import response.
|
1765
|
+
class ImportVariantsResponse
|
1766
|
+
include Google::Apis::Core::Hashable
|
1767
|
+
|
1768
|
+
# IDs of the call sets created during the import.
|
1769
|
+
# Corresponds to the JSON property `callSetIds`
|
1770
|
+
# @return [Array<String>]
|
1771
|
+
attr_accessor :call_set_ids
|
1772
|
+
|
1773
|
+
def initialize(**args)
|
1774
|
+
update!(**args)
|
1775
|
+
end
|
1776
|
+
|
1777
|
+
# Update properties of this object
|
1778
|
+
def update!(**args)
|
1779
|
+
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
1780
|
+
end
|
1781
|
+
end
|
1782
|
+
|
1783
|
+
# A read group is all the data that's processed the same way by the sequencer.
|
1784
|
+
class ReadGroup
|
1785
|
+
include Google::Apis::Core::Hashable
|
1786
|
+
|
1787
|
+
# The reference set the reads in this read group are aligned to.
|
1788
|
+
# Corresponds to the JSON property `referenceSetId`
|
1789
|
+
# @return [String]
|
1790
|
+
attr_accessor :reference_set_id
|
1791
|
+
|
1792
|
+
# A map of additional read group information. This must be of the form
|
1793
|
+
# map<string, string[]> (string key mapping to a list of string values).
|
1794
|
+
# Corresponds to the JSON property `info`
|
1795
|
+
# @return [Hash<String,Array<Object>>]
|
1796
|
+
attr_accessor :info
|
1797
|
+
|
1798
|
+
# The server-generated read group ID, unique for all read groups.
|
1799
|
+
# Note: This is different than the @RG ID field in the SAM spec. For that
|
1800
|
+
# value, see name.
|
1801
|
+
# Corresponds to the JSON property `id`
|
1802
|
+
# @return [String]
|
1803
|
+
attr_accessor :id
|
1804
|
+
|
1805
|
+
# The predicted insert size of this read group. The insert size is the length
|
1806
|
+
# the sequenced DNA fragment from end-to-end, not including the adapters.
|
1807
|
+
# Corresponds to the JSON property `predictedInsertSize`
|
1808
|
+
# @return [Fixnum]
|
1809
|
+
attr_accessor :predicted_insert_size
|
1810
|
+
|
1811
|
+
# The programs used to generate this read group. Programs are always
|
1812
|
+
# identical for all read groups within a read group set. For this reason,
|
1813
|
+
# only the first read group in a returned set will have this field
|
1814
|
+
# populated.
|
1815
|
+
# Corresponds to the JSON property `programs`
|
1816
|
+
# @return [Array<Google::Apis::GenomicsV1::Program>]
|
1817
|
+
attr_accessor :programs
|
1818
|
+
|
1819
|
+
# A free-form text description of this read group.
|
1820
|
+
# Corresponds to the JSON property `description`
|
1821
|
+
# @return [String]
|
1822
|
+
attr_accessor :description
|
1823
|
+
|
1824
|
+
# A client-supplied sample identifier for the reads in this read group.
|
1825
|
+
# Corresponds to the JSON property `sampleId`
|
1826
|
+
# @return [String]
|
1827
|
+
attr_accessor :sample_id
|
1828
|
+
|
1829
|
+
# The dataset to which this read group belongs.
|
1830
|
+
# Corresponds to the JSON property `datasetId`
|
1831
|
+
# @return [String]
|
1832
|
+
attr_accessor :dataset_id
|
1833
|
+
|
1834
|
+
# The experiment used to generate this read group.
|
1835
|
+
# Corresponds to the JSON property `experiment`
|
1836
|
+
# @return [Google::Apis::GenomicsV1::Experiment]
|
1837
|
+
attr_accessor :experiment
|
1838
|
+
|
1839
|
+
# The read group name. This corresponds to the @RG ID field in the SAM spec.
|
1840
|
+
# Corresponds to the JSON property `name`
|
1841
|
+
# @return [String]
|
1842
|
+
attr_accessor :name
|
1843
|
+
|
1844
|
+
def initialize(**args)
|
1845
|
+
update!(**args)
|
1846
|
+
end
|
1847
|
+
|
1848
|
+
# Update properties of this object
|
1849
|
+
def update!(**args)
|
1850
|
+
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
1851
|
+
@info = args[:info] if args.key?(:info)
|
1852
|
+
@id = args[:id] if args.key?(:id)
|
1853
|
+
@predicted_insert_size = args[:predicted_insert_size] if args.key?(:predicted_insert_size)
|
1854
|
+
@programs = args[:programs] if args.key?(:programs)
|
1855
|
+
@description = args[:description] if args.key?(:description)
|
1856
|
+
@sample_id = args[:sample_id] if args.key?(:sample_id)
|
1857
|
+
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
1858
|
+
@experiment = args[:experiment] if args.key?(:experiment)
|
1859
|
+
@name = args[:name] if args.key?(:name)
|
1860
|
+
end
|
1861
|
+
end
|
1862
|
+
|
1863
|
+
# A read group set is a logical collection of read groups, which are
|
1864
|
+
# collections of reads produced by a sequencer. A read group set typically
|
1865
|
+
# models reads corresponding to one sample, sequenced one way, and aligned one
|
1866
|
+
# way.
|
1867
|
+
# * A read group set belongs to one dataset.
|
1868
|
+
# * A read group belongs to one read group set.
|
1869
|
+
# * A read belongs to one read group.
|
1870
|
+
# For more genomics resource definitions, see [Fundamentals of Google
|
1871
|
+
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
1872
|
+
class ReadGroupSet
|
1873
|
+
include Google::Apis::Core::Hashable
|
1874
|
+
|
1875
|
+
# The read groups in this set. There are typically 1-10 read groups in a read
|
1876
|
+
# group set.
|
1877
|
+
# Corresponds to the JSON property `readGroups`
|
1878
|
+
# @return [Array<Google::Apis::GenomicsV1::ReadGroup>]
|
1879
|
+
attr_accessor :read_groups
|
1880
|
+
|
1881
|
+
# The filename of the original source file for this read group set, if any.
|
1882
|
+
# Corresponds to the JSON property `filename`
|
1883
|
+
# @return [String]
|
1884
|
+
attr_accessor :filename
|
1885
|
+
|
1886
|
+
# The read group set name. By default this will be initialized to the sample
|
1887
|
+
# name of the sequenced data contained in this set.
|
1888
|
+
# Corresponds to the JSON property `name`
|
1889
|
+
# @return [String]
|
1890
|
+
attr_accessor :name
|
1891
|
+
|
1892
|
+
# The reference set to which the reads in this read group set are aligned.
|
1893
|
+
# Corresponds to the JSON property `referenceSetId`
|
1894
|
+
# @return [String]
|
1895
|
+
attr_accessor :reference_set_id
|
1896
|
+
|
1897
|
+
# A map of additional read group set information.
|
1898
|
+
# Corresponds to the JSON property `info`
|
1899
|
+
# @return [Hash<String,Array<Object>>]
|
1900
|
+
attr_accessor :info
|
1901
|
+
|
1902
|
+
# The server-generated read group set ID, unique for all read group sets.
|
1903
|
+
# Corresponds to the JSON property `id`
|
1904
|
+
# @return [String]
|
1905
|
+
attr_accessor :id
|
1906
|
+
|
1907
|
+
# The dataset to which this read group set belongs.
|
1908
|
+
# Corresponds to the JSON property `datasetId`
|
1909
|
+
# @return [String]
|
1910
|
+
attr_accessor :dataset_id
|
1911
|
+
|
1912
|
+
def initialize(**args)
|
1913
|
+
update!(**args)
|
1914
|
+
end
|
1915
|
+
|
1916
|
+
# Update properties of this object
|
1917
|
+
def update!(**args)
|
1918
|
+
@read_groups = args[:read_groups] if args.key?(:read_groups)
|
1919
|
+
@filename = args[:filename] if args.key?(:filename)
|
1920
|
+
@name = args[:name] if args.key?(:name)
|
1921
|
+
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
1922
|
+
@info = args[:info] if args.key?(:info)
|
1923
|
+
@id = args[:id] if args.key?(:id)
|
1924
|
+
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
1925
|
+
end
|
1926
|
+
end
|
1927
|
+
|
1928
|
+
# The search variant sets response.
|
1929
|
+
class SearchVariantSetsResponse
|
1930
|
+
include Google::Apis::Core::Hashable
|
1931
|
+
|
1932
|
+
# The continuation token, which is used to page through large result sets.
|
1933
|
+
# Provide this value in a subsequent request to return the next page of
|
1934
|
+
# results. This field will be empty if there aren't any additional results.
|
1935
|
+
# Corresponds to the JSON property `nextPageToken`
|
1936
|
+
# @return [String]
|
1937
|
+
attr_accessor :next_page_token
|
1938
|
+
|
1939
|
+
# The variant sets belonging to the requested dataset.
|
1940
|
+
# Corresponds to the JSON property `variantSets`
|
1941
|
+
# @return [Array<Google::Apis::GenomicsV1::VariantSet>]
|
1942
|
+
attr_accessor :variant_sets
|
1943
|
+
|
1944
|
+
def initialize(**args)
|
1945
|
+
update!(**args)
|
1946
|
+
end
|
1947
|
+
|
1948
|
+
# Update properties of this object
|
1949
|
+
def update!(**args)
|
1950
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
1951
|
+
@variant_sets = args[:variant_sets] if args.key?(:variant_sets)
|
1952
|
+
end
|
1953
|
+
end
|
1954
|
+
|
1955
|
+
# A generic empty message that you can re-use to avoid defining duplicated
|
1956
|
+
# empty messages in your APIs. A typical example is to use it as the request
|
1957
|
+
# or the response type of an API method. For instance:
|
1958
|
+
# service Foo `
|
1959
|
+
# rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty);
|
1960
|
+
# `
|
1961
|
+
# The JSON representation for `Empty` is empty JSON object ````.
|
1962
|
+
class Empty
|
1963
|
+
include Google::Apis::Core::Hashable
|
1964
|
+
|
1965
|
+
def initialize(**args)
|
1966
|
+
update!(**args)
|
1967
|
+
end
|
1968
|
+
|
1969
|
+
# Update properties of this object
|
1970
|
+
def update!(**args)
|
1971
|
+
end
|
1972
|
+
end
|
1973
|
+
|
1974
|
+
#
|
1975
|
+
class Entry
|
1976
|
+
include Google::Apis::Core::Hashable
|
1977
|
+
|
1978
|
+
# The `Status` type defines a logical error model that is suitable for different
|
1979
|
+
# programming environments, including REST APIs and RPC APIs. It is used by
|
1980
|
+
# [gRPC](https://github.com/grpc). The error model is designed to be:
|
1981
|
+
# - Simple to use and understand for most users
|
1982
|
+
# - Flexible enough to meet unexpected needs
|
1983
|
+
# # Overview
|
1984
|
+
# The `Status` message contains three pieces of data: error code, error message,
|
1985
|
+
# and error details. The error code should be an enum value of
|
1986
|
+
# google.rpc.Code, but it may accept additional error codes if needed. The
|
1987
|
+
# error message should be a developer-facing English message that helps
|
1988
|
+
# developers *understand* and *resolve* the error. If a localized user-facing
|
1989
|
+
# error message is needed, put the localized message in the error details or
|
1990
|
+
# localize it in the client. The optional error details may contain arbitrary
|
1991
|
+
# information about the error. There is a predefined set of error detail types
|
1992
|
+
# in the package `google.rpc` which can be used for common error conditions.
|
1993
|
+
# # Language mapping
|
1994
|
+
# The `Status` message is the logical representation of the error model, but it
|
1995
|
+
# is not necessarily the actual wire format. When the `Status` message is
|
1996
|
+
# exposed in different client libraries and different wire protocols, it can be
|
1997
|
+
# mapped differently. For example, it will likely be mapped to some exceptions
|
1998
|
+
# in Java, but more likely mapped to some error codes in C.
|
1999
|
+
# # Other uses
|
2000
|
+
# The error model and the `Status` message can be used in a variety of
|
2001
|
+
# environments, either with or without APIs, to provide a
|
2002
|
+
# consistent developer experience across different environments.
|
2003
|
+
# Example uses of this error model include:
|
2004
|
+
# - Partial errors. If a service needs to return partial errors to the client,
|
2005
|
+
# it may embed the `Status` in the normal response to indicate the partial
|
2006
|
+
# errors.
|
2007
|
+
# - Workflow errors. A typical workflow has multiple steps. Each step may
|
2008
|
+
# have a `Status` message for error reporting purpose.
|
2009
|
+
# - Batch operations. If a client uses batch request and batch response, the
|
2010
|
+
# `Status` message should be used directly inside batch response, one for
|
2011
|
+
# each error sub-response.
|
2012
|
+
# - Asynchronous operations. If an API call embeds asynchronous operation
|
2013
|
+
# results in its response, the status of those operations should be
|
2014
|
+
# represented directly using the `Status` message.
|
2015
|
+
# - Logging. If some API errors are stored in logs, the message `Status` could
|
2016
|
+
# be used directly after any stripping needed for security/privacy reasons.
|
2017
|
+
# Corresponds to the JSON property `status`
|
2018
|
+
# @return [Google::Apis::GenomicsV1::Status]
|
2019
|
+
attr_accessor :status
|
2020
|
+
|
2021
|
+
# An annotation describes a region of reference genome. The value of an
|
2022
|
+
# annotation may be one of several canonical types, supplemented by arbitrary
|
2023
|
+
# info tags. An annotation is not inherently associated with a specific
|
2024
|
+
# sample or individual (though a client could choose to use annotations in
|
2025
|
+
# this way). Example canonical annotation types are `GENE` and
|
2026
|
+
# `VARIANT`.
|
2027
|
+
# Corresponds to the JSON property `annotation`
|
2028
|
+
# @return [Google::Apis::GenomicsV1::Annotation]
|
2029
|
+
attr_accessor :annotation
|
2030
|
+
|
2031
|
+
def initialize(**args)
|
2032
|
+
update!(**args)
|
2033
|
+
end
|
2034
|
+
|
2035
|
+
# Update properties of this object
|
2036
|
+
def update!(**args)
|
2037
|
+
@status = args[:status] if args.key?(:status)
|
2038
|
+
@annotation = args[:annotation] if args.key?(:annotation)
|
2039
|
+
end
|
2040
|
+
end
|
2041
|
+
|
2042
|
+
# An abstraction for referring to a genomic position, in relation to some
|
2043
|
+
# already known reference. For now, represents a genomic position as a
|
2044
|
+
# reference name, a base number on that reference (0-based), and a
|
2045
|
+
# determination of forward or reverse strand.
|
2046
|
+
class Position
|
2047
|
+
include Google::Apis::Core::Hashable
|
2048
|
+
|
2049
|
+
# Whether this position is on the reverse strand, as opposed to the forward
|
2050
|
+
# strand.
|
2051
|
+
# Corresponds to the JSON property `reverseStrand`
|
2052
|
+
# @return [Boolean]
|
2053
|
+
attr_accessor :reverse_strand
|
2054
|
+
alias_method :reverse_strand?, :reverse_strand
|
2055
|
+
|
2056
|
+
# The 0-based offset from the start of the forward strand for that reference.
|
2057
|
+
# Corresponds to the JSON property `position`
|
2058
|
+
# @return [String]
|
2059
|
+
attr_accessor :position
|
2060
|
+
|
2061
|
+
# The name of the reference in whatever reference set is being used.
|
2062
|
+
# Corresponds to the JSON property `referenceName`
|
2063
|
+
# @return [String]
|
2064
|
+
attr_accessor :reference_name
|
2065
|
+
|
2066
|
+
def initialize(**args)
|
2067
|
+
update!(**args)
|
2068
|
+
end
|
2069
|
+
|
2070
|
+
# Update properties of this object
|
2071
|
+
def update!(**args)
|
2072
|
+
@reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
|
2073
|
+
@position = args[:position] if args.key?(:position)
|
2074
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
2075
|
+
end
|
2076
|
+
end
|
2077
|
+
|
2078
|
+
#
|
2079
|
+
class SearchReferenceSetsResponse
|
2080
|
+
include Google::Apis::Core::Hashable
|
2081
|
+
|
2082
|
+
# The matching references sets.
|
2083
|
+
# Corresponds to the JSON property `referenceSets`
|
2084
|
+
# @return [Array<Google::Apis::GenomicsV1::ReferenceSet>]
|
2085
|
+
attr_accessor :reference_sets
|
2086
|
+
|
2087
|
+
# The continuation token, which is used to page through large result sets.
|
2088
|
+
# Provide this value in a subsequent request to return the next page of
|
2089
|
+
# results. This field will be empty if there aren't any additional results.
|
2090
|
+
# Corresponds to the JSON property `nextPageToken`
|
2091
|
+
# @return [String]
|
2092
|
+
attr_accessor :next_page_token
|
2093
|
+
|
2094
|
+
def initialize(**args)
|
2095
|
+
update!(**args)
|
2096
|
+
end
|
2097
|
+
|
2098
|
+
# Update properties of this object
|
2099
|
+
def update!(**args)
|
2100
|
+
@reference_sets = args[:reference_sets] if args.key?(:reference_sets)
|
2101
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2102
|
+
end
|
2103
|
+
end
|
2104
|
+
|
2105
|
+
# The call set search request.
|
2106
|
+
class SearchCallSetsRequest
|
2107
|
+
include Google::Apis::Core::Hashable
|
2108
|
+
|
2109
|
+
# Restrict the query to call sets within the given variant sets. At least one
|
2110
|
+
# ID must be provided.
|
2111
|
+
# Corresponds to the JSON property `variantSetIds`
|
2112
|
+
# @return [Array<String>]
|
2113
|
+
attr_accessor :variant_set_ids
|
2114
|
+
|
2115
|
+
# Only return call sets for which a substring of the name matches this
|
2116
|
+
# string.
|
2117
|
+
# Corresponds to the JSON property `name`
|
2118
|
+
# @return [String]
|
2119
|
+
attr_accessor :name
|
2120
|
+
|
2121
|
+
# The continuation token, which is used to page through large result sets.
|
2122
|
+
# To get the next page of results, set this parameter to the value of
|
2123
|
+
# `nextPageToken` from the previous response.
|
2124
|
+
# Corresponds to the JSON property `pageToken`
|
2125
|
+
# @return [String]
|
2126
|
+
attr_accessor :page_token
|
2127
|
+
|
2128
|
+
# The maximum number of results to return in a single page. If unspecified,
|
2129
|
+
# defaults to 1024.
|
2130
|
+
# Corresponds to the JSON property `pageSize`
|
2131
|
+
# @return [Fixnum]
|
2132
|
+
attr_accessor :page_size
|
2133
|
+
|
2134
|
+
def initialize(**args)
|
2135
|
+
update!(**args)
|
2136
|
+
end
|
2137
|
+
|
2138
|
+
# Update properties of this object
|
2139
|
+
def update!(**args)
|
2140
|
+
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
2141
|
+
@name = args[:name] if args.key?(:name)
|
2142
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
2143
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
2144
|
+
end
|
2145
|
+
end
|
2146
|
+
|
2147
|
+
# The read group set import request.
|
2148
|
+
class ImportReadGroupSetsRequest
|
2149
|
+
include Google::Apis::Core::Hashable
|
2150
|
+
|
2151
|
+
# The reference set to which the imported read group sets are aligned to, if
|
2152
|
+
# any. The reference names of this reference set must be a superset of those
|
2153
|
+
# found in the imported file headers. If no reference set id is provided, a
|
2154
|
+
# best effort is made to associate with a matching reference set.
|
2155
|
+
# Corresponds to the JSON property `referenceSetId`
|
2156
|
+
# @return [String]
|
2157
|
+
attr_accessor :reference_set_id
|
2158
|
+
|
2159
|
+
# The partition strategy describes how read groups are partitioned into read
|
2160
|
+
# group sets.
|
2161
|
+
# Corresponds to the JSON property `partitionStrategy`
|
2162
|
+
# @return [String]
|
2163
|
+
attr_accessor :partition_strategy
|
2164
|
+
|
2165
|
+
# Required. The ID of the dataset these read group sets will belong to. The
|
2166
|
+
# caller must have WRITE permissions to this dataset.
|
2167
|
+
# Corresponds to the JSON property `datasetId`
|
2168
|
+
# @return [String]
|
2169
|
+
attr_accessor :dataset_id
|
2170
|
+
|
2171
|
+
# A list of URIs pointing at [BAM
|
2172
|
+
# files](https://samtools.github.io/hts-specs/SAMv1.pdf)
|
2173
|
+
# in Google Cloud Storage.
|
2174
|
+
# Those URIs can include wildcards (*), but do not add or remove
|
2175
|
+
# matching files before import has completed.
|
2176
|
+
# Note that Google Cloud Storage object listing is only eventually
|
2177
|
+
# consistent: files added may be not be immediately visible to
|
2178
|
+
# everyone. Thus, if using a wildcard it is preferable not to start
|
2179
|
+
# the import immediately after the files are created.
|
2180
|
+
# Corresponds to the JSON property `sourceUris`
|
2181
|
+
# @return [Array<String>]
|
2182
|
+
attr_accessor :source_uris
|
2183
|
+
|
2184
|
+
def initialize(**args)
|
2185
|
+
update!(**args)
|
2186
|
+
end
|
2187
|
+
|
2188
|
+
# Update properties of this object
|
2189
|
+
def update!(**args)
|
2190
|
+
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
2191
|
+
@partition_strategy = args[:partition_strategy] if args.key?(:partition_strategy)
|
2192
|
+
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
2193
|
+
@source_uris = args[:source_uris] if args.key?(:source_uris)
|
2194
|
+
end
|
2195
|
+
end
|
2196
|
+
|
2197
|
+
# Defines an Identity and Access Management (IAM) policy. It is used to
|
2198
|
+
# specify access control policies for Cloud Platform resources.
|
2199
|
+
# A `Policy` consists of a list of `bindings`. A `Binding` binds a list of
|
2200
|
+
# `members` to a `role`, where the members can be user accounts, Google groups,
|
2201
|
+
# Google domains, and service accounts. A `role` is a named list of permissions
|
2202
|
+
# defined by IAM.
|
2203
|
+
# **Example**
|
2204
|
+
# `
|
2205
|
+
# "bindings": [
|
2206
|
+
# `
|
2207
|
+
# "role": "roles/owner",
|
2208
|
+
# "members": [
|
2209
|
+
# "user:mike@example.com",
|
2210
|
+
# "group:admins@example.com",
|
2211
|
+
# "domain:google.com",
|
2212
|
+
# "serviceAccount:my-other-app@appspot.gserviceaccount.com",
|
2213
|
+
# ]
|
2214
|
+
# `,
|
2215
|
+
# `
|
2216
|
+
# "role": "roles/viewer",
|
2217
|
+
# "members": ["user:sean@example.com"]
|
2218
|
+
# `
|
2219
|
+
# ]
|
2220
|
+
# `
|
2221
|
+
# For a description of IAM and its features, see the
|
2222
|
+
# [IAM developer's guide](https://cloud.google.com/iam).
|
2223
|
+
class Policy
|
2224
|
+
include Google::Apis::Core::Hashable
|
2225
|
+
|
2226
|
+
# `etag` is used for optimistic concurrency control as a way to help
|
2227
|
+
# prevent simultaneous updates of a policy from overwriting each other.
|
2228
|
+
# It is strongly suggested that systems make use of the `etag` in the
|
2229
|
+
# read-modify-write cycle to perform policy updates in order to avoid race
|
2230
|
+
# conditions: An `etag` is returned in the response to `getIamPolicy`, and
|
2231
|
+
# systems are expected to put that etag in the request to `setIamPolicy` to
|
2232
|
+
# ensure that their change will be applied to the same version of the policy.
|
2233
|
+
# If no `etag` is provided in the call to `setIamPolicy`, then the existing
|
2234
|
+
# policy is overwritten blindly.
|
2235
|
+
# Corresponds to the JSON property `etag`
|
2236
|
+
# @return [String]
|
2237
|
+
attr_accessor :etag
|
2238
|
+
|
2239
|
+
# Version of the `Policy`. The default version is 0.
|
2240
|
+
# Corresponds to the JSON property `version`
|
2241
|
+
# @return [Fixnum]
|
2242
|
+
attr_accessor :version
|
2243
|
+
|
2244
|
+
# Associates a list of `members` to a `role`.
|
2245
|
+
# Multiple `bindings` must not be specified for the same `role`.
|
2246
|
+
# `bindings` with no members will result in an error.
|
2247
|
+
# Corresponds to the JSON property `bindings`
|
2248
|
+
# @return [Array<Google::Apis::GenomicsV1::Binding>]
|
2249
|
+
attr_accessor :bindings
|
2250
|
+
|
2251
|
+
def initialize(**args)
|
2252
|
+
update!(**args)
|
2253
|
+
end
|
2254
|
+
|
2255
|
+
# Update properties of this object
|
2256
|
+
def update!(**args)
|
2257
|
+
@etag = args[:etag] if args.key?(:etag)
|
2258
|
+
@version = args[:version] if args.key?(:version)
|
2259
|
+
@bindings = args[:bindings] if args.key?(:bindings)
|
2260
|
+
end
|
2261
|
+
end
|
2262
|
+
|
2263
|
+
# The read search request.
|
2264
|
+
class SearchReadsRequest
|
2265
|
+
include Google::Apis::Core::Hashable
|
2266
|
+
|
2267
|
+
# The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to
|
2268
|
+
# `*`, only unmapped reads are returned. If unspecified, all reads (mapped
|
2269
|
+
# and unmapped) are returned.
|
2270
|
+
# Corresponds to the JSON property `referenceName`
|
2271
|
+
# @return [String]
|
2272
|
+
attr_accessor :reference_name
|
2273
|
+
|
2274
|
+
# The IDs of the read groups sets within which to search for reads. All
|
2275
|
+
# specified read group sets must be aligned against a common set of reference
|
2276
|
+
# sequences; this defines the genomic coordinates for the query. Must specify
|
2277
|
+
# one of `readGroupSetIds` or `readGroupIds`.
|
2278
|
+
# Corresponds to the JSON property `readGroupSetIds`
|
2279
|
+
# @return [Array<String>]
|
2280
|
+
attr_accessor :read_group_set_ids
|
2281
|
+
|
2282
|
+
# The IDs of the read groups within which to search for reads. All specified
|
2283
|
+
# read groups must belong to the same read group sets. Must specify one of
|
2284
|
+
# `readGroupSetIds` or `readGroupIds`.
|
2285
|
+
# Corresponds to the JSON property `readGroupIds`
|
2286
|
+
# @return [Array<String>]
|
2287
|
+
attr_accessor :read_group_ids
|
2288
|
+
|
2289
|
+
# The end position of the range on the reference, 0-based exclusive. If
|
2290
|
+
# specified, `referenceName` must also be specified.
|
2291
|
+
# Corresponds to the JSON property `end`
|
2292
|
+
# @return [String]
|
2293
|
+
attr_accessor :end
|
2294
|
+
|
2295
|
+
# The continuation token, which is used to page through large result sets.
|
2296
|
+
# To get the next page of results, set this parameter to the value of
|
2297
|
+
# `nextPageToken` from the previous response.
|
2298
|
+
# Corresponds to the JSON property `pageToken`
|
2299
|
+
# @return [String]
|
2300
|
+
attr_accessor :page_token
|
2301
|
+
|
2302
|
+
# The maximum number of results to return in a single page. If unspecified,
|
2303
|
+
# defaults to 256. The maximum value is 2048.
|
2304
|
+
# Corresponds to the JSON property `pageSize`
|
2305
|
+
# @return [Fixnum]
|
2306
|
+
attr_accessor :page_size
|
2307
|
+
|
2308
|
+
# The start position of the range on the reference, 0-based inclusive. If
|
2309
|
+
# specified, `referenceName` must also be specified.
|
2310
|
+
# Corresponds to the JSON property `start`
|
2311
|
+
# @return [String]
|
2312
|
+
attr_accessor :start
|
2313
|
+
|
2314
|
+
def initialize(**args)
|
2315
|
+
update!(**args)
|
2316
|
+
end
|
2317
|
+
|
2318
|
+
# Update properties of this object
|
2319
|
+
def update!(**args)
|
2320
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
2321
|
+
@read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids)
|
2322
|
+
@read_group_ids = args[:read_group_ids] if args.key?(:read_group_ids)
|
2323
|
+
@end = args[:end] if args.key?(:end)
|
2324
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
2325
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
2326
|
+
@start = args[:start] if args.key?(:start)
|
2327
|
+
end
|
2328
|
+
end
|
2329
|
+
|
2330
|
+
# The request message for Operations.CancelOperation.
|
2331
|
+
class CancelOperationRequest
|
2332
|
+
include Google::Apis::Core::Hashable
|
2333
|
+
|
2334
|
+
def initialize(**args)
|
2335
|
+
update!(**args)
|
2336
|
+
end
|
2337
|
+
|
2338
|
+
# Update properties of this object
|
2339
|
+
def update!(**args)
|
2340
|
+
end
|
2341
|
+
end
|
2342
|
+
|
2343
|
+
# An annotation describes a region of reference genome. The value of an
|
2344
|
+
# annotation may be one of several canonical types, supplemented by arbitrary
|
2345
|
+
# info tags. An annotation is not inherently associated with a specific
|
2346
|
+
# sample or individual (though a client could choose to use annotations in
|
2347
|
+
# this way). Example canonical annotation types are `GENE` and
|
2348
|
+
# `VARIANT`.
|
2349
|
+
class Annotation
|
2350
|
+
include Google::Apis::Core::Hashable
|
2351
|
+
|
2352
|
+
# A transcript represents the assertion that a particular region of the
|
2353
|
+
# reference genome may be transcribed as RNA.
|
2354
|
+
# Corresponds to the JSON property `transcript`
|
2355
|
+
# @return [Google::Apis::GenomicsV1::Transcript]
|
2356
|
+
attr_accessor :transcript
|
2357
|
+
|
2358
|
+
# The start position of the range on the reference, 0-based inclusive.
|
2359
|
+
# Corresponds to the JSON property `start`
|
2360
|
+
# @return [String]
|
2361
|
+
attr_accessor :start
|
2362
|
+
|
2363
|
+
# The annotation set to which this annotation belongs.
|
2364
|
+
# Corresponds to the JSON property `annotationSetId`
|
2365
|
+
# @return [String]
|
2366
|
+
attr_accessor :annotation_set_id
|
2367
|
+
|
2368
|
+
# The display name of this annotation.
|
2369
|
+
# Corresponds to the JSON property `name`
|
2370
|
+
# @return [String]
|
2371
|
+
attr_accessor :name
|
2372
|
+
|
2373
|
+
# A variant annotation, which describes the effect of a variant on the
|
2374
|
+
# genome, the coding sequence, and/or higher level consequences at the
|
2375
|
+
# organism level e.g. pathogenicity. This field is only set for annotations
|
2376
|
+
# of type `VARIANT`.
|
2377
|
+
# Corresponds to the JSON property `variant`
|
2378
|
+
# @return [Google::Apis::GenomicsV1::VariantAnnotation]
|
2379
|
+
attr_accessor :variant
|
2380
|
+
|
2381
|
+
# The ID of the Google Genomics reference associated with this range.
|
2382
|
+
# Corresponds to the JSON property `referenceId`
|
2383
|
+
# @return [String]
|
2384
|
+
attr_accessor :reference_id
|
2385
|
+
|
2386
|
+
# The server-generated annotation ID, unique across all annotations.
|
2387
|
+
# Corresponds to the JSON property `id`
|
2388
|
+
# @return [String]
|
2389
|
+
attr_accessor :id
|
2390
|
+
|
2391
|
+
# Whether this range refers to the reverse strand, as opposed to the forward
|
2392
|
+
# strand. Note that regardless of this field, the start/end position of the
|
2393
|
+
# range always refer to the forward strand.
|
2394
|
+
# Corresponds to the JSON property `reverseStrand`
|
2395
|
+
# @return [Boolean]
|
2396
|
+
attr_accessor :reverse_strand
|
2397
|
+
alias_method :reverse_strand?, :reverse_strand
|
2398
|
+
|
2399
|
+
# The display name corresponding to the reference specified by
|
2400
|
+
# `referenceId`, for example `chr1`, `1`, or `chrX`.
|
2401
|
+
# Corresponds to the JSON property `referenceName`
|
2402
|
+
# @return [String]
|
2403
|
+
attr_accessor :reference_name
|
2404
|
+
|
2405
|
+
# The data type for this annotation. Must match the containing annotation
|
2406
|
+
# set's type.
|
2407
|
+
# Corresponds to the JSON property `type`
|
2408
|
+
# @return [String]
|
2409
|
+
attr_accessor :type
|
2410
|
+
|
2411
|
+
# A map of additional read alignment information. This must be of the form
|
2412
|
+
# map<string, string[]> (string key mapping to a list of string values).
|
2413
|
+
# Corresponds to the JSON property `info`
|
2414
|
+
# @return [Hash<String,Array<Object>>]
|
2415
|
+
attr_accessor :info
|
2416
|
+
|
2417
|
+
# The end position of the range on the reference, 0-based exclusive.
|
2418
|
+
# Corresponds to the JSON property `end`
|
2419
|
+
# @return [String]
|
2420
|
+
attr_accessor :end
|
2421
|
+
|
2422
|
+
def initialize(**args)
|
2423
|
+
update!(**args)
|
2424
|
+
end
|
2425
|
+
|
2426
|
+
# Update properties of this object
|
2427
|
+
def update!(**args)
|
2428
|
+
@transcript = args[:transcript] if args.key?(:transcript)
|
2429
|
+
@start = args[:start] if args.key?(:start)
|
2430
|
+
@annotation_set_id = args[:annotation_set_id] if args.key?(:annotation_set_id)
|
2431
|
+
@name = args[:name] if args.key?(:name)
|
2432
|
+
@variant = args[:variant] if args.key?(:variant)
|
2433
|
+
@reference_id = args[:reference_id] if args.key?(:reference_id)
|
2434
|
+
@id = args[:id] if args.key?(:id)
|
2435
|
+
@reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
|
2436
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
2437
|
+
@type = args[:type] if args.key?(:type)
|
2438
|
+
@info = args[:info] if args.key?(:info)
|
2439
|
+
@end = args[:end] if args.key?(:end)
|
2440
|
+
end
|
2441
|
+
end
|
2442
|
+
|
2443
|
+
# This resource represents a long-running operation that is the result of a
|
2444
|
+
# network API call.
|
2445
|
+
class Operation
|
2446
|
+
include Google::Apis::Core::Hashable
|
2447
|
+
|
2448
|
+
# If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If
|
2449
|
+
# importing Variants, an ImportVariantsResponse is returned. For pipelines and
|
2450
|
+
# exports, an empty response is returned.
|
2451
|
+
# Corresponds to the JSON property `response`
|
2452
|
+
# @return [Hash<String,Object>]
|
2453
|
+
attr_accessor :response
|
2454
|
+
|
2455
|
+
# The server-assigned name, which is only unique within the same service that
|
2456
|
+
# originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-
|
2457
|
+
# qzoWAgEw`
|
2458
|
+
# Corresponds to the JSON property `name`
|
2459
|
+
# @return [String]
|
2460
|
+
attr_accessor :name
|
2461
|
+
|
2462
|
+
# The `Status` type defines a logical error model that is suitable for different
|
2463
|
+
# programming environments, including REST APIs and RPC APIs. It is used by
|
2464
|
+
# [gRPC](https://github.com/grpc). The error model is designed to be:
|
2465
|
+
# - Simple to use and understand for most users
|
2466
|
+
# - Flexible enough to meet unexpected needs
|
2467
|
+
# # Overview
|
2468
|
+
# The `Status` message contains three pieces of data: error code, error message,
|
2469
|
+
# and error details. The error code should be an enum value of
|
2470
|
+
# google.rpc.Code, but it may accept additional error codes if needed. The
|
2471
|
+
# error message should be a developer-facing English message that helps
|
2472
|
+
# developers *understand* and *resolve* the error. If a localized user-facing
|
2473
|
+
# error message is needed, put the localized message in the error details or
|
2474
|
+
# localize it in the client. The optional error details may contain arbitrary
|
2475
|
+
# information about the error. There is a predefined set of error detail types
|
2476
|
+
# in the package `google.rpc` which can be used for common error conditions.
|
2477
|
+
# # Language mapping
|
2478
|
+
# The `Status` message is the logical representation of the error model, but it
|
2479
|
+
# is not necessarily the actual wire format. When the `Status` message is
|
2480
|
+
# exposed in different client libraries and different wire protocols, it can be
|
2481
|
+
# mapped differently. For example, it will likely be mapped to some exceptions
|
2482
|
+
# in Java, but more likely mapped to some error codes in C.
|
2483
|
+
# # Other uses
|
2484
|
+
# The error model and the `Status` message can be used in a variety of
|
2485
|
+
# environments, either with or without APIs, to provide a
|
2486
|
+
# consistent developer experience across different environments.
|
2487
|
+
# Example uses of this error model include:
|
2488
|
+
# - Partial errors. If a service needs to return partial errors to the client,
|
2489
|
+
# it may embed the `Status` in the normal response to indicate the partial
|
2490
|
+
# errors.
|
2491
|
+
# - Workflow errors. A typical workflow has multiple steps. Each step may
|
2492
|
+
# have a `Status` message for error reporting purpose.
|
2493
|
+
# - Batch operations. If a client uses batch request and batch response, the
|
2494
|
+
# `Status` message should be used directly inside batch response, one for
|
2495
|
+
# each error sub-response.
|
2496
|
+
# - Asynchronous operations. If an API call embeds asynchronous operation
|
2497
|
+
# results in its response, the status of those operations should be
|
2498
|
+
# represented directly using the `Status` message.
|
2499
|
+
# - Logging. If some API errors are stored in logs, the message `Status` could
|
2500
|
+
# be used directly after any stripping needed for security/privacy reasons.
|
2501
|
+
# Corresponds to the JSON property `error`
|
2502
|
+
# @return [Google::Apis::GenomicsV1::Status]
|
2503
|
+
attr_accessor :error
|
2504
|
+
|
2505
|
+
# An OperationMetadata object. This will always be returned with the Operation.
|
2506
|
+
# Corresponds to the JSON property `metadata`
|
2507
|
+
# @return [Hash<String,Object>]
|
2508
|
+
attr_accessor :metadata
|
2509
|
+
|
2510
|
+
# If the value is `false`, it means the operation is still in progress.
|
2511
|
+
# If true, the operation is completed, and either `error` or `response` is
|
2512
|
+
# available.
|
2513
|
+
# Corresponds to the JSON property `done`
|
2514
|
+
# @return [Boolean]
|
2515
|
+
attr_accessor :done
|
2516
|
+
alias_method :done?, :done
|
2517
|
+
|
2518
|
+
def initialize(**args)
|
2519
|
+
update!(**args)
|
2520
|
+
end
|
2521
|
+
|
2522
|
+
# Update properties of this object
|
2523
|
+
def update!(**args)
|
2524
|
+
@response = args[:response] if args.key?(:response)
|
2525
|
+
@name = args[:name] if args.key?(:name)
|
2526
|
+
@error = args[:error] if args.key?(:error)
|
2527
|
+
@metadata = args[:metadata] if args.key?(:metadata)
|
2528
|
+
@done = args[:done] if args.key?(:done)
|
2529
|
+
end
|
2530
|
+
end
|
2531
|
+
|
2532
|
+
# Runtime metadata that will be populated in the
|
2533
|
+
# runtimeMetadata
|
2534
|
+
# field of the Operation associated with a RunPipeline execution.
|
2535
|
+
class RuntimeMetadata
|
2536
|
+
include Google::Apis::Core::Hashable
|
2537
|
+
|
2538
|
+
# Describes a Compute Engine resource that is being managed by a running
|
2539
|
+
# pipeline.
|
2540
|
+
# Corresponds to the JSON property `computeEngine`
|
2541
|
+
# @return [Google::Apis::GenomicsV1::ComputeEngine]
|
2542
|
+
attr_accessor :compute_engine
|
2543
|
+
|
2544
|
+
def initialize(**args)
|
2545
|
+
update!(**args)
|
2546
|
+
end
|
2547
|
+
|
2548
|
+
# Update properties of this object
|
2549
|
+
def update!(**args)
|
2550
|
+
@compute_engine = args[:compute_engine] if args.key?(:compute_engine)
|
2551
|
+
end
|
2552
|
+
end
|
2553
|
+
|
2554
|
+
# The read group set import response.
|
2555
|
+
class ImportReadGroupSetsResponse
|
2556
|
+
include Google::Apis::Core::Hashable
|
2557
|
+
|
2558
|
+
# IDs of the read group sets that were created.
|
2559
|
+
# Corresponds to the JSON property `readGroupSetIds`
|
2560
|
+
# @return [Array<String>]
|
2561
|
+
attr_accessor :read_group_set_ids
|
2562
|
+
|
2563
|
+
def initialize(**args)
|
2564
|
+
update!(**args)
|
2565
|
+
end
|
2566
|
+
|
2567
|
+
# Update properties of this object
|
2568
|
+
def update!(**args)
|
2569
|
+
@read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids)
|
2570
|
+
end
|
2571
|
+
end
|
2572
|
+
|
2573
|
+
# A call represents the determination of genotype with respect to a particular
|
2574
|
+
# variant. It may include associated information such as quality and phasing.
|
2575
|
+
# For example, a call might assign a probability of 0.32 to the occurrence of
|
2576
|
+
# a SNP named rs1234 in a call set with the name NA12345.
|
2577
|
+
class VariantCall
|
2578
|
+
include Google::Apis::Core::Hashable
|
2579
|
+
|
2580
|
+
# If this field is present, this variant call's genotype ordering implies
|
2581
|
+
# the phase of the bases and is consistent with any other variant calls in
|
2582
|
+
# the same reference sequence which have the same phaseset value.
|
2583
|
+
# When importing data from VCF, if the genotype data was phased but no
|
2584
|
+
# phase set was specified this field will be set to `*`.
|
2585
|
+
# Corresponds to the JSON property `phaseset`
|
2586
|
+
# @return [String]
|
2587
|
+
attr_accessor :phaseset
|
2588
|
+
|
2589
|
+
# A map of additional variant call information. This must be of the form
|
2590
|
+
# map<string, string[]> (string key mapping to a list of string values).
|
2591
|
+
# Corresponds to the JSON property `info`
|
2592
|
+
# @return [Hash<String,Array<Object>>]
|
2593
|
+
attr_accessor :info
|
2594
|
+
|
2595
|
+
# The name of the call set this variant call belongs to.
|
2596
|
+
# Corresponds to the JSON property `callSetName`
|
2597
|
+
# @return [String]
|
2598
|
+
attr_accessor :call_set_name
|
2599
|
+
|
2600
|
+
# The genotype likelihoods for this variant call. Each array entry
|
2601
|
+
# represents how likely a specific genotype is for this call. The value
|
2602
|
+
# ordering is defined by the GL tag in the VCF spec.
|
2603
|
+
# If Phred-scaled genotype likelihood scores (PL) are available and
|
2604
|
+
# log10(P) genotype likelihood scores (GL) are not, PL scores are converted
|
2605
|
+
# to GL scores. If both are available, PL scores are stored in `info`.
|
2606
|
+
# Corresponds to the JSON property `genotypeLikelihood`
|
2607
|
+
# @return [Array<Float>]
|
2608
|
+
attr_accessor :genotype_likelihood
|
2609
|
+
|
2610
|
+
# The ID of the call set this variant call belongs to.
|
2611
|
+
# Corresponds to the JSON property `callSetId`
|
2612
|
+
# @return [String]
|
2613
|
+
attr_accessor :call_set_id
|
2614
|
+
|
2615
|
+
# The genotype of this variant call. Each value represents either the value
|
2616
|
+
# of the `referenceBases` field or a 1-based index into
|
2617
|
+
# `alternateBases`. If a variant had a `referenceBases`
|
2618
|
+
# value of `T` and an `alternateBases`
|
2619
|
+
# value of `["A", "C"]`, and the `genotype` was
|
2620
|
+
# `[2, 1]`, that would mean the call
|
2621
|
+
# represented the heterozygous value `CA` for this variant.
|
2622
|
+
# If the `genotype` was instead `[0, 1]`, the
|
2623
|
+
# represented value would be `TA`. Ordering of the
|
2624
|
+
# genotype values is important if the `phaseset` is present.
|
2625
|
+
# If a genotype is not called (that is, a `.` is present in the
|
2626
|
+
# GT string) -1 is returned.
|
2627
|
+
# Corresponds to the JSON property `genotype`
|
2628
|
+
# @return [Array<Fixnum>]
|
2629
|
+
attr_accessor :genotype
|
2630
|
+
|
2631
|
+
def initialize(**args)
|
2632
|
+
update!(**args)
|
2633
|
+
end
|
2634
|
+
|
2635
|
+
# Update properties of this object
|
2636
|
+
def update!(**args)
|
2637
|
+
@phaseset = args[:phaseset] if args.key?(:phaseset)
|
2638
|
+
@info = args[:info] if args.key?(:info)
|
2639
|
+
@call_set_name = args[:call_set_name] if args.key?(:call_set_name)
|
2640
|
+
@genotype_likelihood = args[:genotype_likelihood] if args.key?(:genotype_likelihood)
|
2641
|
+
@call_set_id = args[:call_set_id] if args.key?(:call_set_id)
|
2642
|
+
@genotype = args[:genotype] if args.key?(:genotype)
|
2643
|
+
end
|
2644
|
+
end
|
2645
|
+
|
2646
|
+
# The variant search response.
|
2647
|
+
class SearchVariantsResponse
|
2648
|
+
include Google::Apis::Core::Hashable
|
2649
|
+
|
2650
|
+
# The continuation token, which is used to page through large result sets.
|
2651
|
+
# Provide this value in a subsequent request to return the next page of
|
2652
|
+
# results. This field will be empty if there aren't any additional results.
|
2653
|
+
# Corresponds to the JSON property `nextPageToken`
|
2654
|
+
# @return [String]
|
2655
|
+
attr_accessor :next_page_token
|
2656
|
+
|
2657
|
+
# The list of matching Variants.
|
2658
|
+
# Corresponds to the JSON property `variants`
|
2659
|
+
# @return [Array<Google::Apis::GenomicsV1::Variant>]
|
2660
|
+
attr_accessor :variants
|
2661
|
+
|
2662
|
+
def initialize(**args)
|
2663
|
+
update!(**args)
|
2664
|
+
end
|
2665
|
+
|
2666
|
+
# Update properties of this object
|
2667
|
+
def update!(**args)
|
2668
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2669
|
+
@variants = args[:variants] if args.key?(:variants)
|
2670
|
+
end
|
2671
|
+
end
|
2672
|
+
|
2673
|
+
#
|
2674
|
+
class ListBasesResponse
|
2675
|
+
include Google::Apis::Core::Hashable
|
2676
|
+
|
2677
|
+
# A substring of the bases that make up this reference.
|
2678
|
+
# Corresponds to the JSON property `sequence`
|
2679
|
+
# @return [String]
|
2680
|
+
attr_accessor :sequence
|
2681
|
+
|
2682
|
+
# The offset position (0-based) of the given `sequence` from the
|
2683
|
+
# start of this `Reference`. This value will differ for each page
|
2684
|
+
# in a paginated request.
|
2685
|
+
# Corresponds to the JSON property `offset`
|
2686
|
+
# @return [String]
|
2687
|
+
attr_accessor :offset
|
2688
|
+
|
2689
|
+
# The continuation token, which is used to page through large result sets.
|
2690
|
+
# Provide this value in a subsequent request to return the next page of
|
2691
|
+
# results. This field will be empty if there aren't any additional results.
|
2692
|
+
# Corresponds to the JSON property `nextPageToken`
|
2693
|
+
# @return [String]
|
2694
|
+
attr_accessor :next_page_token
|
2695
|
+
|
2696
|
+
def initialize(**args)
|
2697
|
+
update!(**args)
|
2698
|
+
end
|
2699
|
+
|
2700
|
+
# Update properties of this object
|
2701
|
+
def update!(**args)
|
2702
|
+
@sequence = args[:sequence] if args.key?(:sequence)
|
2703
|
+
@offset = args[:offset] if args.key?(:offset)
|
2704
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2705
|
+
end
|
2706
|
+
end
|
2707
|
+
|
2708
|
+
# The `Status` type defines a logical error model that is suitable for different
|
2709
|
+
# programming environments, including REST APIs and RPC APIs. It is used by
|
2710
|
+
# [gRPC](https://github.com/grpc). The error model is designed to be:
|
2711
|
+
# - Simple to use and understand for most users
|
2712
|
+
# - Flexible enough to meet unexpected needs
|
2713
|
+
# # Overview
|
2714
|
+
# The `Status` message contains three pieces of data: error code, error message,
|
2715
|
+
# and error details. The error code should be an enum value of
|
2716
|
+
# google.rpc.Code, but it may accept additional error codes if needed. The
|
2717
|
+
# error message should be a developer-facing English message that helps
|
2718
|
+
# developers *understand* and *resolve* the error. If a localized user-facing
|
2719
|
+
# error message is needed, put the localized message in the error details or
|
2720
|
+
# localize it in the client. The optional error details may contain arbitrary
|
2721
|
+
# information about the error. There is a predefined set of error detail types
|
2722
|
+
# in the package `google.rpc` which can be used for common error conditions.
|
2723
|
+
# # Language mapping
|
2724
|
+
# The `Status` message is the logical representation of the error model, but it
|
2725
|
+
# is not necessarily the actual wire format. When the `Status` message is
|
2726
|
+
# exposed in different client libraries and different wire protocols, it can be
|
2727
|
+
# mapped differently. For example, it will likely be mapped to some exceptions
|
2728
|
+
# in Java, but more likely mapped to some error codes in C.
|
2729
|
+
# # Other uses
|
2730
|
+
# The error model and the `Status` message can be used in a variety of
|
2731
|
+
# environments, either with or without APIs, to provide a
|
2732
|
+
# consistent developer experience across different environments.
|
2733
|
+
# Example uses of this error model include:
|
2734
|
+
# - Partial errors. If a service needs to return partial errors to the client,
|
2735
|
+
# it may embed the `Status` in the normal response to indicate the partial
|
2736
|
+
# errors.
|
2737
|
+
# - Workflow errors. A typical workflow has multiple steps. Each step may
|
2738
|
+
# have a `Status` message for error reporting purpose.
|
2739
|
+
# - Batch operations. If a client uses batch request and batch response, the
|
2740
|
+
# `Status` message should be used directly inside batch response, one for
|
2741
|
+
# each error sub-response.
|
2742
|
+
# - Asynchronous operations. If an API call embeds asynchronous operation
|
2743
|
+
# results in its response, the status of those operations should be
|
2744
|
+
# represented directly using the `Status` message.
|
2745
|
+
# - Logging. If some API errors are stored in logs, the message `Status` could
|
2746
|
+
# be used directly after any stripping needed for security/privacy reasons.
|
2747
|
+
class Status
|
2748
|
+
include Google::Apis::Core::Hashable
|
2749
|
+
|
2750
|
+
# A developer-facing error message, which should be in English. Any
|
2751
|
+
# user-facing error message should be localized and sent in the
|
2752
|
+
# google.rpc.Status.details field, or localized by the client.
|
2753
|
+
# Corresponds to the JSON property `message`
|
2754
|
+
# @return [String]
|
2755
|
+
attr_accessor :message
|
2756
|
+
|
2757
|
+
# A list of messages that carry the error details. There will be a
|
2758
|
+
# common set of message types for APIs to use.
|
2759
|
+
# Corresponds to the JSON property `details`
|
2760
|
+
# @return [Array<Hash<String,Object>>]
|
2761
|
+
attr_accessor :details
|
2762
|
+
|
2763
|
+
# The status code, which should be an enum value of google.rpc.Code.
|
2764
|
+
# Corresponds to the JSON property `code`
|
2765
|
+
# @return [Fixnum]
|
2766
|
+
attr_accessor :code
|
2767
|
+
|
2768
|
+
def initialize(**args)
|
2769
|
+
update!(**args)
|
2770
|
+
end
|
2771
|
+
|
2772
|
+
# Update properties of this object
|
2773
|
+
def update!(**args)
|
2774
|
+
@message = args[:message] if args.key?(:message)
|
2775
|
+
@details = args[:details] if args.key?(:details)
|
2776
|
+
@code = args[:code] if args.key?(:code)
|
2777
|
+
end
|
2778
|
+
end
|
2779
|
+
|
2780
|
+
#
|
2781
|
+
class UndeleteDatasetRequest
|
2782
|
+
include Google::Apis::Core::Hashable
|
2783
|
+
|
2784
|
+
def initialize(**args)
|
2785
|
+
update!(**args)
|
2786
|
+
end
|
2787
|
+
|
2788
|
+
# Update properties of this object
|
2789
|
+
def update!(**args)
|
2790
|
+
end
|
2791
|
+
end
|
2792
|
+
|
2793
|
+
# Associates `members` with a `role`.
|
2794
|
+
class Binding
|
2795
|
+
include Google::Apis::Core::Hashable
|
2796
|
+
|
2797
|
+
# Specifies the identities requesting access for a Cloud Platform resource.
|
2798
|
+
# `members` can have the following values:
|
2799
|
+
# * `allUsers`: A special identifier that represents anyone who is
|
2800
|
+
# on the internet; with or without a Google account.
|
2801
|
+
# * `allAuthenticatedUsers`: A special identifier that represents anyone
|
2802
|
+
# who is authenticated with a Google account or a service account.
|
2803
|
+
# * `user:`emailid``: An email address that represents a specific Google
|
2804
|
+
# account. For example, `alice@gmail.com` or `joe@example.com`.
|
2805
|
+
# * `serviceAccount:`emailid``: An email address that represents a service
|
2806
|
+
# account. For example, `my-other-app@appspot.gserviceaccount.com`.
|
2807
|
+
# * `group:`emailid``: An email address that represents a Google group.
|
2808
|
+
# For example, `admins@example.com`.
|
2809
|
+
# * `domain:`domain``: A Google Apps domain name that represents all the
|
2810
|
+
# users of that domain. For example, `google.com` or `example.com`.
|
2811
|
+
# Corresponds to the JSON property `members`
|
2812
|
+
# @return [Array<String>]
|
2813
|
+
attr_accessor :members
|
2814
|
+
|
2815
|
+
# Role that is assigned to `members`.
|
2816
|
+
# For example, `roles/viewer`, `roles/editor`, or `roles/owner`.
|
2817
|
+
# Required
|
2818
|
+
# Corresponds to the JSON property `role`
|
2819
|
+
# @return [String]
|
2820
|
+
attr_accessor :role
|
2821
|
+
|
2822
|
+
def initialize(**args)
|
2823
|
+
update!(**args)
|
2824
|
+
end
|
2825
|
+
|
2826
|
+
# Update properties of this object
|
2827
|
+
def update!(**args)
|
2828
|
+
@members = args[:members] if args.key?(:members)
|
2829
|
+
@role = args[:role] if args.key?(:role)
|
2830
|
+
end
|
2831
|
+
end
|
2832
|
+
|
2833
|
+
# A 0-based half-open genomic coordinate range for search requests.
|
2834
|
+
class Range
|
2835
|
+
include Google::Apis::Core::Hashable
|
2836
|
+
|
2837
|
+
# The start position of the range on the reference, 0-based inclusive.
|
2838
|
+
# Corresponds to the JSON property `start`
|
2839
|
+
# @return [String]
|
2840
|
+
attr_accessor :start
|
2841
|
+
|
2842
|
+
# The end position of the range on the reference, 0-based exclusive.
|
2843
|
+
# Corresponds to the JSON property `end`
|
2844
|
+
# @return [String]
|
2845
|
+
attr_accessor :end
|
2846
|
+
|
2847
|
+
# The reference sequence name, for example `chr1`,
|
2848
|
+
# `1`, or `chrX`.
|
2849
|
+
# Corresponds to the JSON property `referenceName`
|
2850
|
+
# @return [String]
|
2851
|
+
attr_accessor :reference_name
|
2852
|
+
|
2853
|
+
def initialize(**args)
|
2854
|
+
update!(**args)
|
2855
|
+
end
|
2856
|
+
|
2857
|
+
# Update properties of this object
|
2858
|
+
def update!(**args)
|
2859
|
+
@start = args[:start] if args.key?(:start)
|
2860
|
+
@end = args[:end] if args.key?(:end)
|
2861
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
2862
|
+
end
|
2863
|
+
end
|
2864
|
+
|
2865
|
+
# A variant set is a collection of call sets and variants. It contains summary
|
2866
|
+
# statistics of those contents. A variant set belongs to a dataset.
|
2867
|
+
# For more genomics resource definitions, see [Fundamentals of Google
|
2868
|
+
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
2869
|
+
class VariantSet
|
2870
|
+
include Google::Apis::Core::Hashable
|
2871
|
+
|
2872
|
+
# The metadata associated with this variant set.
|
2873
|
+
# Corresponds to the JSON property `metadata`
|
2874
|
+
# @return [Array<Google::Apis::GenomicsV1::VariantSetMetadata>]
|
2875
|
+
attr_accessor :metadata
|
2876
|
+
|
2877
|
+
# A list of all references used by the variants in a variant set
|
2878
|
+
# with associated coordinate upper bounds for each one.
|
2879
|
+
# Corresponds to the JSON property `referenceBounds`
|
2880
|
+
# @return [Array<Google::Apis::GenomicsV1::ReferenceBound>]
|
2881
|
+
attr_accessor :reference_bounds
|
2882
|
+
|
2883
|
+
# The server-generated variant set ID, unique across all variant sets.
|
2884
|
+
# Corresponds to the JSON property `id`
|
2885
|
+
# @return [String]
|
2886
|
+
attr_accessor :id
|
2887
|
+
|
2888
|
+
# A textual description of this variant set.
|
2889
|
+
# Corresponds to the JSON property `description`
|
2890
|
+
# @return [String]
|
2891
|
+
attr_accessor :description
|
2892
|
+
|
2893
|
+
# The dataset to which this variant set belongs.
|
2894
|
+
# Corresponds to the JSON property `datasetId`
|
2895
|
+
# @return [String]
|
2896
|
+
attr_accessor :dataset_id
|
2897
|
+
|
2898
|
+
# User-specified, mutable name.
|
2899
|
+
# Corresponds to the JSON property `name`
|
2900
|
+
# @return [String]
|
2901
|
+
attr_accessor :name
|
2902
|
+
|
2903
|
+
# The reference set to which the variant set is mapped. The reference set
|
2904
|
+
# describes the alignment provenance of the variant set, while the
|
2905
|
+
# `referenceBounds` describe the shape of the actual variant data. The
|
2906
|
+
# reference set's reference names are a superset of those found in the
|
2907
|
+
# `referenceBounds`.
|
2908
|
+
# For example, given a variant set that is mapped to the GRCh38 reference set
|
2909
|
+
# and contains a single variant on reference 'X', `referenceBounds` would
|
2910
|
+
# contain only an entry for 'X', while the associated reference set
|
2911
|
+
# enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
|
2912
|
+
# Corresponds to the JSON property `referenceSetId`
|
2913
|
+
# @return [String]
|
2914
|
+
attr_accessor :reference_set_id
|
2915
|
+
|
2916
|
+
def initialize(**args)
|
2917
|
+
update!(**args)
|
2918
|
+
end
|
2919
|
+
|
2920
|
+
# Update properties of this object
|
2921
|
+
def update!(**args)
|
2922
|
+
@metadata = args[:metadata] if args.key?(:metadata)
|
2923
|
+
@reference_bounds = args[:reference_bounds] if args.key?(:reference_bounds)
|
2924
|
+
@id = args[:id] if args.key?(:id)
|
2925
|
+
@description = args[:description] if args.key?(:description)
|
2926
|
+
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
2927
|
+
@name = args[:name] if args.key?(:name)
|
2928
|
+
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
2929
|
+
end
|
2930
|
+
end
|
2931
|
+
|
2932
|
+
#
|
2933
|
+
class BatchCreateAnnotationsResponse
|
2934
|
+
include Google::Apis::Core::Hashable
|
2935
|
+
|
2936
|
+
# The resulting per-annotation entries, ordered consistently with the
|
2937
|
+
# original request.
|
2938
|
+
# Corresponds to the JSON property `entries`
|
2939
|
+
# @return [Array<Google::Apis::GenomicsV1::Entry>]
|
2940
|
+
attr_accessor :entries
|
2941
|
+
|
2942
|
+
def initialize(**args)
|
2943
|
+
update!(**args)
|
2944
|
+
end
|
2945
|
+
|
2946
|
+
# Update properties of this object
|
2947
|
+
def update!(**args)
|
2948
|
+
@entries = args[:entries] if args.key?(:entries)
|
2949
|
+
end
|
2950
|
+
end
|
2951
|
+
|
2952
|
+
# ReferenceBound records an upper bound for the starting coordinate of
|
2953
|
+
# variants in a particular reference.
|
2954
|
+
class ReferenceBound
|
2955
|
+
include Google::Apis::Core::Hashable
|
2956
|
+
|
2957
|
+
# An upper bound (inclusive) on the starting coordinate of any
|
2958
|
+
# variant in the reference sequence.
|
2959
|
+
# Corresponds to the JSON property `upperBound`
|
2960
|
+
# @return [String]
|
2961
|
+
attr_accessor :upper_bound
|
2962
|
+
|
2963
|
+
# The name of the reference associated with this reference bound.
|
2964
|
+
# Corresponds to the JSON property `referenceName`
|
2965
|
+
# @return [String]
|
2966
|
+
attr_accessor :reference_name
|
2967
|
+
|
2968
|
+
def initialize(**args)
|
2969
|
+
update!(**args)
|
2970
|
+
end
|
2971
|
+
|
2972
|
+
# Update properties of this object
|
2973
|
+
def update!(**args)
|
2974
|
+
@upper_bound = args[:upper_bound] if args.key?(:upper_bound)
|
2975
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
2976
|
+
end
|
2977
|
+
end
|
2978
|
+
|
2979
|
+
# The call set search response.
|
2980
|
+
class SearchCallSetsResponse
|
2981
|
+
include Google::Apis::Core::Hashable
|
2982
|
+
|
2983
|
+
# The continuation token, which is used to page through large result sets.
|
2984
|
+
# Provide this value in a subsequent request to return the next page of
|
2985
|
+
# results. This field will be empty if there aren't any additional results.
|
2986
|
+
# Corresponds to the JSON property `nextPageToken`
|
2987
|
+
# @return [String]
|
2988
|
+
attr_accessor :next_page_token
|
2989
|
+
|
2990
|
+
# The list of matching call sets.
|
2991
|
+
# Corresponds to the JSON property `callSets`
|
2992
|
+
# @return [Array<Google::Apis::GenomicsV1::CallSet>]
|
2993
|
+
attr_accessor :call_sets
|
2994
|
+
|
2995
|
+
def initialize(**args)
|
2996
|
+
update!(**args)
|
2997
|
+
end
|
2998
|
+
|
2999
|
+
# Update properties of this object
|
3000
|
+
def update!(**args)
|
3001
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
3002
|
+
@call_sets = args[:call_sets] if args.key?(:call_sets)
|
3003
|
+
end
|
3004
|
+
end
|
3005
|
+
|
3006
|
+
# A variant represents a change in DNA sequence relative to a reference
|
3007
|
+
# sequence. For example, a variant could represent a SNP or an insertion.
|
3008
|
+
# Variants belong to a variant set.
|
3009
|
+
# For more genomics resource definitions, see [Fundamentals of Google
|
3010
|
+
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
3011
|
+
# Each of the calls on a variant represent a determination of genotype with
|
3012
|
+
# respect to that variant. For example, a call might assign probability of 0.32
|
3013
|
+
# to the occurrence of a SNP named rs1234 in a sample named NA12345. A call
|
3014
|
+
# belongs to a call set, which contains related calls typically from one
|
3015
|
+
# sample.
|
3016
|
+
class Variant
|
3017
|
+
include Google::Apis::Core::Hashable
|
3018
|
+
|
3019
|
+
# A measure of how likely this variant is to be real.
|
3020
|
+
# A higher value is better.
|
3021
|
+
# Corresponds to the JSON property `quality`
|
3022
|
+
# @return [Float]
|
3023
|
+
attr_accessor :quality
|
3024
|
+
|
3025
|
+
# The server-generated variant ID, unique across all variants.
|
3026
|
+
# Corresponds to the JSON property `id`
|
3027
|
+
# @return [String]
|
3028
|
+
attr_accessor :id
|
3029
|
+
|
3030
|
+
# The ID of the variant set this variant belongs to.
|
3031
|
+
# Corresponds to the JSON property `variantSetId`
|
3032
|
+
# @return [String]
|
3033
|
+
attr_accessor :variant_set_id
|
3034
|
+
|
3035
|
+
# The reference on which this variant occurs.
|
3036
|
+
# (such as `chr20` or `X`)
|
3037
|
+
# Corresponds to the JSON property `referenceName`
|
3038
|
+
# @return [String]
|
3039
|
+
attr_accessor :reference_name
|
3040
|
+
|
3041
|
+
# A map of additional variant information. This must be of the form
|
3042
|
+
# map<string, string[]> (string key mapping to a list of string values).
|
3043
|
+
# Corresponds to the JSON property `info`
|
3044
|
+
# @return [Hash<String,Array<Object>>]
|
3045
|
+
attr_accessor :info
|
3046
|
+
|
3047
|
+
# The reference bases for this variant. They start at the given
|
3048
|
+
# position.
|
3049
|
+
# Corresponds to the JSON property `referenceBases`
|
3050
|
+
# @return [String]
|
3051
|
+
attr_accessor :reference_bases
|
3052
|
+
|
3053
|
+
# Names for the variant, for example a RefSNP ID.
|
3054
|
+
# Corresponds to the JSON property `names`
|
3055
|
+
# @return [Array<String>]
|
3056
|
+
attr_accessor :names
|
3057
|
+
|
3058
|
+
# The bases that appear instead of the reference bases.
|
3059
|
+
# Corresponds to the JSON property `alternateBases`
|
3060
|
+
# @return [Array<String>]
|
3061
|
+
attr_accessor :alternate_bases
|
3062
|
+
|
3063
|
+
# The end position (0-based) of this variant. This corresponds to the first
|
3064
|
+
# base after the last base in the reference allele. So, the length of
|
3065
|
+
# the reference allele is (end - start). This is useful for variants
|
3066
|
+
# that don't explicitly give alternate bases, for example large deletions.
|
3067
|
+
# Corresponds to the JSON property `end`
|
3068
|
+
# @return [String]
|
3069
|
+
attr_accessor :end
|
3070
|
+
|
3071
|
+
# A list of filters (normally quality filters) this variant has failed.
|
3072
|
+
# `PASS` indicates this variant has passed all filters.
|
3073
|
+
# Corresponds to the JSON property `filter`
|
3074
|
+
# @return [Array<String>]
|
3075
|
+
attr_accessor :filter
|
3076
|
+
|
3077
|
+
# The variant calls for this particular variant. Each one represents the
|
3078
|
+
# determination of genotype with respect to this variant.
|
3079
|
+
# Corresponds to the JSON property `calls`
|
3080
|
+
# @return [Array<Google::Apis::GenomicsV1::VariantCall>]
|
3081
|
+
attr_accessor :calls
|
3082
|
+
|
3083
|
+
# The date this variant was created, in milliseconds from the epoch.
|
3084
|
+
# Corresponds to the JSON property `created`
|
3085
|
+
# @return [String]
|
3086
|
+
attr_accessor :created
|
3087
|
+
|
3088
|
+
# The position at which this variant occurs (0-based).
|
3089
|
+
# This corresponds to the first base of the string of reference bases.
|
3090
|
+
# Corresponds to the JSON property `start`
|
3091
|
+
# @return [String]
|
3092
|
+
attr_accessor :start
|
3093
|
+
|
3094
|
+
def initialize(**args)
|
3095
|
+
update!(**args)
|
3096
|
+
end
|
3097
|
+
|
3098
|
+
# Update properties of this object
|
3099
|
+
def update!(**args)
|
3100
|
+
@quality = args[:quality] if args.key?(:quality)
|
3101
|
+
@id = args[:id] if args.key?(:id)
|
3102
|
+
@variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
|
3103
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
3104
|
+
@info = args[:info] if args.key?(:info)
|
3105
|
+
@reference_bases = args[:reference_bases] if args.key?(:reference_bases)
|
3106
|
+
@names = args[:names] if args.key?(:names)
|
3107
|
+
@alternate_bases = args[:alternate_bases] if args.key?(:alternate_bases)
|
3108
|
+
@end = args[:end] if args.key?(:end)
|
3109
|
+
@filter = args[:filter] if args.key?(:filter)
|
3110
|
+
@calls = args[:calls] if args.key?(:calls)
|
3111
|
+
@created = args[:created] if args.key?(:created)
|
3112
|
+
@start = args[:start] if args.key?(:start)
|
3113
|
+
end
|
3114
|
+
end
|
3115
|
+
|
3116
|
+
# The response message for Operations.ListOperations.
|
3117
|
+
class ListOperationsResponse
|
3118
|
+
include Google::Apis::Core::Hashable
|
3119
|
+
|
3120
|
+
# The standard List next-page token.
|
3121
|
+
# Corresponds to the JSON property `nextPageToken`
|
3122
|
+
# @return [String]
|
3123
|
+
attr_accessor :next_page_token
|
3124
|
+
|
3125
|
+
# A list of operations that matches the specified filter in the request.
|
3126
|
+
# Corresponds to the JSON property `operations`
|
3127
|
+
# @return [Array<Google::Apis::GenomicsV1::Operation>]
|
3128
|
+
attr_accessor :operations
|
3129
|
+
|
3130
|
+
def initialize(**args)
|
3131
|
+
update!(**args)
|
3132
|
+
end
|
3133
|
+
|
3134
|
+
# Update properties of this object
|
3135
|
+
def update!(**args)
|
3136
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
3137
|
+
@operations = args[:operations] if args.key?(:operations)
|
3138
|
+
end
|
3139
|
+
end
|
3140
|
+
|
3141
|
+
# Metadata describing an Operation.
|
3142
|
+
class OperationMetadata
|
3143
|
+
include Google::Apis::Core::Hashable
|
3144
|
+
|
3145
|
+
# Optional event messages that were generated during the job's execution.
|
3146
|
+
# This also contains any warnings that were generated during import
|
3147
|
+
# or export.
|
3148
|
+
# Corresponds to the JSON property `events`
|
3149
|
+
# @return [Array<Google::Apis::GenomicsV1::OperationEvent>]
|
3150
|
+
attr_accessor :events
|
3151
|
+
|
3152
|
+
# The time at which the job stopped running.
|
3153
|
+
# Corresponds to the JSON property `endTime`
|
3154
|
+
# @return [String]
|
3155
|
+
attr_accessor :end_time
|
3156
|
+
|
3157
|
+
# The time at which the job began to run.
|
3158
|
+
# Corresponds to the JSON property `startTime`
|
3159
|
+
# @return [String]
|
3160
|
+
attr_accessor :start_time
|
3161
|
+
|
3162
|
+
# The original request that started the operation. Note that this will be in
|
3163
|
+
# current version of the API. If the operation was started with v1beta2 API
|
3164
|
+
# and a GetOperation is performed on v1 API, a v1 request will be returned.
|
3165
|
+
# Corresponds to the JSON property `request`
|
3166
|
+
# @return [Hash<String,Object>]
|
3167
|
+
attr_accessor :request
|
3168
|
+
|
3169
|
+
# Runtime metadata on this Operation.
|
3170
|
+
# Corresponds to the JSON property `runtimeMetadata`
|
3171
|
+
# @return [Hash<String,Object>]
|
3172
|
+
attr_accessor :runtime_metadata
|
3173
|
+
|
3174
|
+
# The time at which the job was submitted to the Genomics service.
|
3175
|
+
# Corresponds to the JSON property `createTime`
|
3176
|
+
# @return [String]
|
3177
|
+
attr_accessor :create_time
|
3178
|
+
|
3179
|
+
# Optionally provided by the caller when submitting the request that creates
|
3180
|
+
# the operation.
|
3181
|
+
# Corresponds to the JSON property `labels`
|
3182
|
+
# @return [Hash<String,String>]
|
3183
|
+
attr_accessor :labels
|
3184
|
+
|
3185
|
+
# The Google Cloud Project in which the job is scoped.
|
3186
|
+
# Corresponds to the JSON property `projectId`
|
3187
|
+
# @return [String]
|
3188
|
+
attr_accessor :project_id
|
3189
|
+
|
3190
|
+
# This field is deprecated. Use `labels` instead. Optionally provided by the
|
3191
|
+
# caller when submitting the request that creates the operation.
|
3192
|
+
# Corresponds to the JSON property `clientId`
|
3193
|
+
# @return [String]
|
3194
|
+
attr_accessor :client_id
|
3195
|
+
|
3196
|
+
def initialize(**args)
|
3197
|
+
update!(**args)
|
3198
|
+
end
|
3199
|
+
|
3200
|
+
# Update properties of this object
|
3201
|
+
def update!(**args)
|
3202
|
+
@events = args[:events] if args.key?(:events)
|
3203
|
+
@end_time = args[:end_time] if args.key?(:end_time)
|
3204
|
+
@start_time = args[:start_time] if args.key?(:start_time)
|
3205
|
+
@request = args[:request] if args.key?(:request)
|
3206
|
+
@runtime_metadata = args[:runtime_metadata] if args.key?(:runtime_metadata)
|
3207
|
+
@create_time = args[:create_time] if args.key?(:create_time)
|
3208
|
+
@labels = args[:labels] if args.key?(:labels)
|
3209
|
+
@project_id = args[:project_id] if args.key?(:project_id)
|
3210
|
+
@client_id = args[:client_id] if args.key?(:client_id)
|
3211
|
+
end
|
3212
|
+
end
|
3213
|
+
|
3214
|
+
# The variant search request.
|
3215
|
+
class SearchVariantsRequest
|
3216
|
+
include Google::Apis::Core::Hashable
|
3217
|
+
|
3218
|
+
# The maximum number of variants to return in a single page. If unspecified,
|
3219
|
+
# defaults to 5000. The maximum value is 10000.
|
3220
|
+
# Corresponds to the JSON property `pageSize`
|
3221
|
+
# @return [Fixnum]
|
3222
|
+
attr_accessor :page_size
|
3223
|
+
|
3224
|
+
# Only return variant calls which belong to call sets with these ids.
|
3225
|
+
# Leaving this blank returns all variant calls. If a variant has no
|
3226
|
+
# calls belonging to any of these call sets, it won't be returned at all.
|
3227
|
+
# Corresponds to the JSON property `callSetIds`
|
3228
|
+
# @return [Array<String>]
|
3229
|
+
attr_accessor :call_set_ids
|
3230
|
+
|
3231
|
+
# Only return variants which have exactly this name.
|
3232
|
+
# Corresponds to the JSON property `variantName`
|
3233
|
+
# @return [String]
|
3234
|
+
attr_accessor :variant_name
|
3235
|
+
|
3236
|
+
# The beginning of the window (0-based, inclusive) for which
|
3237
|
+
# overlapping variants should be returned. If unspecified, defaults to 0.
|
3238
|
+
# Corresponds to the JSON property `start`
|
3239
|
+
# @return [String]
|
3240
|
+
attr_accessor :start
|
3241
|
+
|
3242
|
+
# Required. Only return variants in this reference sequence.
|
3243
|
+
# Corresponds to the JSON property `referenceName`
|
3244
|
+
# @return [String]
|
3245
|
+
attr_accessor :reference_name
|
3246
|
+
|
3247
|
+
# At most one variant set ID must be provided. Only variants from this
|
3248
|
+
# variant set will be returned. If omitted, a call set id must be included in
|
3249
|
+
# the request.
|
3250
|
+
# Corresponds to the JSON property `variantSetIds`
|
3251
|
+
# @return [Array<String>]
|
3252
|
+
attr_accessor :variant_set_ids
|
3253
|
+
|
3254
|
+
# The end of the window, 0-based exclusive. If unspecified or 0, defaults to
|
3255
|
+
# the length of the reference.
|
3256
|
+
# Corresponds to the JSON property `end`
|
3257
|
+
# @return [String]
|
3258
|
+
attr_accessor :end
|
3259
|
+
|
3260
|
+
# The continuation token, which is used to page through large result sets.
|
3261
|
+
# To get the next page of results, set this parameter to the value of
|
3262
|
+
# `nextPageToken` from the previous response.
|
3263
|
+
# Corresponds to the JSON property `pageToken`
|
3264
|
+
# @return [String]
|
3265
|
+
attr_accessor :page_token
|
3266
|
+
|
3267
|
+
# The maximum number of calls to return in a single page. Note that this
|
3268
|
+
# limit may be exceeded in the event that a matching variant contains more
|
3269
|
+
# calls than the requested maximum. If unspecified, defaults to 5000. The
|
3270
|
+
# maximum value is 10000.
|
3271
|
+
# Corresponds to the JSON property `maxCalls`
|
3272
|
+
# @return [Fixnum]
|
3273
|
+
attr_accessor :max_calls
|
3274
|
+
|
3275
|
+
def initialize(**args)
|
3276
|
+
update!(**args)
|
3277
|
+
end
|
3278
|
+
|
3279
|
+
# Update properties of this object
|
3280
|
+
def update!(**args)
|
3281
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
3282
|
+
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
3283
|
+
@variant_name = args[:variant_name] if args.key?(:variant_name)
|
3284
|
+
@start = args[:start] if args.key?(:start)
|
3285
|
+
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
3286
|
+
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
3287
|
+
@end = args[:end] if args.key?(:end)
|
3288
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
3289
|
+
@max_calls = args[:max_calls] if args.key?(:max_calls)
|
3290
|
+
end
|
3291
|
+
end
|
3292
|
+
|
3293
|
+
# The read group set search request.
|
3294
|
+
class SearchReadGroupSetsRequest
|
3295
|
+
include Google::Apis::Core::Hashable
|
3296
|
+
|
3297
|
+
# Restricts this query to read group sets within the given datasets. At least
|
3298
|
+
# one ID must be provided.
|
3299
|
+
# Corresponds to the JSON property `datasetIds`
|
3300
|
+
# @return [Array<String>]
|
3301
|
+
attr_accessor :dataset_ids
|
3302
|
+
|
3303
|
+
# Only return read group sets for which a substring of the name matches this
|
3304
|
+
# string.
|
3305
|
+
# Corresponds to the JSON property `name`
|
3306
|
+
# @return [String]
|
3307
|
+
attr_accessor :name
|
3308
|
+
|
3309
|
+
# The continuation token, which is used to page through large result sets.
|
3310
|
+
# To get the next page of results, set this parameter to the value of
|
3311
|
+
# `nextPageToken` from the previous response.
|
3312
|
+
# Corresponds to the JSON property `pageToken`
|
3313
|
+
# @return [String]
|
3314
|
+
attr_accessor :page_token
|
3315
|
+
|
3316
|
+
# The maximum number of results to return in a single page. If unspecified,
|
3317
|
+
# defaults to 256. The maximum value is 1024.
|
3318
|
+
# Corresponds to the JSON property `pageSize`
|
3319
|
+
# @return [Fixnum]
|
3320
|
+
attr_accessor :page_size
|
3321
|
+
|
3322
|
+
def initialize(**args)
|
3323
|
+
update!(**args)
|
3324
|
+
end
|
3325
|
+
|
3326
|
+
# Update properties of this object
|
3327
|
+
def update!(**args)
|
3328
|
+
@dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
|
3329
|
+
@name = args[:name] if args.key?(:name)
|
3330
|
+
@page_token = args[:page_token] if args.key?(:page_token)
|
3331
|
+
@page_size = args[:page_size] if args.key?(:page_size)
|
3332
|
+
end
|
3333
|
+
end
|
3334
|
+
|
3335
|
+
#
|
3336
|
+
class SearchAnnotationsResponse
|
3337
|
+
include Google::Apis::Core::Hashable
|
3338
|
+
|
3339
|
+
# The continuation token, which is used to page through large result sets.
|
3340
|
+
# Provide this value in a subsequent request to return the next page of
|
3341
|
+
# results. This field will be empty if there aren't any additional results.
|
3342
|
+
# Corresponds to the JSON property `nextPageToken`
|
3343
|
+
# @return [String]
|
3344
|
+
attr_accessor :next_page_token
|
3345
|
+
|
3346
|
+
# The matching annotations.
|
3347
|
+
# Corresponds to the JSON property `annotations`
|
3348
|
+
# @return [Array<Google::Apis::GenomicsV1::Annotation>]
|
3349
|
+
attr_accessor :annotations
|
3350
|
+
|
3351
|
+
def initialize(**args)
|
3352
|
+
update!(**args)
|
3353
|
+
end
|
3354
|
+
|
3355
|
+
# Update properties of this object
|
3356
|
+
def update!(**args)
|
3357
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
3358
|
+
@annotations = args[:annotations] if args.key?(:annotations)
|
3359
|
+
end
|
3360
|
+
end
|
3361
|
+
|
3362
|
+
#
|
3363
|
+
class ClinicalCondition
|
3364
|
+
include Google::Apis::Core::Hashable
|
3365
|
+
|
3366
|
+
# The OMIM id for this condition.
|
3367
|
+
# Search for these IDs at http://omim.org/
|
3368
|
+
# Corresponds to the JSON property `omimId`
|
3369
|
+
# @return [String]
|
3370
|
+
attr_accessor :omim_id
|
3371
|
+
|
3372
|
+
# The set of external IDs for this condition.
|
3373
|
+
# Corresponds to the JSON property `externalIds`
|
3374
|
+
# @return [Array<Google::Apis::GenomicsV1::ExternalId>]
|
3375
|
+
attr_accessor :external_ids
|
3376
|
+
|
3377
|
+
# The MedGen concept id associated with this gene.
|
3378
|
+
# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
|
3379
|
+
# Corresponds to the JSON property `conceptId`
|
3380
|
+
# @return [String]
|
3381
|
+
attr_accessor :concept_id
|
3382
|
+
|
3383
|
+
# A set of names for the condition.
|
3384
|
+
# Corresponds to the JSON property `names`
|
3385
|
+
# @return [Array<String>]
|
3386
|
+
attr_accessor :names
|
3387
|
+
|
3388
|
+
def initialize(**args)
|
3389
|
+
update!(**args)
|
3390
|
+
end
|
3391
|
+
|
3392
|
+
# Update properties of this object
|
3393
|
+
def update!(**args)
|
3394
|
+
@omim_id = args[:omim_id] if args.key?(:omim_id)
|
3395
|
+
@external_ids = args[:external_ids] if args.key?(:external_ids)
|
3396
|
+
@concept_id = args[:concept_id] if args.key?(:concept_id)
|
3397
|
+
@names = args[:names] if args.key?(:names)
|
3398
|
+
end
|
3399
|
+
end
|
3400
|
+
|
3401
|
+
# The read search response.
|
3402
|
+
class SearchReadsResponse
|
3403
|
+
include Google::Apis::Core::Hashable
|
3404
|
+
|
3405
|
+
# The continuation token, which is used to page through large result sets.
|
3406
|
+
# Provide this value in a subsequent request to return the next page of
|
3407
|
+
# results. This field will be empty if there aren't any additional results.
|
3408
|
+
# Corresponds to the JSON property `nextPageToken`
|
3409
|
+
# @return [String]
|
3410
|
+
attr_accessor :next_page_token
|
3411
|
+
|
3412
|
+
# The list of matching alignments sorted by mapped genomic coordinate,
|
3413
|
+
# if any, ascending in position within the same reference. Unmapped reads,
|
3414
|
+
# which have no position, are returned contiguously and are sorted in
|
3415
|
+
# ascending lexicographic order by fragment name.
|
3416
|
+
# Corresponds to the JSON property `alignments`
|
3417
|
+
# @return [Array<Google::Apis::GenomicsV1::Read>]
|
3418
|
+
attr_accessor :alignments
|
3419
|
+
|
3420
|
+
def initialize(**args)
|
3421
|
+
update!(**args)
|
3422
|
+
end
|
3423
|
+
|
3424
|
+
# Update properties of this object
|
3425
|
+
def update!(**args)
|
3426
|
+
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
3427
|
+
@alignments = args[:alignments] if args.key?(:alignments)
|
3428
|
+
end
|
3429
|
+
end
|
3430
|
+
|
3431
|
+
#
|
3432
|
+
class Program
|
3433
|
+
include Google::Apis::Core::Hashable
|
3434
|
+
|
3435
|
+
# The display name of the program. This is typically the colloquial name of
|
3436
|
+
# the tool used, for example 'bwa' or 'picard'.
|
3437
|
+
# Corresponds to the JSON property `name`
|
3438
|
+
# @return [String]
|
3439
|
+
attr_accessor :name
|
3440
|
+
|
3441
|
+
# The command line used to run this program.
|
3442
|
+
# Corresponds to the JSON property `commandLine`
|
3443
|
+
# @return [String]
|
3444
|
+
attr_accessor :command_line
|
3445
|
+
|
3446
|
+
# The ID of the program run before this one.
|
3447
|
+
# Corresponds to the JSON property `prevProgramId`
|
3448
|
+
# @return [String]
|
3449
|
+
attr_accessor :prev_program_id
|
3450
|
+
|
3451
|
+
# The user specified locally unique ID of the program. Used along with
|
3452
|
+
# `prevProgramId` to define an ordering between programs.
|
3453
|
+
# Corresponds to the JSON property `id`
|
3454
|
+
# @return [String]
|
3455
|
+
attr_accessor :id
|
3456
|
+
|
3457
|
+
# The version of the program run.
|
3458
|
+
# Corresponds to the JSON property `version`
|
3459
|
+
# @return [String]
|
3460
|
+
attr_accessor :version
|
3461
|
+
|
3462
|
+
def initialize(**args)
|
3463
|
+
update!(**args)
|
3464
|
+
end
|
3465
|
+
|
3466
|
+
# Update properties of this object
|
3467
|
+
def update!(**args)
|
3468
|
+
@name = args[:name] if args.key?(:name)
|
3469
|
+
@command_line = args[:command_line] if args.key?(:command_line)
|
3470
|
+
@prev_program_id = args[:prev_program_id] if args.key?(:prev_program_id)
|
3471
|
+
@id = args[:id] if args.key?(:id)
|
3472
|
+
@version = args[:version] if args.key?(:version)
|
3473
|
+
end
|
3474
|
+
end
|
3475
|
+
end
|
3476
|
+
end
|
3477
|
+
end
|