google-api-client 0.11.3 → 0.12.0

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Files changed (397) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +51 -0
  3. data/api_names.yaml +32317 -34465
  4. data/generated/google/apis/acceleratedmobilepageurl_v1/classes.rb +44 -44
  5. data/generated/google/apis/acceleratedmobilepageurl_v1/representations.rb +14 -14
  6. data/generated/google/apis/acceleratedmobilepageurl_v1/service.rb +10 -10
  7. data/generated/google/apis/adexchangebuyer2_v2beta1.rb +1 -1
  8. data/generated/google/apis/adexchangebuyer2_v2beta1/classes.rb +305 -305
  9. data/generated/google/apis/adexchangebuyer2_v2beta1/representations.rb +82 -82
  10. data/generated/google/apis/adexchangebuyer2_v2beta1/service.rb +106 -106
  11. data/generated/google/apis/adexchangebuyer_v1_4/classes.rb +6 -6
  12. data/generated/google/apis/adexchangebuyer_v1_4/representations.rb +3 -3
  13. data/generated/google/apis/adexchangebuyer_v1_4/service.rb +3 -3
  14. data/generated/google/apis/adexchangeseller_v2_0/service.rb +10 -10
  15. data/generated/google/apis/admin_directory_v1/service.rb +26 -26
  16. data/generated/google/apis/adsense_v1_4.rb +1 -1
  17. data/generated/google/apis/adsense_v1_4/classes.rb +2 -2
  18. data/generated/google/apis/adsense_v1_4/representations.rb +3 -3
  19. data/generated/google/apis/adsense_v1_4/service.rb +44 -44
  20. data/generated/google/apis/adsensehost_v4_1.rb +1 -1
  21. data/generated/google/apis/adsensehost_v4_1/service.rb +22 -22
  22. data/generated/google/apis/analytics_v3/classes.rb +3 -3
  23. data/generated/google/apis/analytics_v3/representations.rb +3 -3
  24. data/generated/google/apis/analytics_v3/service.rb +82 -82
  25. data/generated/google/apis/analyticsreporting_v4.rb +1 -1
  26. data/generated/google/apis/analyticsreporting_v4/classes.rb +916 -916
  27. data/generated/google/apis/analyticsreporting_v4/representations.rb +167 -167
  28. data/generated/google/apis/analyticsreporting_v4/service.rb +7 -7
  29. data/generated/google/apis/androidenterprise_v1.rb +1 -1
  30. data/generated/google/apis/androidenterprise_v1/classes.rb +10 -10
  31. data/generated/google/apis/androidenterprise_v1/representations.rb +20 -20
  32. data/generated/google/apis/androidenterprise_v1/service.rb +43 -43
  33. data/generated/google/apis/androidpublisher_v2/classes.rb +26 -26
  34. data/generated/google/apis/androidpublisher_v2/representations.rb +46 -46
  35. data/generated/google/apis/androidpublisher_v2/service.rb +95 -95
  36. data/generated/google/apis/appengine_v1.rb +1 -1
  37. data/generated/google/apis/appengine_v1/classes.rb +825 -817
  38. data/generated/google/apis/appengine_v1/representations.rb +185 -184
  39. data/generated/google/apis/appengine_v1/service.rb +220 -216
  40. data/generated/google/apis/appstate_v1.rb +1 -1
  41. data/generated/google/apis/bigquery_v2.rb +1 -1
  42. data/generated/google/apis/bigquery_v2/classes.rb +9 -7
  43. data/generated/google/apis/bigquery_v2/representations.rb +8 -8
  44. data/generated/google/apis/bigquery_v2/service.rb +13 -13
  45. data/generated/google/apis/blogger_v3/service.rb +3 -3
  46. data/generated/google/apis/books_v1/classes.rb +55 -55
  47. data/generated/google/apis/books_v1/representations.rb +67 -67
  48. data/generated/google/apis/books_v1/service.rb +82 -82
  49. data/generated/google/apis/calendar_v3.rb +1 -1
  50. data/generated/google/apis/calendar_v3/classes.rb +6 -6
  51. data/generated/google/apis/calendar_v3/representations.rb +3 -3
  52. data/generated/google/apis/calendar_v3/service.rb +2 -2
  53. data/generated/google/apis/civicinfo_v2/classes.rb +1 -1
  54. data/generated/google/apis/civicinfo_v2/representations.rb +2 -2
  55. data/generated/google/apis/civicinfo_v2/service.rb +8 -8
  56. data/generated/google/apis/classroom_v1.rb +24 -24
  57. data/generated/google/apis/classroom_v1/classes.rb +381 -381
  58. data/generated/google/apis/classroom_v1/representations.rb +108 -108
  59. data/generated/google/apis/classroom_v1/service.rb +503 -503
  60. data/generated/google/apis/cloudbuild_v1.rb +1 -1
  61. data/generated/google/apis/cloudbuild_v1/classes.rb +219 -219
  62. data/generated/google/apis/cloudbuild_v1/representations.rb +62 -62
  63. data/generated/google/apis/cloudbuild_v1/service.rb +165 -165
  64. data/generated/google/apis/clouddebugger_v2.rb +1 -1
  65. data/generated/google/apis/clouddebugger_v2/classes.rb +133 -133
  66. data/generated/google/apis/clouddebugger_v2/representations.rb +29 -29
  67. data/generated/google/apis/clouddebugger_v2/service.rb +54 -54
  68. data/generated/google/apis/clouderrorreporting_v1beta1.rb +1 -1
  69. data/generated/google/apis/clouderrorreporting_v1beta1/classes.rb +177 -177
  70. data/generated/google/apis/clouderrorreporting_v1beta1/representations.rb +47 -47
  71. data/generated/google/apis/clouderrorreporting_v1beta1/service.rb +123 -123
  72. data/generated/google/apis/cloudfunctions_v1.rb +1 -1
  73. data/generated/google/apis/cloudfunctions_v1/service.rb +6 -6
  74. data/generated/google/apis/cloudkms_v1.rb +3 -3
  75. data/generated/google/apis/cloudkms_v1/classes.rb +229 -229
  76. data/generated/google/apis/cloudkms_v1/representations.rb +54 -54
  77. data/generated/google/apis/cloudkms_v1/service.rb +224 -224
  78. data/generated/google/apis/cloudresourcemanager_v1.rb +3 -3
  79. data/generated/google/apis/cloudresourcemanager_v1/classes.rb +1199 -1199
  80. data/generated/google/apis/cloudresourcemanager_v1/representations.rb +192 -192
  81. data/generated/google/apis/cloudresourcemanager_v1/service.rb +122 -122
  82. data/generated/google/apis/cloudresourcemanager_v1beta1/classes.rb +495 -495
  83. data/generated/google/apis/cloudresourcemanager_v1beta1/representations.rb +92 -92
  84. data/generated/google/apis/cloudresourcemanager_v1beta1/service.rb +320 -320
  85. data/generated/google/apis/cloudtrace_v1.rb +4 -4
  86. data/generated/google/apis/cloudtrace_v1/classes.rb +44 -44
  87. data/generated/google/apis/cloudtrace_v1/representations.rb +13 -13
  88. data/generated/google/apis/cloudtrace_v1/service.rb +28 -28
  89. data/generated/google/apis/compute_beta.rb +1 -1
  90. data/generated/google/apis/compute_beta/classes.rb +57 -15
  91. data/generated/google/apis/compute_beta/representations.rb +30 -14
  92. data/generated/google/apis/compute_beta/service.rb +52 -52
  93. data/generated/google/apis/compute_v1.rb +1 -1
  94. data/generated/google/apis/compute_v1/classes.rb +223 -10
  95. data/generated/google/apis/compute_v1/representations.rb +85 -16
  96. data/generated/google/apis/compute_v1/service.rb +327 -51
  97. data/generated/google/apis/container_v1/classes.rb +267 -267
  98. data/generated/google/apis/container_v1/representations.rb +61 -61
  99. data/generated/google/apis/container_v1/service.rb +123 -123
  100. data/generated/google/apis/content_v2.rb +1 -1
  101. data/generated/google/apis/content_v2/classes.rb +71 -71
  102. data/generated/google/apis/content_v2/representations.rb +105 -105
  103. data/generated/google/apis/content_v2/service.rb +120 -120
  104. data/generated/google/apis/dataflow_v1b3.rb +4 -4
  105. data/generated/google/apis/dataflow_v1b3/classes.rb +3442 -3452
  106. data/generated/google/apis/dataflow_v1b3/representations.rb +388 -389
  107. data/generated/google/apis/dataflow_v1b3/service.rb +265 -265
  108. data/generated/google/apis/dataproc_v1.rb +1 -1
  109. data/generated/google/apis/dataproc_v1/classes.rb +1059 -1059
  110. data/generated/google/apis/dataproc_v1/representations.rb +147 -147
  111. data/generated/google/apis/dataproc_v1/service.rb +309 -305
  112. data/generated/google/apis/datastore_v1.rb +1 -1
  113. data/generated/google/apis/datastore_v1/classes.rb +818 -818
  114. data/generated/google/apis/datastore_v1/representations.rb +151 -151
  115. data/generated/google/apis/datastore_v1/service.rb +62 -62
  116. data/generated/google/apis/deploymentmanager_v2/classes.rb +5 -5
  117. data/generated/google/apis/deploymentmanager_v2/representations.rb +10 -10
  118. data/generated/google/apis/deploymentmanager_v2/service.rb +20 -20
  119. data/generated/google/apis/discovery_v1/classes.rb +4 -4
  120. data/generated/google/apis/discovery_v1/representations.rb +2 -2
  121. data/generated/google/apis/discovery_v1/service.rb +1 -1
  122. data/generated/google/apis/dns_v1.rb +1 -1
  123. data/generated/google/apis/dns_v1/classes.rb +3 -3
  124. data/generated/google/apis/dns_v1/representations.rb +6 -6
  125. data/generated/google/apis/dns_v1/service.rb +12 -12
  126. data/generated/google/apis/dns_v2beta1.rb +1 -1
  127. data/generated/google/apis/doubleclickbidmanager_v1.rb +1 -1
  128. data/generated/google/apis/doubleclickbidmanager_v1/service.rb +8 -8
  129. data/generated/google/apis/doubleclicksearch_v2.rb +1 -1
  130. data/generated/google/apis/drive_v2/service.rb +1 -1
  131. data/generated/google/apis/drive_v3/service.rb +1 -1
  132. data/generated/google/apis/firebasedynamiclinks_v1.rb +1 -1
  133. data/generated/google/apis/firebasedynamiclinks_v1/classes.rb +188 -188
  134. data/generated/google/apis/firebasedynamiclinks_v1/representations.rb +62 -62
  135. data/generated/google/apis/firebasedynamiclinks_v1/service.rb +4 -4
  136. data/generated/google/apis/firebaserules_v1.rb +1 -1
  137. data/generated/google/apis/firebaserules_v1/classes.rb +403 -206
  138. data/generated/google/apis/firebaserules_v1/representations.rb +134 -54
  139. data/generated/google/apis/firebaserules_v1/service.rb +89 -89
  140. data/generated/google/apis/fusiontables_v2/service.rb +2 -2
  141. data/generated/google/apis/games_configuration_v1configuration.rb +1 -1
  142. data/generated/google/apis/games_configuration_v1configuration/classes.rb +2 -2
  143. data/generated/google/apis/games_configuration_v1configuration/representations.rb +4 -4
  144. data/generated/google/apis/games_configuration_v1configuration/service.rb +8 -8
  145. data/generated/google/apis/games_management_v1management.rb +1 -1
  146. data/generated/google/apis/games_v1.rb +1 -1
  147. data/generated/google/apis/games_v1/classes.rb +23 -23
  148. data/generated/google/apis/games_v1/representations.rb +43 -43
  149. data/generated/google/apis/games_v1/service.rb +72 -72
  150. data/generated/google/apis/genomics_v1.rb +7 -7
  151. data/generated/google/apis/genomics_v1/classes.rb +2296 -2297
  152. data/generated/google/apis/genomics_v1/representations.rb +298 -298
  153. data/generated/google/apis/genomics_v1/service.rb +1160 -1160
  154. data/generated/google/apis/groupssettings_v1/service.rb +0 -3
  155. data/generated/google/apis/iam_v1.rb +1 -1
  156. data/generated/google/apis/iam_v1/classes.rb +235 -235
  157. data/generated/google/apis/iam_v1/representations.rb +72 -72
  158. data/generated/google/apis/iam_v1/service.rb +189 -189
  159. data/generated/google/apis/identitytoolkit_v3/classes.rb +15 -15
  160. data/generated/google/apis/identitytoolkit_v3/representations.rb +30 -30
  161. data/generated/google/apis/identitytoolkit_v3/service.rb +64 -64
  162. data/generated/google/apis/kgsearch_v1/classes.rb +6 -6
  163. data/generated/google/apis/kgsearch_v1/representations.rb +1 -1
  164. data/generated/google/apis/kgsearch_v1/service.rb +10 -10
  165. data/generated/google/apis/language_v1/classes.rb +220 -220
  166. data/generated/google/apis/language_v1/representations.rb +81 -81
  167. data/generated/google/apis/language_v1/service.rb +43 -43
  168. data/generated/google/apis/language_v1beta1/classes.rb +448 -448
  169. data/generated/google/apis/language_v1beta1/representations.rb +106 -106
  170. data/generated/google/apis/language_v1beta1/service.rb +31 -31
  171. data/generated/google/apis/licensing_v1/service.rb +2 -2
  172. data/generated/google/apis/logging_v2/classes.rb +737 -737
  173. data/generated/google/apis/logging_v2/representations.rb +120 -120
  174. data/generated/google/apis/logging_v2/service.rb +479 -479
  175. data/generated/google/apis/logging_v2beta1/classes.rb +293 -293
  176. data/generated/google/apis/logging_v2beta1/representations.rb +54 -54
  177. data/generated/google/apis/logging_v2beta1/service.rb +349 -349
  178. data/generated/google/apis/manufacturers_v1/classes.rb +423 -423
  179. data/generated/google/apis/manufacturers_v1/representations.rb +61 -61
  180. data/generated/google/apis/manufacturers_v1/service.rb +8 -8
  181. data/generated/google/apis/mirror_v1/classes.rb +5 -5
  182. data/generated/google/apis/mirror_v1/representations.rb +10 -10
  183. data/generated/google/apis/mirror_v1/service.rb +20 -20
  184. data/generated/google/apis/ml_v1.rb +1 -1
  185. data/generated/google/apis/ml_v1/classes.rb +1285 -1205
  186. data/generated/google/apis/ml_v1/representations.rb +204 -174
  187. data/generated/google/apis/ml_v1/service.rb +150 -145
  188. data/generated/google/apis/monitoring_v3.rb +1 -1
  189. data/generated/google/apis/monitoring_v3/classes.rb +880 -880
  190. data/generated/google/apis/monitoring_v3/representations.rb +154 -154
  191. data/generated/google/apis/monitoring_v3/service.rb +299 -299
  192. data/generated/google/apis/mybusiness_v3/service.rb +5 -5
  193. data/generated/google/apis/oauth2_v2/service.rb +1 -1
  194. data/generated/google/apis/pagespeedonline_v2/classes.rb +11 -11
  195. data/generated/google/apis/pagespeedonline_v2/representations.rb +13 -13
  196. data/generated/google/apis/pagespeedonline_v2/service.rb +1 -1
  197. data/generated/google/apis/partners_v2.rb +1 -1
  198. data/generated/google/apis/partners_v2/classes.rb +524 -509
  199. data/generated/google/apis/partners_v2/representations.rb +115 -111
  200. data/generated/google/apis/partners_v2/service.rb +287 -287
  201. data/generated/google/apis/people_v1.rb +13 -13
  202. data/generated/google/apis/people_v1/classes.rb +1150 -1150
  203. data/generated/google/apis/people_v1/representations.rb +258 -258
  204. data/generated/google/apis/people_v1/service.rb +7 -7
  205. data/generated/google/apis/plus_domains_v1.rb +1 -1
  206. data/generated/google/apis/plus_domains_v1/service.rb +4 -4
  207. data/generated/google/apis/plus_v1.rb +1 -1
  208. data/generated/google/apis/plus_v1/service.rb +1 -1
  209. data/generated/google/apis/prediction_v1_6/service.rb +8 -8
  210. data/generated/google/apis/proximitybeacon_v1beta1/classes.rb +554 -554
  211. data/generated/google/apis/proximitybeacon_v1beta1/representations.rb +108 -108
  212. data/generated/google/apis/proximitybeacon_v1beta1/service.rb +224 -224
  213. data/generated/google/apis/pubsub_v1/classes.rb +228 -228
  214. data/generated/google/apis/pubsub_v1/representations.rb +69 -69
  215. data/generated/google/apis/pubsub_v1/service.rb +182 -182
  216. data/generated/google/apis/qpx_express_v1/classes.rb +2 -2
  217. data/generated/google/apis/qpx_express_v1/representations.rb +4 -4
  218. data/generated/google/apis/qpx_express_v1/service.rb +8 -8
  219. data/generated/google/apis/replicapool_v1beta2/classes.rb +5 -5
  220. data/generated/google/apis/replicapool_v1beta2/representations.rb +10 -10
  221. data/generated/google/apis/replicapool_v1beta2/service.rb +21 -21
  222. data/generated/google/apis/replicapoolupdater_v1beta1/service.rb +1 -1
  223. data/generated/google/apis/resourceviews_v1beta2/classes.rb +5 -5
  224. data/generated/google/apis/resourceviews_v1beta2/representations.rb +10 -10
  225. data/generated/google/apis/resourceviews_v1beta2/service.rb +20 -20
  226. data/generated/google/apis/runtimeconfig_v1.rb +3 -3
  227. data/generated/google/apis/runtimeconfig_v1/classes.rb +19 -19
  228. data/generated/google/apis/runtimeconfig_v1/representations.rb +10 -10
  229. data/generated/google/apis/runtimeconfig_v1/service.rb +4 -4
  230. data/generated/google/apis/script_v1.rb +9 -9
  231. data/generated/google/apis/script_v1/classes.rb +94 -94
  232. data/generated/google/apis/script_v1/representations.rb +26 -26
  233. data/generated/google/apis/searchconsole_v1.rb +1 -1
  234. data/generated/google/apis/searchconsole_v1/classes.rb +65 -65
  235. data/generated/google/apis/searchconsole_v1/representations.rb +27 -27
  236. data/generated/google/apis/searchconsole_v1/service.rb +6 -6
  237. data/generated/google/apis/servicecontrol_v1/classes.rb +1131 -1131
  238. data/generated/google/apis/servicecontrol_v1/representations.rb +195 -195
  239. data/generated/google/apis/servicecontrol_v1/service.rb +57 -57
  240. data/generated/google/apis/servicemanagement_v1.rb +7 -7
  241. data/generated/google/apis/servicemanagement_v1/classes.rb +3543 -3585
  242. data/generated/google/apis/servicemanagement_v1/representations.rb +556 -556
  243. data/generated/google/apis/servicemanagement_v1/service.rb +309 -309
  244. data/generated/google/apis/serviceuser_v1.rb +4 -4
  245. data/generated/google/apis/serviceuser_v1/classes.rb +2734 -2776
  246. data/generated/google/apis/serviceuser_v1/representations.rb +398 -398
  247. data/generated/google/apis/serviceuser_v1/service.rb +16 -16
  248. data/generated/google/apis/sheets_v4/classes.rb +1489 -1489
  249. data/generated/google/apis/sheets_v4/representations.rb +324 -324
  250. data/generated/google/apis/sheets_v4/service.rb +49 -49
  251. data/generated/google/apis/site_verification_v1/classes.rb +6 -6
  252. data/generated/google/apis/site_verification_v1/representations.rb +8 -8
  253. data/generated/google/apis/site_verification_v1/service.rb +12 -12
  254. data/generated/google/apis/slides_v1.rb +4 -4
  255. data/generated/google/apis/slides_v1/classes.rb +2907 -2907
  256. data/generated/google/apis/slides_v1/representations.rb +695 -695
  257. data/generated/google/apis/slides_v1/service.rb +40 -40
  258. data/generated/google/apis/sourcerepo_v1.rb +7 -1
  259. data/generated/google/apis/sourcerepo_v1/classes.rb +459 -452
  260. data/generated/google/apis/sourcerepo_v1/representations.rb +90 -89
  261. data/generated/google/apis/sourcerepo_v1/service.rb +101 -100
  262. data/generated/google/apis/spanner_v1/classes.rb +2557 -2557
  263. data/generated/google/apis/spanner_v1/representations.rb +205 -205
  264. data/generated/google/apis/spanner_v1/service.rb +525 -525
  265. data/generated/google/apis/speech_v1beta1.rb +1 -1
  266. data/generated/google/apis/speech_v1beta1/classes.rb +73 -73
  267. data/generated/google/apis/speech_v1beta1/representations.rb +25 -25
  268. data/generated/google/apis/speech_v1beta1/service.rb +33 -33
  269. data/generated/google/apis/sqladmin_v1beta4.rb +1 -1
  270. data/generated/google/apis/sqladmin_v1beta4/classes.rb +16 -15
  271. data/generated/google/apis/sqladmin_v1beta4/representations.rb +28 -28
  272. data/generated/google/apis/sqladmin_v1beta4/service.rb +58 -57
  273. data/generated/google/apis/storage_v1/classes.rb +6 -6
  274. data/generated/google/apis/storage_v1/representations.rb +4 -4
  275. data/generated/google/apis/storage_v1/service.rb +1 -1
  276. data/generated/google/apis/storagetransfer_v1.rb +1 -1
  277. data/generated/google/apis/storagetransfer_v1/classes.rb +357 -357
  278. data/generated/google/apis/storagetransfer_v1/representations.rb +87 -87
  279. data/generated/google/apis/storagetransfer_v1/service.rb +53 -48
  280. data/generated/google/apis/tagmanager_v1/service.rb +33 -33
  281. data/generated/google/apis/toolresults_v1beta3.rb +1 -1
  282. data/generated/google/apis/translate_v2.rb +1 -1
  283. data/generated/google/apis/translate_v2/classes.rb +46 -46
  284. data/generated/google/apis/translate_v2/representations.rb +22 -22
  285. data/generated/google/apis/translate_v2/service.rb +81 -74
  286. data/generated/google/apis/vision_v1/classes.rb +1290 -1290
  287. data/generated/google/apis/vision_v1/representations.rb +166 -166
  288. data/generated/google/apis/vision_v1/service.rb +6 -6
  289. data/generated/google/apis/webmasters_v3/classes.rb +4 -4
  290. data/generated/google/apis/webmasters_v3/representations.rb +8 -8
  291. data/generated/google/apis/webmasters_v3/service.rb +21 -21
  292. data/generated/google/apis/youtube_analytics_v1.rb +1 -1
  293. data/generated/google/apis/youtube_analytics_v1/classes.rb +2 -2
  294. data/generated/google/apis/youtube_analytics_v1/representations.rb +4 -4
  295. data/generated/google/apis/youtube_analytics_v1/service.rb +8 -8
  296. data/generated/google/apis/youtube_v3/classes.rb +20 -20
  297. data/generated/google/apis/youtube_v3/representations.rb +40 -40
  298. data/generated/google/apis/youtube_v3/service.rb +80 -80
  299. data/generated/google/apis/youtubereporting_v1.rb +1 -1
  300. data/generated/google/apis/youtubereporting_v1/classes.rb +127 -127
  301. data/generated/google/apis/youtubereporting_v1/representations.rb +36 -36
  302. data/generated/google/apis/youtubereporting_v1/service.rb +90 -90
  303. data/google-api-client.gemspec +3 -3
  304. data/lib/google/apis/core/base_service.rb +6 -0
  305. data/lib/google/apis/generator/annotator.rb +2 -2
  306. data/lib/google/apis/generator/model.rb +2 -2
  307. data/lib/google/apis/version.rb +1 -1
  308. metadata +11 -94
  309. data/dl.rb +0 -0
  310. data/generated/google/apis/adexchangebuyer_v1_3.rb +0 -35
  311. data/generated/google/apis/adexchangebuyer_v1_3/classes.rb +0 -1335
  312. data/generated/google/apis/adexchangebuyer_v1_3/representations.rb +0 -446
  313. data/generated/google/apis/adexchangebuyer_v1_3/service.rb +0 -872
  314. data/generated/google/apis/appengine_v1beta4.rb +0 -35
  315. data/generated/google/apis/appengine_v1beta4/classes.rb +0 -1585
  316. data/generated/google/apis/appengine_v1beta4/representations.rb +0 -542
  317. data/generated/google/apis/appengine_v1beta4/service.rb +0 -477
  318. data/generated/google/apis/appengine_v1beta5.rb +0 -40
  319. data/generated/google/apis/appengine_v1beta5/classes.rb +0 -2094
  320. data/generated/google/apis/appengine_v1beta5/representations.rb +0 -802
  321. data/generated/google/apis/appengine_v1beta5/service.rb +0 -867
  322. data/generated/google/apis/autoscaler_v1beta2.rb +0 -38
  323. data/generated/google/apis/autoscaler_v1beta2/classes.rb +0 -710
  324. data/generated/google/apis/autoscaler_v1beta2/representations.rb +0 -296
  325. data/generated/google/apis/autoscaler_v1beta2/service.rb +0 -478
  326. data/generated/google/apis/classroom_v1beta1.rb +0 -49
  327. data/generated/google/apis/classroom_v1beta1/classes.rb +0 -447
  328. data/generated/google/apis/classroom_v1beta1/representations.rb +0 -190
  329. data/generated/google/apis/classroom_v1beta1/service.rb +0 -791
  330. data/generated/google/apis/cloudkms_v1beta1.rb +0 -35
  331. data/generated/google/apis/cloudkms_v1beta1/classes.rb +0 -1039
  332. data/generated/google/apis/cloudkms_v1beta1/representations.rb +0 -448
  333. data/generated/google/apis/cloudkms_v1beta1/service.rb +0 -933
  334. data/generated/google/apis/cloudlatencytest_v2.rb +0 -34
  335. data/generated/google/apis/cloudlatencytest_v2/classes.rb +0 -195
  336. data/generated/google/apis/cloudlatencytest_v2/representations.rb +0 -127
  337. data/generated/google/apis/cloudlatencytest_v2/service.rb +0 -135
  338. data/generated/google/apis/container_v1beta1.rb +0 -35
  339. data/generated/google/apis/container_v1beta1/classes.rb +0 -466
  340. data/generated/google/apis/container_v1beta1/representations.rb +0 -177
  341. data/generated/google/apis/container_v1beta1/service.rb +0 -394
  342. data/generated/google/apis/coordinate_v1.rb +0 -37
  343. data/generated/google/apis/coordinate_v1/classes.rb +0 -669
  344. data/generated/google/apis/coordinate_v1/representations.rb +0 -321
  345. data/generated/google/apis/coordinate_v1/service.rb +0 -678
  346. data/generated/google/apis/datastore_v1beta2.rb +0 -40
  347. data/generated/google/apis/datastore_v1beta2/classes.rb +0 -1186
  348. data/generated/google/apis/datastore_v1beta2/representations.rb +0 -594
  349. data/generated/google/apis/datastore_v1beta2/service.rb +0 -294
  350. data/generated/google/apis/datastore_v1beta3.rb +0 -38
  351. data/generated/google/apis/datastore_v1beta3/classes.rb +0 -1284
  352. data/generated/google/apis/datastore_v1beta3/representations.rb +0 -572
  353. data/generated/google/apis/datastore_v1beta3/service.rb +0 -259
  354. data/generated/google/apis/deploymentmanager_v2beta2.rb +0 -44
  355. data/generated/google/apis/deploymentmanager_v2beta2/classes.rb +0 -843
  356. data/generated/google/apis/deploymentmanager_v2beta2/representations.rb +0 -306
  357. data/generated/google/apis/deploymentmanager_v2beta2/service.rb +0 -689
  358. data/generated/google/apis/dfareporting_v2_1.rb +0 -37
  359. data/generated/google/apis/dfareporting_v2_1/classes.rb +0 -10770
  360. data/generated/google/apis/dfareporting_v2_1/representations.rb +0 -3438
  361. data/generated/google/apis/dfareporting_v2_1/service.rb +0 -8585
  362. data/generated/google/apis/dfareporting_v2_3.rb +0 -37
  363. data/generated/google/apis/dfareporting_v2_3/classes.rb +0 -10839
  364. data/generated/google/apis/dfareporting_v2_3/representations.rb +0 -3829
  365. data/generated/google/apis/dfareporting_v2_3/service.rb +0 -8581
  366. data/generated/google/apis/dfareporting_v2_5.rb +0 -40
  367. data/generated/google/apis/dfareporting_v2_5/classes.rb +0 -11225
  368. data/generated/google/apis/dfareporting_v2_5/representations.rb +0 -3982
  369. data/generated/google/apis/dfareporting_v2_5/service.rb +0 -8755
  370. data/generated/google/apis/dfareporting_v2_6.rb +0 -40
  371. data/generated/google/apis/dfareporting_v2_6/classes.rb +0 -11599
  372. data/generated/google/apis/dfareporting_v2_6/representations.rb +0 -4119
  373. data/generated/google/apis/dfareporting_v2_6/service.rb +0 -9026
  374. data/generated/google/apis/gan_v1beta1.rb +0 -31
  375. data/generated/google/apis/gan_v1beta1/classes.rb +0 -1428
  376. data/generated/google/apis/gan_v1beta1/representations.rb +0 -462
  377. data/generated/google/apis/gan_v1beta1/service.rb +0 -682
  378. data/generated/google/apis/genomics_v1beta2.rb +0 -46
  379. data/generated/google/apis/genomics_v1beta2/classes.rb +0 -3288
  380. data/generated/google/apis/genomics_v1beta2/representations.rb +0 -1194
  381. data/generated/google/apis/genomics_v1beta2/service.rb +0 -2392
  382. data/generated/google/apis/logging_v1beta3.rb +0 -47
  383. data/generated/google/apis/logging_v1beta3/classes.rb +0 -1079
  384. data/generated/google/apis/logging_v1beta3/representations.rb +0 -366
  385. data/generated/google/apis/logging_v1beta3/service.rb +0 -1001
  386. data/generated/google/apis/manager_v1beta2.rb +0 -53
  387. data/generated/google/apis/manager_v1beta2/classes.rb +0 -1287
  388. data/generated/google/apis/manager_v1beta2/representations.rb +0 -606
  389. data/generated/google/apis/manager_v1beta2/service.rb +0 -372
  390. data/generated/google/apis/pubsub_v1beta2.rb +0 -37
  391. data/generated/google/apis/pubsub_v1beta2/classes.rb +0 -620
  392. data/generated/google/apis/pubsub_v1beta2/representations.rb +0 -282
  393. data/generated/google/apis/pubsub_v1beta2/service.rb +0 -774
  394. data/generated/google/apis/tracing_v1.rb +0 -40
  395. data/generated/google/apis/tracing_v1/classes.rb +0 -664
  396. data/generated/google/apis/tracing_v1/representations.rb +0 -279
  397. data/generated/google/apis/tracing_v1/service.rb +0 -226
@@ -1,46 +0,0 @@
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_v1beta2/service.rb'
16
- require 'google/apis/genomics_v1beta2/classes.rb'
17
- require 'google/apis/genomics_v1beta2/representations.rb'
18
-
19
- module Google
20
- module Apis
21
- # Genomics API
22
- #
23
- # Provides access to Genomics data.
24
- #
25
- # @see https://developers.google.com/genomics/v1beta2/reference
26
- module GenomicsV1beta2
27
- VERSION = 'V1beta2'
28
- REVISION = '20150715'
29
-
30
- # View and manage your data in Google BigQuery
31
- AUTH_BIGQUERY = 'https://www.googleapis.com/auth/bigquery'
32
-
33
- # View and manage your data across Google Cloud Platform services
34
- AUTH_CLOUD_PLATFORM = 'https://www.googleapis.com/auth/cloud-platform'
35
-
36
- # Manage your data in Google Cloud Storage
37
- AUTH_DEVSTORAGE_READ_WRITE = 'https://www.googleapis.com/auth/devstorage.read_write'
38
-
39
- # View and manage Genomics data
40
- AUTH_GENOMICS = 'https://www.googleapis.com/auth/genomics'
41
-
42
- # View Genomics data
43
- AUTH_GENOMICS_READONLY = 'https://www.googleapis.com/auth/genomics.readonly'
44
- end
45
- end
46
- end
@@ -1,3288 +0,0 @@
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 GenomicsV1beta2
24
-
25
- # The read group set align request.
26
- class AlignReadGroupSetsRequest
27
- include Google::Apis::Core::Hashable
28
-
29
- # The BAM source files for alignment. Exactly one of readGroupSetId,
30
- # bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided.
31
- # The caller must have READ permissions for these files.
32
- # Corresponds to the JSON property `bamSourceUris`
33
- # @return [Array<String>]
34
- attr_accessor :bam_source_uris
35
-
36
- # Required. The ID of the dataset the newly aligned read group sets will belong
37
- # to. The caller must have WRITE permissions to this dataset.
38
- # Corresponds to the JSON property `datasetId`
39
- # @return [String]
40
- attr_accessor :dataset_id
41
-
42
- # Describes an interleaved FASTQ file source for alignment.
43
- # Corresponds to the JSON property `interleavedFastqSource`
44
- # @return [Google::Apis::GenomicsV1beta2::InterleavedFastqSource]
45
- attr_accessor :interleaved_fastq_source
46
-
47
- # Describes a paired-end FASTQ file source for alignment.
48
- # Corresponds to the JSON property `pairedFastqSource`
49
- # @return [Google::Apis::GenomicsV1beta2::PairedFastqSource]
50
- attr_accessor :paired_fastq_source
51
-
52
- # The ID of the read group set which will be aligned. A new read group set will
53
- # be generated to hold the aligned data, the originals will not be modified. The
54
- # caller must have READ permissions for this read group set. Exactly one of
55
- # readGroupSetId, bamSourceUris, interleavedFastqSource or pairedFastqSource
56
- # must be provided.
57
- # Corresponds to the JSON property `readGroupSetId`
58
- # @return [String]
59
- attr_accessor :read_group_set_id
60
-
61
- def initialize(**args)
62
- update!(**args)
63
- end
64
-
65
- # Update properties of this object
66
- def update!(**args)
67
- @bam_source_uris = args[:bam_source_uris] unless args[:bam_source_uris].nil?
68
- @dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
69
- @interleaved_fastq_source = args[:interleaved_fastq_source] unless args[:interleaved_fastq_source].nil?
70
- @paired_fastq_source = args[:paired_fastq_source] unless args[:paired_fastq_source].nil?
71
- @read_group_set_id = args[:read_group_set_id] unless args[:read_group_set_id].nil?
72
- end
73
- end
74
-
75
- # The read group set align response.
76
- class AlignReadGroupSetsResponse
77
- include Google::Apis::Core::Hashable
78
-
79
- # A job ID that can be used to get status information.
80
- # Corresponds to the JSON property `jobId`
81
- # @return [String]
82
- attr_accessor :job_id
83
-
84
- def initialize(**args)
85
- update!(**args)
86
- end
87
-
88
- # Update properties of this object
89
- def update!(**args)
90
- @job_id = args[:job_id] unless args[:job_id].nil?
91
- end
92
- end
93
-
94
- # An annotation describes a region of reference genome. The value of an
95
- # annotation may be one of several canonical types, supplemented by arbitrary
96
- # info tags. A variant annotation is represented by one or more of these
97
- # canonical types. An annotation is not inherently associated with a specific
98
- # sample or individual (though a client could choose to use annotations in this
99
- # way). Example canonical annotation types are 'Gene' and 'Variant'.
100
- class Annotation
101
- include Google::Apis::Core::Hashable
102
-
103
- # The ID of the containing annotation set.
104
- # Corresponds to the JSON property `annotationSetId`
105
- # @return [String]
106
- attr_accessor :annotation_set_id
107
-
108
- # The generated unique ID for this annotation.
109
- # Corresponds to the JSON property `id`
110
- # @return [String]
111
- attr_accessor :id
112
-
113
- # A string which maps to an array of values.
114
- # Corresponds to the JSON property `info`
115
- # @return [Hash<String,Array<String>>]
116
- attr_accessor :info
117
-
118
- # The display name of this annotation.
119
- # Corresponds to the JSON property `name`
120
- # @return [String]
121
- attr_accessor :name
122
-
123
- # A 0-based half-open genomic coordinate range over a reference sequence, for
124
- # representing the position of a genomic resource.
125
- # Corresponds to the JSON property `position`
126
- # @return [Google::Apis::GenomicsV1beta2::RangePosition]
127
- attr_accessor :position
128
-
129
- # A transcript represents the assertion that a particular region of the
130
- # reference genome may be transcribed as RNA.
131
- # Corresponds to the JSON property `transcript`
132
- # @return [Google::Apis::GenomicsV1beta2::Transcript]
133
- attr_accessor :transcript
134
-
135
- # The data type for this annotation. Must match the containing annotation set's
136
- # type.
137
- # Corresponds to the JSON property `type`
138
- # @return [String]
139
- attr_accessor :type
140
-
141
- # A Variant annotation.
142
- # Corresponds to the JSON property `variant`
143
- # @return [Google::Apis::GenomicsV1beta2::VariantAnnotation]
144
- attr_accessor :variant
145
-
146
- def initialize(**args)
147
- update!(**args)
148
- end
149
-
150
- # Update properties of this object
151
- def update!(**args)
152
- @annotation_set_id = args[:annotation_set_id] unless args[:annotation_set_id].nil?
153
- @id = args[:id] unless args[:id].nil?
154
- @info = args[:info] unless args[:info].nil?
155
- @name = args[:name] unless args[:name].nil?
156
- @position = args[:position] unless args[:position].nil?
157
- @transcript = args[:transcript] unless args[:transcript].nil?
158
- @type = args[:type] unless args[:type].nil?
159
- @variant = args[:variant] unless args[:variant].nil?
160
- end
161
- end
162
-
163
- # An annotation set is a logical grouping of annotations that share consistent
164
- # type information and provenance. Examples of annotation sets include 'all
165
- # genes from refseq', and 'all variant annotations from ClinVar'.
166
- class AnnotationSet
167
- include Google::Apis::Core::Hashable
168
-
169
- # The ID of the containing dataset.
170
- # Corresponds to the JSON property `datasetId`
171
- # @return [String]
172
- attr_accessor :dataset_id
173
-
174
- # The generated unique ID for this annotation set.
175
- # Corresponds to the JSON property `id`
176
- # @return [String]
177
- attr_accessor :id
178
-
179
- # A string which maps to an array of values.
180
- # Corresponds to the JSON property `info`
181
- # @return [Hash<String,Array<String>>]
182
- attr_accessor :info
183
-
184
- # The display name for this annotation set.
185
- # Corresponds to the JSON property `name`
186
- # @return [String]
187
- attr_accessor :name
188
-
189
- # The ID of the reference set that defines the coordinate space for this set's
190
- # annotations.
191
- # Corresponds to the JSON property `referenceSetId`
192
- # @return [String]
193
- attr_accessor :reference_set_id
194
-
195
- # The source URI describing the file from which this annotation set was
196
- # generated, if any.
197
- # Corresponds to the JSON property `sourceUri`
198
- # @return [String]
199
- attr_accessor :source_uri
200
-
201
- # The type of annotations contained within this set.
202
- # Corresponds to the JSON property `type`
203
- # @return [String]
204
- attr_accessor :type
205
-
206
- def initialize(**args)
207
- update!(**args)
208
- end
209
-
210
- # Update properties of this object
211
- def update!(**args)
212
- @dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
213
- @id = args[:id] unless args[:id].nil?
214
- @info = args[:info] unless args[:info].nil?
215
- @name = args[:name] unless args[:name].nil?
216
- @reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
217
- @source_uri = args[:source_uri] unless args[:source_uri].nil?
218
- @type = args[:type] unless args[:type].nil?
219
- end
220
- end
221
-
222
- #
223
- class BatchAnnotationsResponse
224
- include Google::Apis::Core::Hashable
225
-
226
- # The resulting per-annotation entries, ordered consistently with the original
227
- # request.
228
- # Corresponds to the JSON property `entries`
229
- # @return [Array<Google::Apis::GenomicsV1beta2::BatchAnnotationsResponseEntry>]
230
- attr_accessor :entries
231
-
232
- def initialize(**args)
233
- update!(**args)
234
- end
235
-
236
- # Update properties of this object
237
- def update!(**args)
238
- @entries = args[:entries] unless args[:entries].nil?
239
- end
240
- end
241
-
242
- #
243
- class BatchAnnotationsResponseEntry
244
- include Google::Apis::Core::Hashable
245
-
246
- # An annotation describes a region of reference genome. The value of an
247
- # annotation may be one of several canonical types, supplemented by arbitrary
248
- # info tags. A variant annotation is represented by one or more of these
249
- # canonical types. An annotation is not inherently associated with a specific
250
- # sample or individual (though a client could choose to use annotations in this
251
- # way). Example canonical annotation types are 'Gene' and 'Variant'.
252
- # Corresponds to the JSON property `annotation`
253
- # @return [Google::Apis::GenomicsV1beta2::Annotation]
254
- attr_accessor :annotation
255
-
256
- #
257
- # Corresponds to the JSON property `status`
258
- # @return [Google::Apis::GenomicsV1beta2::BatchAnnotationsResponseEntryStatus]
259
- attr_accessor :status
260
-
261
- def initialize(**args)
262
- update!(**args)
263
- end
264
-
265
- # Update properties of this object
266
- def update!(**args)
267
- @annotation = args[:annotation] unless args[:annotation].nil?
268
- @status = args[:status] unless args[:status].nil?
269
- end
270
- end
271
-
272
- #
273
- class BatchAnnotationsResponseEntryStatus
274
- include Google::Apis::Core::Hashable
275
-
276
- # The HTTP status code for this operation.
277
- # Corresponds to the JSON property `code`
278
- # @return [Fixnum]
279
- attr_accessor :code
280
-
281
- # Error message for this status, if any.
282
- # Corresponds to the JSON property `message`
283
- # @return [String]
284
- attr_accessor :message
285
-
286
- def initialize(**args)
287
- update!(**args)
288
- end
289
-
290
- # Update properties of this object
291
- def update!(**args)
292
- @code = args[:code] unless args[:code].nil?
293
- @message = args[:message] unless args[:message].nil?
294
- end
295
- end
296
-
297
- #
298
- class BatchCreateAnnotationsRequest
299
- include Google::Apis::Core::Hashable
300
-
301
- # The annotations to be created. At most 4096 can be specified in a single
302
- # request.
303
- # Corresponds to the JSON property `annotations`
304
- # @return [Array<Google::Apis::GenomicsV1beta2::Annotation>]
305
- attr_accessor :annotations
306
-
307
- def initialize(**args)
308
- update!(**args)
309
- end
310
-
311
- # Update properties of this object
312
- def update!(**args)
313
- @annotations = args[:annotations] unless args[:annotations].nil?
314
- end
315
- end
316
-
317
- # A call represents the determination of genotype with respect to a particular
318
- # variant. It may include associated information such as quality and phasing.
319
- # For example, a call might assign a probability of 0.32 to the occurrence of a
320
- # SNP named rs1234 in a call set with the name NA12345.
321
- class Call
322
- include Google::Apis::Core::Hashable
323
-
324
- # The ID of the call set this variant call belongs to.
325
- # Corresponds to the JSON property `callSetId`
326
- # @return [String]
327
- attr_accessor :call_set_id
328
-
329
- # The name of the call set this variant call belongs to.
330
- # Corresponds to the JSON property `callSetName`
331
- # @return [String]
332
- attr_accessor :call_set_name
333
-
334
- # The genotype of this variant call. Each value represents either the value of
335
- # the referenceBases field or a 1-based index into alternateBases. If a variant
336
- # had a referenceBases value of T and an alternateBases value of ["A", "C"], and
337
- # the genotype was [2, 1], that would mean the call represented the heterozygous
338
- # value CA for this variant. If the genotype was instead [0, 1], the represented
339
- # value would be TA. Ordering of the genotype values is important if the
340
- # phaseset is present. If a genotype is not called (that is, a . is present in
341
- # the GT string) -1 is returned.
342
- # Corresponds to the JSON property `genotype`
343
- # @return [Array<Fixnum>]
344
- attr_accessor :genotype
345
-
346
- # The genotype likelihoods for this variant call. Each array entry represents
347
- # how likely a specific genotype is for this call. The value ordering is defined
348
- # by the GL tag in the VCF spec. If Phred-scaled genotype likelihood scores (PL)
349
- # are available and log10(P) genotype likelihood scores (GL) are not, PL scores
350
- # are converted to GL scores. If both are available, PL scores are stored in
351
- # info.
352
- # Corresponds to the JSON property `genotypeLikelihood`
353
- # @return [Array<Float>]
354
- attr_accessor :genotype_likelihood
355
-
356
- # A string which maps to an array of values.
357
- # Corresponds to the JSON property `info`
358
- # @return [Hash<String,Array<String>>]
359
- attr_accessor :info
360
-
361
- # If this field is present, this variant call's genotype ordering implies the
362
- # phase of the bases and is consistent with any other variant calls in the same
363
- # reference sequence which have the same phaseset value. When importing data
364
- # from VCF, if the genotype data was phased but no phase set was specified this
365
- # field will be set to *.
366
- # Corresponds to the JSON property `phaseset`
367
- # @return [String]
368
- attr_accessor :phaseset
369
-
370
- def initialize(**args)
371
- update!(**args)
372
- end
373
-
374
- # Update properties of this object
375
- def update!(**args)
376
- @call_set_id = args[:call_set_id] unless args[:call_set_id].nil?
377
- @call_set_name = args[:call_set_name] unless args[:call_set_name].nil?
378
- @genotype = args[:genotype] unless args[:genotype].nil?
379
- @genotype_likelihood = args[:genotype_likelihood] unless args[:genotype_likelihood].nil?
380
- @info = args[:info] unless args[:info].nil?
381
- @phaseset = args[:phaseset] unless args[:phaseset].nil?
382
- end
383
- end
384
-
385
- # The read group set call request.
386
- class CallReadGroupSetsRequest
387
- include Google::Apis::Core::Hashable
388
-
389
- # Required. The ID of the dataset the called variants will belong to. The caller
390
- # must have WRITE permissions to this dataset.
391
- # Corresponds to the JSON property `datasetId`
392
- # @return [String]
393
- attr_accessor :dataset_id
394
-
395
- # The IDs of the read group sets which will be called. The caller must have READ
396
- # permissions for these read group sets. One of readGroupSetId or sourceUris
397
- # must be provided.
398
- # Corresponds to the JSON property `readGroupSetId`
399
- # @return [String]
400
- attr_accessor :read_group_set_id
401
-
402
- # A list of URIs pointing at BAM files in Google Cloud Storage which will be
403
- # called. FASTQ files are not allowed. The caller must have READ permissions for
404
- # these files. One of readGroupSetId or sourceUris must be provided.
405
- # Corresponds to the JSON property `sourceUris`
406
- # @return [Array<String>]
407
- attr_accessor :source_uris
408
-
409
- def initialize(**args)
410
- update!(**args)
411
- end
412
-
413
- # Update properties of this object
414
- def update!(**args)
415
- @dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
416
- @read_group_set_id = args[:read_group_set_id] unless args[:read_group_set_id].nil?
417
- @source_uris = args[:source_uris] unless args[:source_uris].nil?
418
- end
419
- end
420
-
421
- # The read group set call response.
422
- class CallReadGroupSetsResponse
423
- include Google::Apis::Core::Hashable
424
-
425
- # A job ID that can be used to get status information.
426
- # Corresponds to the JSON property `jobId`
427
- # @return [String]
428
- attr_accessor :job_id
429
-
430
- def initialize(**args)
431
- update!(**args)
432
- end
433
-
434
- # Update properties of this object
435
- def update!(**args)
436
- @job_id = args[:job_id] unless args[:job_id].nil?
437
- end
438
- end
439
-
440
- # A call set is a collection of variant calls, typically for one sample. It
441
- # belongs to a variant set.
442
- class CallSet
443
- include Google::Apis::Core::Hashable
444
-
445
- # The date this call set was created in milliseconds from the epoch.
446
- # Corresponds to the JSON property `created`
447
- # @return [String]
448
- attr_accessor :created
449
-
450
- # The Google generated ID of the call set, immutable.
451
- # Corresponds to the JSON property `id`
452
- # @return [String]
453
- attr_accessor :id
454
-
455
- # A string which maps to an array of values.
456
- # Corresponds to the JSON property `info`
457
- # @return [Hash<String,Array<String>>]
458
- attr_accessor :info
459
-
460
- # The call set name.
461
- # Corresponds to the JSON property `name`
462
- # @return [String]
463
- attr_accessor :name
464
-
465
- # The sample ID this call set corresponds to.
466
- # Corresponds to the JSON property `sampleId`
467
- # @return [String]
468
- attr_accessor :sample_id
469
-
470
- # The IDs of the variant sets this call set belongs to.
471
- # Corresponds to the JSON property `variantSetIds`
472
- # @return [Array<String>]
473
- attr_accessor :variant_set_ids
474
-
475
- def initialize(**args)
476
- update!(**args)
477
- end
478
-
479
- # Update properties of this object
480
- def update!(**args)
481
- @created = args[:created] unless args[:created].nil?
482
- @id = args[:id] unless args[:id].nil?
483
- @info = args[:info] unless args[:info].nil?
484
- @name = args[:name] unless args[:name].nil?
485
- @sample_id = args[:sample_id] unless args[:sample_id].nil?
486
- @variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil?
487
- end
488
- end
489
-
490
- # A single CIGAR operation.
491
- class CigarUnit
492
- include Google::Apis::Core::Hashable
493
-
494
- #
495
- # Corresponds to the JSON property `operation`
496
- # @return [String]
497
- attr_accessor :operation
498
-
499
- # The number of bases that the operation runs for. Required.
500
- # Corresponds to the JSON property `operationLength`
501
- # @return [String]
502
- attr_accessor :operation_length
503
-
504
- # referenceSequence is only used at mismatches (SEQUENCE_MISMATCH) and deletions
505
- # (DELETE). Filling this field replaces SAM's MD tag. If the relevant
506
- # information is not available, this field is unset.
507
- # Corresponds to the JSON property `referenceSequence`
508
- # @return [String]
509
- attr_accessor :reference_sequence
510
-
511
- def initialize(**args)
512
- update!(**args)
513
- end
514
-
515
- # Update properties of this object
516
- def update!(**args)
517
- @operation = args[:operation] unless args[:operation].nil?
518
- @operation_length = args[:operation_length] unless args[:operation_length].nil?
519
- @reference_sequence = args[:reference_sequence] unless args[:reference_sequence].nil?
520
- end
521
- end
522
-
523
- # A bucket over which read coverage has been precomputed. A bucket corresponds
524
- # to a specific range of the reference sequence.
525
- class CoverageBucket
526
- include Google::Apis::Core::Hashable
527
-
528
- # The average number of reads which are aligned to each individual reference
529
- # base in this bucket.
530
- # Corresponds to the JSON property `meanCoverage`
531
- # @return [Float]
532
- attr_accessor :mean_coverage
533
-
534
- # A 0-based half-open genomic coordinate range over a reference sequence.
535
- # Corresponds to the JSON property `range`
536
- # @return [Google::Apis::GenomicsV1beta2::Range]
537
- attr_accessor :range
538
-
539
- def initialize(**args)
540
- update!(**args)
541
- end
542
-
543
- # Update properties of this object
544
- def update!(**args)
545
- @mean_coverage = args[:mean_coverage] unless args[:mean_coverage].nil?
546
- @range = args[:range] unless args[:range].nil?
547
- end
548
- end
549
-
550
- # A Dataset is a collection of genomic data.
551
- class Dataset
552
- include Google::Apis::Core::Hashable
553
-
554
- # The time this dataset was created, in seconds from the epoch.
555
- # Corresponds to the JSON property `createTime`
556
- # @return [String]
557
- attr_accessor :create_time
558
-
559
- # The Google generated ID of the dataset, immutable.
560
- # Corresponds to the JSON property `id`
561
- # @return [String]
562
- attr_accessor :id
563
-
564
- # Flag indicating whether or not a dataset is publicly viewable. If a dataset is
565
- # not public, it inherits viewing permissions from its project.
566
- # Corresponds to the JSON property `isPublic`
567
- # @return [Boolean]
568
- attr_accessor :is_public
569
- alias_method :is_public?, :is_public
570
-
571
- # The dataset name.
572
- # Corresponds to the JSON property `name`
573
- # @return [String]
574
- attr_accessor :name
575
-
576
- # The Google Developers Console project number that this dataset belongs to.
577
- # Corresponds to the JSON property `projectNumber`
578
- # @return [String]
579
- attr_accessor :project_number
580
-
581
- def initialize(**args)
582
- update!(**args)
583
- end
584
-
585
- # Update properties of this object
586
- def update!(**args)
587
- @create_time = args[:create_time] unless args[:create_time].nil?
588
- @id = args[:id] unless args[:id].nil?
589
- @is_public = args[:is_public] unless args[:is_public].nil?
590
- @name = args[:name] unless args[:name].nil?
591
- @project_number = args[:project_number] unless args[:project_number].nil?
592
- end
593
- end
594
-
595
- # The job creation request.
596
- class ExperimentalCreateJobRequest
597
- include Google::Apis::Core::Hashable
598
-
599
- # Specifies whether or not to run the alignment pipeline. Either align or
600
- # callVariants must be set.
601
- # Corresponds to the JSON property `align`
602
- # @return [Boolean]
603
- attr_accessor :align
604
- alias_method :align?, :align
605
-
606
- # Specifies whether or not to run the variant calling pipeline. Either align or
607
- # callVariants must be set.
608
- # Corresponds to the JSON property `callVariants`
609
- # @return [Boolean]
610
- attr_accessor :call_variants
611
- alias_method :call_variants?, :call_variants
612
-
613
- # Specifies where to copy the results of certain pipelines. This should be in
614
- # the form of gs://bucket/path.
615
- # Corresponds to the JSON property `gcsOutputPath`
616
- # @return [String]
617
- attr_accessor :gcs_output_path
618
-
619
- # A list of Google Cloud Storage URIs of paired end .fastq files to operate upon.
620
- # If specified, this represents the second file of each paired .fastq file. The
621
- # first file of each pair should be specified in sourceUris.
622
- # Corresponds to the JSON property `pairedSourceUris`
623
- # @return [Array<String>]
624
- attr_accessor :paired_source_uris
625
-
626
- # Required. The Google Cloud Project ID with which to associate the request.
627
- # Corresponds to the JSON property `projectNumber`
628
- # @return [String]
629
- attr_accessor :project_number
630
-
631
- # A list of Google Cloud Storage URIs of data files to operate upon. These can
632
- # be .bam, interleaved .fastq, or paired .fastq. If specifying paired .fastq
633
- # files, the first of each pair of files should be listed here, and the second
634
- # of each pair should be listed in pairedSourceUris.
635
- # Corresponds to the JSON property `sourceUris`
636
- # @return [Array<String>]
637
- attr_accessor :source_uris
638
-
639
- def initialize(**args)
640
- update!(**args)
641
- end
642
-
643
- # Update properties of this object
644
- def update!(**args)
645
- @align = args[:align] unless args[:align].nil?
646
- @call_variants = args[:call_variants] unless args[:call_variants].nil?
647
- @gcs_output_path = args[:gcs_output_path] unless args[:gcs_output_path].nil?
648
- @paired_source_uris = args[:paired_source_uris] unless args[:paired_source_uris].nil?
649
- @project_number = args[:project_number] unless args[:project_number].nil?
650
- @source_uris = args[:source_uris] unless args[:source_uris].nil?
651
- end
652
- end
653
-
654
- # The job creation response.
655
- class ExperimentalCreateJobResponse
656
- include Google::Apis::Core::Hashable
657
-
658
- # A job ID that can be used to get status information.
659
- # Corresponds to the JSON property `jobId`
660
- # @return [String]
661
- attr_accessor :job_id
662
-
663
- def initialize(**args)
664
- update!(**args)
665
- end
666
-
667
- # Update properties of this object
668
- def update!(**args)
669
- @job_id = args[:job_id] unless args[:job_id].nil?
670
- end
671
- end
672
-
673
- # The read group set export request.
674
- class ExportReadGroupSetsRequest
675
- include Google::Apis::Core::Hashable
676
-
677
- # Required. A Google Cloud Storage URI for the exported BAM file. The currently
678
- # authenticated user must have write access to the new file. An error will be
679
- # returned if the URI already contains data.
680
- # Corresponds to the JSON property `exportUri`
681
- # @return [String]
682
- attr_accessor :export_uri
683
-
684
- # Required. The Google Developers Console project number that owns this export.
685
- # Corresponds to the JSON property `projectNumber`
686
- # @return [String]
687
- attr_accessor :project_number
688
-
689
- # Required. The IDs of the read group sets to export.
690
- # Corresponds to the JSON property `readGroupSetIds`
691
- # @return [Array<String>]
692
- attr_accessor :read_group_set_ids
693
-
694
- # The reference names to export. If this is not specified, all reference
695
- # sequences, including unmapped reads, are exported. Use * to export only
696
- # unmapped reads.
697
- # Corresponds to the JSON property `referenceNames`
698
- # @return [Array<String>]
699
- attr_accessor :reference_names
700
-
701
- def initialize(**args)
702
- update!(**args)
703
- end
704
-
705
- # Update properties of this object
706
- def update!(**args)
707
- @export_uri = args[:export_uri] unless args[:export_uri].nil?
708
- @project_number = args[:project_number] unless args[:project_number].nil?
709
- @read_group_set_ids = args[:read_group_set_ids] unless args[:read_group_set_ids].nil?
710
- @reference_names = args[:reference_names] unless args[:reference_names].nil?
711
- end
712
- end
713
-
714
- # The read group set export response.
715
- class ExportReadGroupSetsResponse
716
- include Google::Apis::Core::Hashable
717
-
718
- # A job ID that can be used to get status information.
719
- # Corresponds to the JSON property `jobId`
720
- # @return [String]
721
- attr_accessor :job_id
722
-
723
- def initialize(**args)
724
- update!(**args)
725
- end
726
-
727
- # Update properties of this object
728
- def update!(**args)
729
- @job_id = args[:job_id] unless args[:job_id].nil?
730
- end
731
- end
732
-
733
- # The variant data export request.
734
- class ExportVariantSetRequest
735
- include Google::Apis::Core::Hashable
736
-
737
- # Required. The BigQuery dataset to export data to. This dataset must already
738
- # exist. Note that this is distinct from the Genomics concept of "dataset".
739
- # Corresponds to the JSON property `bigqueryDataset`
740
- # @return [String]
741
- attr_accessor :bigquery_dataset
742
-
743
- # Required. The BigQuery table to export data to. If the table doesn't exist, it
744
- # will be created. If it already exists, it will be overwritten.
745
- # Corresponds to the JSON property `bigqueryTable`
746
- # @return [String]
747
- attr_accessor :bigquery_table
748
-
749
- # If provided, only variant call information from the specified call sets will
750
- # be exported. By default all variant calls are exported.
751
- # Corresponds to the JSON property `callSetIds`
752
- # @return [Array<String>]
753
- attr_accessor :call_set_ids
754
-
755
- # The format for the exported data.
756
- # Corresponds to the JSON property `format`
757
- # @return [String]
758
- attr_accessor :format
759
-
760
- # Required. The Google Cloud project number that owns the destination BigQuery
761
- # dataset. The caller must have WRITE access to this project. This project will
762
- # also own the resulting export job.
763
- # Corresponds to the JSON property `projectNumber`
764
- # @return [String]
765
- attr_accessor :project_number
766
-
767
- def initialize(**args)
768
- update!(**args)
769
- end
770
-
771
- # Update properties of this object
772
- def update!(**args)
773
- @bigquery_dataset = args[:bigquery_dataset] unless args[:bigquery_dataset].nil?
774
- @bigquery_table = args[:bigquery_table] unless args[:bigquery_table].nil?
775
- @call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil?
776
- @format = args[:format] unless args[:format].nil?
777
- @project_number = args[:project_number] unless args[:project_number].nil?
778
- end
779
- end
780
-
781
- # The variant data export response.
782
- class ExportVariantSetResponse
783
- include Google::Apis::Core::Hashable
784
-
785
- # A job ID that can be used to get status information.
786
- # Corresponds to the JSON property `jobId`
787
- # @return [String]
788
- attr_accessor :job_id
789
-
790
- def initialize(**args)
791
- update!(**args)
792
- end
793
-
794
- # Update properties of this object
795
- def update!(**args)
796
- @job_id = args[:job_id] unless args[:job_id].nil?
797
- end
798
- end
799
-
800
- #
801
- class ExternalId
802
- include Google::Apis::Core::Hashable
803
-
804
- # The id used by the source of this data.
805
- # Corresponds to the JSON property `id`
806
- # @return [String]
807
- attr_accessor :id
808
-
809
- # The name of the source of this data.
810
- # Corresponds to the JSON property `sourceName`
811
- # @return [String]
812
- attr_accessor :source_name
813
-
814
- def initialize(**args)
815
- update!(**args)
816
- end
817
-
818
- # Update properties of this object
819
- def update!(**args)
820
- @id = args[:id] unless args[:id].nil?
821
- @source_name = args[:source_name] unless args[:source_name].nil?
822
- end
823
- end
824
-
825
- #
826
- class FastqMetadata
827
- include Google::Apis::Core::Hashable
828
-
829
- # Optionally specifies the library name for alignment from FASTQ.
830
- # Corresponds to the JSON property `libraryName`
831
- # @return [String]
832
- attr_accessor :library_name
833
-
834
- # Optionally specifies the platform name for alignment from FASTQ. For example:
835
- # CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, PACBIO.
836
- # Corresponds to the JSON property `platformName`
837
- # @return [String]
838
- attr_accessor :platform_name
839
-
840
- # Optionally specifies the platform unit for alignment from FASTQ. For example:
841
- # flowcell-barcode.lane for Illumina or slide for SOLID.
842
- # Corresponds to the JSON property `platformUnit`
843
- # @return [String]
844
- attr_accessor :platform_unit
845
-
846
- # Optionally specifies the read group name for alignment from FASTQ.
847
- # Corresponds to the JSON property `readGroupName`
848
- # @return [String]
849
- attr_accessor :read_group_name
850
-
851
- # Optionally specifies the sample name for alignment from FASTQ.
852
- # Corresponds to the JSON property `sampleName`
853
- # @return [String]
854
- attr_accessor :sample_name
855
-
856
- def initialize(**args)
857
- update!(**args)
858
- end
859
-
860
- # Update properties of this object
861
- def update!(**args)
862
- @library_name = args[:library_name] unless args[:library_name].nil?
863
- @platform_name = args[:platform_name] unless args[:platform_name].nil?
864
- @platform_unit = args[:platform_unit] unless args[:platform_unit].nil?
865
- @read_group_name = args[:read_group_name] unless args[:read_group_name].nil?
866
- @sample_name = args[:sample_name] unless args[:sample_name].nil?
867
- end
868
- end
869
-
870
- # The read group set import request.
871
- class ImportReadGroupSetsRequest
872
- include Google::Apis::Core::Hashable
873
-
874
- # Required. The ID of the dataset these read group sets will belong to. The
875
- # caller must have WRITE permissions to this dataset.
876
- # Corresponds to the JSON property `datasetId`
877
- # @return [String]
878
- attr_accessor :dataset_id
879
-
880
- # The partition strategy describes how read groups are partitioned into read
881
- # group sets.
882
- # Corresponds to the JSON property `partitionStrategy`
883
- # @return [String]
884
- attr_accessor :partition_strategy
885
-
886
- # The reference set to which the imported read group sets are aligned to, if any.
887
- # The reference names of this reference set must be a superset of those found
888
- # in the imported file headers. If no reference set id is provided, a best
889
- # effort is made to associate with a matching reference set.
890
- # Corresponds to the JSON property `referenceSetId`
891
- # @return [String]
892
- attr_accessor :reference_set_id
893
-
894
- # A list of URIs pointing at BAM files in Google Cloud Storage.
895
- # Corresponds to the JSON property `sourceUris`
896
- # @return [Array<String>]
897
- attr_accessor :source_uris
898
-
899
- def initialize(**args)
900
- update!(**args)
901
- end
902
-
903
- # Update properties of this object
904
- def update!(**args)
905
- @dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
906
- @partition_strategy = args[:partition_strategy] unless args[:partition_strategy].nil?
907
- @reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
908
- @source_uris = args[:source_uris] unless args[:source_uris].nil?
909
- end
910
- end
911
-
912
- # The read group set import response.
913
- class ImportReadGroupSetsResponse
914
- include Google::Apis::Core::Hashable
915
-
916
- # A job ID that can be used to get status information.
917
- # Corresponds to the JSON property `jobId`
918
- # @return [String]
919
- attr_accessor :job_id
920
-
921
- def initialize(**args)
922
- update!(**args)
923
- end
924
-
925
- # Update properties of this object
926
- def update!(**args)
927
- @job_id = args[:job_id] unless args[:job_id].nil?
928
- end
929
- end
930
-
931
- # The variant data import request.
932
- class ImportVariantsRequest
933
- include Google::Apis::Core::Hashable
934
-
935
- # The format of the variant data being imported. If unspecified, defaults to to "
936
- # VCF".
937
- # Corresponds to the JSON property `format`
938
- # @return [String]
939
- attr_accessor :format
940
-
941
- # Convert reference names to the canonical representation. hg19 haploytypes (
942
- # those reference names containing "_hap") are not modified in any way. All
943
- # other reference names are modified according to the following rules: The
944
- # reference name is capitalized. The "chr" prefix is dropped for all autosomes
945
- # and sex chromsomes. For example "chr17" becomes "17" and "chrX" becomes "X".
946
- # All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
947
- # Corresponds to the JSON property `normalizeReferenceNames`
948
- # @return [Boolean]
949
- attr_accessor :normalize_reference_names
950
- alias_method :normalize_reference_names?, :normalize_reference_names
951
-
952
- # A list of URIs referencing variant files in Google Cloud Storage. URIs can
953
- # include wildcards as described here. Note that recursive wildcards ('**') are
954
- # not supported.
955
- # Corresponds to the JSON property `sourceUris`
956
- # @return [Array<String>]
957
- attr_accessor :source_uris
958
-
959
- def initialize(**args)
960
- update!(**args)
961
- end
962
-
963
- # Update properties of this object
964
- def update!(**args)
965
- @format = args[:format] unless args[:format].nil?
966
- @normalize_reference_names = args[:normalize_reference_names] unless args[:normalize_reference_names].nil?
967
- @source_uris = args[:source_uris] unless args[:source_uris].nil?
968
- end
969
- end
970
-
971
- # The variant data import response.
972
- class ImportVariantsResponse
973
- include Google::Apis::Core::Hashable
974
-
975
- # A job ID that can be used to get status information.
976
- # Corresponds to the JSON property `jobId`
977
- # @return [String]
978
- attr_accessor :job_id
979
-
980
- def initialize(**args)
981
- update!(**args)
982
- end
983
-
984
- # Update properties of this object
985
- def update!(**args)
986
- @job_id = args[:job_id] unless args[:job_id].nil?
987
- end
988
- end
989
-
990
- # Wrapper message for `int32`.
991
- # The JSON representation for `Int32Value` is JSON number.
992
- class Int32Value
993
- include Google::Apis::Core::Hashable
994
-
995
- # The int32 value.
996
- # Corresponds to the JSON property `value`
997
- # @return [Fixnum]
998
- attr_accessor :value
999
-
1000
- def initialize(**args)
1001
- update!(**args)
1002
- end
1003
-
1004
- # Update properties of this object
1005
- def update!(**args)
1006
- @value = args[:value] unless args[:value].nil?
1007
- end
1008
- end
1009
-
1010
- # Describes an interleaved FASTQ file source for alignment.
1011
- class InterleavedFastqSource
1012
- include Google::Apis::Core::Hashable
1013
-
1014
- # Optionally specifies the metadata to be associated with the final aligned read
1015
- # group set.
1016
- # Corresponds to the JSON property `metadata`
1017
- # @return [Google::Apis::GenomicsV1beta2::FastqMetadata]
1018
- attr_accessor :metadata
1019
-
1020
- # A list of URIs pointing at interleaved FASTQ files in Google Cloud Storage
1021
- # which will be aligned. The caller must have READ permissions for these files.
1022
- # Corresponds to the JSON property `sourceUris`
1023
- # @return [Array<String>]
1024
- attr_accessor :source_uris
1025
-
1026
- def initialize(**args)
1027
- update!(**args)
1028
- end
1029
-
1030
- # Update properties of this object
1031
- def update!(**args)
1032
- @metadata = args[:metadata] unless args[:metadata].nil?
1033
- @source_uris = args[:source_uris] unless args[:source_uris].nil?
1034
- end
1035
- end
1036
-
1037
- # A Job represents an ongoing process that can be monitored for status
1038
- # information.
1039
- class Job
1040
- include Google::Apis::Core::Hashable
1041
-
1042
- # The date this job was created, in milliseconds from the epoch.
1043
- # Corresponds to the JSON property `created`
1044
- # @return [String]
1045
- attr_accessor :created
1046
-
1047
- # A more detailed description of this job's current status.
1048
- # Corresponds to the JSON property `detailedStatus`
1049
- # @return [String]
1050
- attr_accessor :detailed_status
1051
-
1052
- # Any errors that occurred during processing.
1053
- # Corresponds to the JSON property `errors`
1054
- # @return [Array<String>]
1055
- attr_accessor :errors
1056
-
1057
- # The job ID.
1058
- # Corresponds to the JSON property `id`
1059
- # @return [String]
1060
- attr_accessor :id
1061
-
1062
- # If this Job represents an import, this field will contain the IDs of the
1063
- # objects that were successfully imported.
1064
- # Corresponds to the JSON property `importedIds`
1065
- # @return [Array<String>]
1066
- attr_accessor :imported_ids
1067
-
1068
- # The Google Developers Console project number to which this job belongs.
1069
- # Corresponds to the JSON property `projectNumber`
1070
- # @return [String]
1071
- attr_accessor :project_number
1072
-
1073
- # A summary representation of the service request that spawned the job.
1074
- # Corresponds to the JSON property `request`
1075
- # @return [Google::Apis::GenomicsV1beta2::JobRequest]
1076
- attr_accessor :request
1077
-
1078
- # The status of this job.
1079
- # Corresponds to the JSON property `status`
1080
- # @return [String]
1081
- attr_accessor :status
1082
-
1083
- # Any warnings that occurred during processing.
1084
- # Corresponds to the JSON property `warnings`
1085
- # @return [Array<String>]
1086
- attr_accessor :warnings
1087
-
1088
- def initialize(**args)
1089
- update!(**args)
1090
- end
1091
-
1092
- # Update properties of this object
1093
- def update!(**args)
1094
- @created = args[:created] unless args[:created].nil?
1095
- @detailed_status = args[:detailed_status] unless args[:detailed_status].nil?
1096
- @errors = args[:errors] unless args[:errors].nil?
1097
- @id = args[:id] unless args[:id].nil?
1098
- @imported_ids = args[:imported_ids] unless args[:imported_ids].nil?
1099
- @project_number = args[:project_number] unless args[:project_number].nil?
1100
- @request = args[:request] unless args[:request].nil?
1101
- @status = args[:status] unless args[:status].nil?
1102
- @warnings = args[:warnings] unless args[:warnings].nil?
1103
- end
1104
- end
1105
-
1106
- # A summary representation of the service request that spawned the job.
1107
- class JobRequest
1108
- include Google::Apis::Core::Hashable
1109
-
1110
- # The data destination of the request, for example, a Google BigQuery Table or
1111
- # Dataset ID.
1112
- # Corresponds to the JSON property `destination`
1113
- # @return [Array<String>]
1114
- attr_accessor :destination
1115
-
1116
- # The data source of the request, for example, a Google Cloud Storage object
1117
- # path or Readset ID.
1118
- # Corresponds to the JSON property `source`
1119
- # @return [Array<String>]
1120
- attr_accessor :source
1121
-
1122
- # The original request type.
1123
- # Corresponds to the JSON property `type`
1124
- # @return [String]
1125
- attr_accessor :type
1126
-
1127
- def initialize(**args)
1128
- update!(**args)
1129
- end
1130
-
1131
- # Update properties of this object
1132
- def update!(**args)
1133
- @destination = args[:destination] unless args[:destination].nil?
1134
- @source = args[:source] unless args[:source].nil?
1135
- @type = args[:type] unless args[:type].nil?
1136
- end
1137
- end
1138
-
1139
- # Used to hold basic key value information.
1140
- class KeyValue
1141
- include Google::Apis::Core::Hashable
1142
-
1143
- # A string which maps to an array of values.
1144
- # Corresponds to the JSON property `key`
1145
- # @return [String]
1146
- attr_accessor :key
1147
-
1148
- # The string values.
1149
- # Corresponds to the JSON property `value`
1150
- # @return [Array<String>]
1151
- attr_accessor :value
1152
-
1153
- def initialize(**args)
1154
- update!(**args)
1155
- end
1156
-
1157
- # Update properties of this object
1158
- def update!(**args)
1159
- @key = args[:key] unless args[:key].nil?
1160
- @value = args[:value] unless args[:value].nil?
1161
- end
1162
- end
1163
-
1164
- # A linear alignment can be represented by one CIGAR string. Describes the
1165
- # mapped position and local alignment of the read to the reference.
1166
- class LinearAlignment
1167
- include Google::Apis::Core::Hashable
1168
-
1169
- # Represents the local alignment of this sequence (alignment matches, indels,
1170
- # etc) against the reference.
1171
- # Corresponds to the JSON property `cigar`
1172
- # @return [Array<Google::Apis::GenomicsV1beta2::CigarUnit>]
1173
- attr_accessor :cigar
1174
-
1175
- # The mapping quality of this alignment. Represents how likely the read maps to
1176
- # this position as opposed to other locations.
1177
- # Corresponds to the JSON property `mappingQuality`
1178
- # @return [Fixnum]
1179
- attr_accessor :mapping_quality
1180
-
1181
- # An abstraction for referring to a genomic position, in relation to some
1182
- # already known reference. For now, represents a genomic position as a reference
1183
- # name, a base number on that reference (0-based), and a determination of
1184
- # forward or reverse strand.
1185
- # Corresponds to the JSON property `position`
1186
- # @return [Google::Apis::GenomicsV1beta2::Position]
1187
- attr_accessor :position
1188
-
1189
- def initialize(**args)
1190
- update!(**args)
1191
- end
1192
-
1193
- # Update properties of this object
1194
- def update!(**args)
1195
- @cigar = args[:cigar] unless args[:cigar].nil?
1196
- @mapping_quality = args[:mapping_quality] unless args[:mapping_quality].nil?
1197
- @position = args[:position] unless args[:position].nil?
1198
- end
1199
- end
1200
-
1201
- #
1202
- class ListBasesResponse
1203
- include Google::Apis::Core::Hashable
1204
-
1205
- # The continuation token, which is used to page through large result sets.
1206
- # Provide this value in a subsequent request to return the next page of results.
1207
- # This field will be empty if there aren't any additional results.
1208
- # Corresponds to the JSON property `nextPageToken`
1209
- # @return [String]
1210
- attr_accessor :next_page_token
1211
-
1212
- # The offset position (0-based) of the given sequence from the start of this
1213
- # Reference. This value will differ for each page in a paginated request.
1214
- # Corresponds to the JSON property `offset`
1215
- # @return [String]
1216
- attr_accessor :offset
1217
-
1218
- # A substring of the bases that make up this reference.
1219
- # Corresponds to the JSON property `sequence`
1220
- # @return [String]
1221
- attr_accessor :sequence
1222
-
1223
- def initialize(**args)
1224
- update!(**args)
1225
- end
1226
-
1227
- # Update properties of this object
1228
- def update!(**args)
1229
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
1230
- @offset = args[:offset] unless args[:offset].nil?
1231
- @sequence = args[:sequence] unless args[:sequence].nil?
1232
- end
1233
- end
1234
-
1235
- #
1236
- class ListCoverageBucketsResponse
1237
- include Google::Apis::Core::Hashable
1238
-
1239
- # The length of each coverage bucket in base pairs. Note that buckets at the end
1240
- # of a reference sequence may be shorter. This value is omitted if the bucket
1241
- # width is infinity (the default behaviour, with no range or targetBucketWidth).
1242
- # Corresponds to the JSON property `bucketWidth`
1243
- # @return [String]
1244
- attr_accessor :bucket_width
1245
-
1246
- # The coverage buckets. The list of buckets is sparse; a bucket with 0
1247
- # overlapping reads is not returned. A bucket never crosses more than one
1248
- # reference sequence. Each bucket has width bucketWidth, unless its end is the
1249
- # end of the reference sequence.
1250
- # Corresponds to the JSON property `coverageBuckets`
1251
- # @return [Array<Google::Apis::GenomicsV1beta2::CoverageBucket>]
1252
- attr_accessor :coverage_buckets
1253
-
1254
- # The continuation token, which is used to page through large result sets.
1255
- # Provide this value in a subsequent request to return the next page of results.
1256
- # This field will be empty if there aren't any additional results.
1257
- # Corresponds to the JSON property `nextPageToken`
1258
- # @return [String]
1259
- attr_accessor :next_page_token
1260
-
1261
- def initialize(**args)
1262
- update!(**args)
1263
- end
1264
-
1265
- # Update properties of this object
1266
- def update!(**args)
1267
- @bucket_width = args[:bucket_width] unless args[:bucket_width].nil?
1268
- @coverage_buckets = args[:coverage_buckets] unless args[:coverage_buckets].nil?
1269
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
1270
- end
1271
- end
1272
-
1273
- # The dataset list response.
1274
- class ListDatasetsResponse
1275
- include Google::Apis::Core::Hashable
1276
-
1277
- # The list of matching Datasets.
1278
- # Corresponds to the JSON property `datasets`
1279
- # @return [Array<Google::Apis::GenomicsV1beta2::Dataset>]
1280
- attr_accessor :datasets
1281
-
1282
- # The continuation token, which is used to page through large result sets.
1283
- # Provide this value in a subsequent request to return the next page of results.
1284
- # This field will be empty if there aren't any additional results.
1285
- # Corresponds to the JSON property `nextPageToken`
1286
- # @return [String]
1287
- attr_accessor :next_page_token
1288
-
1289
- def initialize(**args)
1290
- update!(**args)
1291
- end
1292
-
1293
- # Update properties of this object
1294
- def update!(**args)
1295
- @datasets = args[:datasets] unless args[:datasets].nil?
1296
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
1297
- end
1298
- end
1299
-
1300
- #
1301
- class MergeVariantsRequest
1302
- include Google::Apis::Core::Hashable
1303
-
1304
- # The variants to be merged with existing variants.
1305
- # Corresponds to the JSON property `variants`
1306
- # @return [Array<Google::Apis::GenomicsV1beta2::Variant>]
1307
- attr_accessor :variants
1308
-
1309
- def initialize(**args)
1310
- update!(**args)
1311
- end
1312
-
1313
- # Update properties of this object
1314
- def update!(**args)
1315
- @variants = args[:variants] unless args[:variants].nil?
1316
- end
1317
- end
1318
-
1319
- # Metadata describes a single piece of variant call metadata. These data include
1320
- # a top level key and either a single value string (value) or a list of key-
1321
- # value pairs (info.) Value and info are mutually exclusive.
1322
- class Metadata
1323
- include Google::Apis::Core::Hashable
1324
-
1325
- # A textual description of this metadata.
1326
- # Corresponds to the JSON property `description`
1327
- # @return [String]
1328
- attr_accessor :description
1329
-
1330
- # User-provided ID field, not enforced by this API. Two or more pieces of
1331
- # structured metadata with identical id and key fields are considered equivalent.
1332
- # Corresponds to the JSON property `id`
1333
- # @return [String]
1334
- attr_accessor :id
1335
-
1336
- # A string which maps to an array of values.
1337
- # Corresponds to the JSON property `info`
1338
- # @return [Hash<String,Array<String>>]
1339
- attr_accessor :info
1340
-
1341
- # The top-level key.
1342
- # Corresponds to the JSON property `key`
1343
- # @return [String]
1344
- attr_accessor :key
1345
-
1346
- # The number of values that can be included in a field described by this
1347
- # metadata.
1348
- # Corresponds to the JSON property `number`
1349
- # @return [String]
1350
- attr_accessor :number
1351
-
1352
- # The type of data. Possible types include: Integer, Float, Flag, Character, and
1353
- # String.
1354
- # Corresponds to the JSON property `type`
1355
- # @return [String]
1356
- attr_accessor :type
1357
-
1358
- # The value field for simple metadata
1359
- # Corresponds to the JSON property `value`
1360
- # @return [String]
1361
- attr_accessor :value
1362
-
1363
- def initialize(**args)
1364
- update!(**args)
1365
- end
1366
-
1367
- # Update properties of this object
1368
- def update!(**args)
1369
- @description = args[:description] unless args[:description].nil?
1370
- @id = args[:id] unless args[:id].nil?
1371
- @info = args[:info] unless args[:info].nil?
1372
- @key = args[:key] unless args[:key].nil?
1373
- @number = args[:number] unless args[:number].nil?
1374
- @type = args[:type] unless args[:type].nil?
1375
- @value = args[:value] unless args[:value].nil?
1376
- end
1377
- end
1378
-
1379
- # Describes a paired-end FASTQ file source for alignment.
1380
- class PairedFastqSource
1381
- include Google::Apis::Core::Hashable
1382
-
1383
- # A list of URIs pointing at paired end FASTQ files in Google Cloud Storage
1384
- # which will be aligned. The first of each paired file should be specified here,
1385
- # in an order that matches the second of each paired file specified in
1386
- # secondSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq],
1387
- # secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ
1388
- # permissions for these files.
1389
- # Corresponds to the JSON property `firstSourceUris`
1390
- # @return [Array<String>]
1391
- attr_accessor :first_source_uris
1392
-
1393
- # Optionally specifies the metadata to be associated with the final aligned read
1394
- # group set.
1395
- # Corresponds to the JSON property `metadata`
1396
- # @return [Google::Apis::GenomicsV1beta2::FastqMetadata]
1397
- attr_accessor :metadata
1398
-
1399
- # A list of URIs pointing at paired end FASTQ files in Google Cloud Storage
1400
- # which will be aligned. The second of each paired file should be specified here,
1401
- # in an order that matches the first of each paired file specified in
1402
- # firstSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq],
1403
- # secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ
1404
- # permissions for these files.
1405
- # Corresponds to the JSON property `secondSourceUris`
1406
- # @return [Array<String>]
1407
- attr_accessor :second_source_uris
1408
-
1409
- def initialize(**args)
1410
- update!(**args)
1411
- end
1412
-
1413
- # Update properties of this object
1414
- def update!(**args)
1415
- @first_source_uris = args[:first_source_uris] unless args[:first_source_uris].nil?
1416
- @metadata = args[:metadata] unless args[:metadata].nil?
1417
- @second_source_uris = args[:second_source_uris] unless args[:second_source_uris].nil?
1418
- end
1419
- end
1420
-
1421
- # An abstraction for referring to a genomic position, in relation to some
1422
- # already known reference. For now, represents a genomic position as a reference
1423
- # name, a base number on that reference (0-based), and a determination of
1424
- # forward or reverse strand.
1425
- class Position
1426
- include Google::Apis::Core::Hashable
1427
-
1428
- # The 0-based offset from the start of the forward strand for that reference.
1429
- # Corresponds to the JSON property `position`
1430
- # @return [String]
1431
- attr_accessor :position
1432
-
1433
- # The name of the reference in whatever reference set is being used.
1434
- # Corresponds to the JSON property `referenceName`
1435
- # @return [String]
1436
- attr_accessor :reference_name
1437
-
1438
- # Whether this position is on the reverse strand, as opposed to the forward
1439
- # strand.
1440
- # Corresponds to the JSON property `reverseStrand`
1441
- # @return [Boolean]
1442
- attr_accessor :reverse_strand
1443
- alias_method :reverse_strand?, :reverse_strand
1444
-
1445
- def initialize(**args)
1446
- update!(**args)
1447
- end
1448
-
1449
- # Update properties of this object
1450
- def update!(**args)
1451
- @position = args[:position] unless args[:position].nil?
1452
- @reference_name = args[:reference_name] unless args[:reference_name].nil?
1453
- @reverse_strand = args[:reverse_strand] unless args[:reverse_strand].nil?
1454
- end
1455
- end
1456
-
1457
- # A 0-based half-open genomic coordinate range for search requests.
1458
- class QueryRange
1459
- include Google::Apis::Core::Hashable
1460
-
1461
- # The end position of the range on the reference, 0-based exclusive. If
1462
- # specified, referenceId or referenceName must also be specified. If unset or 0,
1463
- # defaults to the length of the reference.
1464
- # Corresponds to the JSON property `end`
1465
- # @return [String]
1466
- attr_accessor :end
1467
-
1468
- # The ID of the reference to query. At most one of referenceId and referenceName
1469
- # should be specified.
1470
- # Corresponds to the JSON property `referenceId`
1471
- # @return [String]
1472
- attr_accessor :reference_id
1473
-
1474
- # The name of the reference to query, within the reference set associated with
1475
- # this query. At most one of referenceId and referenceName pshould be specified.
1476
- # Corresponds to the JSON property `referenceName`
1477
- # @return [String]
1478
- attr_accessor :reference_name
1479
-
1480
- # The start position of the range on the reference, 0-based inclusive. If
1481
- # specified, referenceId or referenceName must also be specified. Defaults to 0.
1482
- # Corresponds to the JSON property `start`
1483
- # @return [String]
1484
- attr_accessor :start
1485
-
1486
- def initialize(**args)
1487
- update!(**args)
1488
- end
1489
-
1490
- # Update properties of this object
1491
- def update!(**args)
1492
- @end = args[:end] unless args[:end].nil?
1493
- @reference_id = args[:reference_id] unless args[:reference_id].nil?
1494
- @reference_name = args[:reference_name] unless args[:reference_name].nil?
1495
- @start = args[:start] unless args[:start].nil?
1496
- end
1497
- end
1498
-
1499
- # A 0-based half-open genomic coordinate range over a reference sequence.
1500
- class Range
1501
- include Google::Apis::Core::Hashable
1502
-
1503
- # The end position of the range on the reference, 0-based exclusive. If
1504
- # specified, referenceName must also be specified.
1505
- # Corresponds to the JSON property `end`
1506
- # @return [String]
1507
- attr_accessor :end
1508
-
1509
- # The reference sequence name, for example chr1, 1, or chrX.
1510
- # Corresponds to the JSON property `referenceName`
1511
- # @return [String]
1512
- attr_accessor :reference_name
1513
-
1514
- # The start position of the range on the reference, 0-based inclusive. If
1515
- # specified, referenceName must also be specified.
1516
- # Corresponds to the JSON property `start`
1517
- # @return [String]
1518
- attr_accessor :start
1519
-
1520
- def initialize(**args)
1521
- update!(**args)
1522
- end
1523
-
1524
- # Update properties of this object
1525
- def update!(**args)
1526
- @end = args[:end] unless args[:end].nil?
1527
- @reference_name = args[:reference_name] unless args[:reference_name].nil?
1528
- @start = args[:start] unless args[:start].nil?
1529
- end
1530
- end
1531
-
1532
- # A 0-based half-open genomic coordinate range over a reference sequence, for
1533
- # representing the position of a genomic resource.
1534
- class RangePosition
1535
- include Google::Apis::Core::Hashable
1536
-
1537
- # The end position of the range on the reference, 0-based exclusive.
1538
- # Corresponds to the JSON property `end`
1539
- # @return [String]
1540
- attr_accessor :end
1541
-
1542
- # The ID of the Google Genomics reference associated with this range.
1543
- # Corresponds to the JSON property `referenceId`
1544
- # @return [String]
1545
- attr_accessor :reference_id
1546
-
1547
- # The display name corresponding to the reference specified by referenceId, for
1548
- # example chr1, 1, or chrX.
1549
- # Corresponds to the JSON property `referenceName`
1550
- # @return [String]
1551
- attr_accessor :reference_name
1552
-
1553
- # Whether this range refers to the reverse strand, as opposed to the forward
1554
- # strand. Note that regardless of this field, the start/end position of the
1555
- # range always refer to the forward strand.
1556
- # Corresponds to the JSON property `reverseStrand`
1557
- # @return [Boolean]
1558
- attr_accessor :reverse_strand
1559
- alias_method :reverse_strand?, :reverse_strand
1560
-
1561
- # The start position of the range on the reference, 0-based inclusive.
1562
- # Corresponds to the JSON property `start`
1563
- # @return [String]
1564
- attr_accessor :start
1565
-
1566
- def initialize(**args)
1567
- update!(**args)
1568
- end
1569
-
1570
- # Update properties of this object
1571
- def update!(**args)
1572
- @end = args[:end] unless args[:end].nil?
1573
- @reference_id = args[:reference_id] unless args[:reference_id].nil?
1574
- @reference_name = args[:reference_name] unless args[:reference_name].nil?
1575
- @reverse_strand = args[:reverse_strand] unless args[:reverse_strand].nil?
1576
- @start = args[:start] unless args[:start].nil?
1577
- end
1578
- end
1579
-
1580
- # A read alignment describes a linear alignment of a string of DNA to a
1581
- # reference sequence, in addition to metadata about the fragment (the molecule
1582
- # of DNA sequenced) and the read (the bases which were read by the sequencer). A
1583
- # read is equivalent to a line in a SAM file. A read belongs to exactly one read
1584
- # group and exactly one read group set. Generating a reference-aligned sequence
1585
- # string When interacting with mapped reads, it's often useful to produce a
1586
- # string representing the local alignment of the read to reference. The
1587
- # following pseudocode demonstrates one way of doing this:
1588
- # out = "" offset = 0 for c in read.alignment.cigar ` switch c.operation ` case "
1589
- # ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out += read.
1590
- # alignedSequence[offset:offset+c.operationLength] offset += c.operationLength
1591
- # break case "CLIP_SOFT", "INSERT": offset += c.operationLength break case "PAD":
1592
- # out += repeat("*", c.operationLength) break case "DELETE": out += repeat("-",
1593
- # c.operationLength) break case "SKIP": out += repeat(" ", c.operationLength)
1594
- # break case "CLIP_HARD": break ` ` return out
1595
- # Converting to SAM's CIGAR string The following pseudocode generates a SAM
1596
- # CIGAR string from the cigar field. Note that this is a lossy conversion (cigar.
1597
- # referenceSequence is lost).
1598
- # cigarMap = ` "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N",
1599
- # "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=", "
1600
- # SEQUENCE_MISMATCH": "X", ` cigarStr = "" for c in read.alignment.cigar `
1601
- # cigarStr += c.operationLength + cigarMap[c.operation] ` return cigarStr
1602
- class Read
1603
- include Google::Apis::Core::Hashable
1604
-
1605
- # The quality of the read sequence contained in this alignment record.
1606
- # alignedSequence and alignedQuality may be shorter than the full read sequence
1607
- # and quality. This will occur if the alignment is part of a chimeric alignment,
1608
- # or if the read was trimmed. When this occurs, the CIGAR for this read will
1609
- # begin/end with a hard clip operator that will indicate the length of the
1610
- # excised sequence.
1611
- # Corresponds to the JSON property `alignedQuality`
1612
- # @return [Array<Fixnum>]
1613
- attr_accessor :aligned_quality
1614
-
1615
- # The bases of the read sequence contained in this alignment record, without
1616
- # CIGAR operations applied. alignedSequence and alignedQuality may be shorter
1617
- # than the full read sequence and quality. This will occur if the alignment is
1618
- # part of a chimeric alignment, or if the read was trimmed. When this occurs,
1619
- # the CIGAR for this read will begin/end with a hard clip operator that will
1620
- # indicate the length of the excised sequence.
1621
- # Corresponds to the JSON property `alignedSequence`
1622
- # @return [String]
1623
- attr_accessor :aligned_sequence
1624
-
1625
- # A linear alignment can be represented by one CIGAR string. Describes the
1626
- # mapped position and local alignment of the read to the reference.
1627
- # Corresponds to the JSON property `alignment`
1628
- # @return [Google::Apis::GenomicsV1beta2::LinearAlignment]
1629
- attr_accessor :alignment
1630
-
1631
- # The fragment is a PCR or optical duplicate (SAM flag 0x400)
1632
- # Corresponds to the JSON property `duplicateFragment`
1633
- # @return [Boolean]
1634
- attr_accessor :duplicate_fragment
1635
- alias_method :duplicate_fragment?, :duplicate_fragment
1636
-
1637
- # SAM flag 0x200
1638
- # Corresponds to the JSON property `failedVendorQualityChecks`
1639
- # @return [Boolean]
1640
- attr_accessor :failed_vendor_quality_checks
1641
- alias_method :failed_vendor_quality_checks?, :failed_vendor_quality_checks
1642
-
1643
- # The observed length of the fragment, equivalent to TLEN in SAM.
1644
- # Corresponds to the JSON property `fragmentLength`
1645
- # @return [Fixnum]
1646
- attr_accessor :fragment_length
1647
-
1648
- # The fragment name. Equivalent to QNAME (query template name) in SAM.
1649
- # Corresponds to the JSON property `fragmentName`
1650
- # @return [String]
1651
- attr_accessor :fragment_name
1652
-
1653
- # The unique ID for this read. This is a generated unique ID, not to be confused
1654
- # with fragmentName.
1655
- # Corresponds to the JSON property `id`
1656
- # @return [String]
1657
- attr_accessor :id
1658
-
1659
- # A string which maps to an array of values.
1660
- # Corresponds to the JSON property `info`
1661
- # @return [Hash<String,Array<String>>]
1662
- attr_accessor :info
1663
-
1664
- # An abstraction for referring to a genomic position, in relation to some
1665
- # already known reference. For now, represents a genomic position as a reference
1666
- # name, a base number on that reference (0-based), and a determination of
1667
- # forward or reverse strand.
1668
- # Corresponds to the JSON property `nextMatePosition`
1669
- # @return [Google::Apis::GenomicsV1beta2::Position]
1670
- attr_accessor :next_mate_position
1671
-
1672
- # The number of reads in the fragment (extension to SAM flag 0x1).
1673
- # Corresponds to the JSON property `numberReads`
1674
- # @return [Fixnum]
1675
- attr_accessor :number_reads
1676
-
1677
- # The orientation and the distance between reads from the fragment are
1678
- # consistent with the sequencing protocol (SAM flag 0x2)
1679
- # Corresponds to the JSON property `properPlacement`
1680
- # @return [Boolean]
1681
- attr_accessor :proper_placement
1682
- alias_method :proper_placement?, :proper_placement
1683
-
1684
- # The ID of the read group this read belongs to. (Every read must belong to
1685
- # exactly one read group.)
1686
- # Corresponds to the JSON property `readGroupId`
1687
- # @return [String]
1688
- attr_accessor :read_group_id
1689
-
1690
- # The ID of the read group set this read belongs to. (Every read must belong to
1691
- # exactly one read group set.)
1692
- # Corresponds to the JSON property `readGroupSetId`
1693
- # @return [String]
1694
- attr_accessor :read_group_set_id
1695
-
1696
- # The read number in sequencing. 0-based and less than numberReads. This field
1697
- # replaces SAM flag 0x40 and 0x80.
1698
- # Corresponds to the JSON property `readNumber`
1699
- # @return [Fixnum]
1700
- attr_accessor :read_number
1701
-
1702
- # Whether this alignment is secondary. Equivalent to SAM flag 0x100. A secondary
1703
- # alignment represents an alternative to the primary alignment for this read.
1704
- # Aligners may return secondary alignments if a read can map ambiguously to
1705
- # multiple coordinates in the genome. By convention, each read has one and only
1706
- # one alignment where both secondaryAlignment and supplementaryAlignment are
1707
- # false.
1708
- # Corresponds to the JSON property `secondaryAlignment`
1709
- # @return [Boolean]
1710
- attr_accessor :secondary_alignment
1711
- alias_method :secondary_alignment?, :secondary_alignment
1712
-
1713
- # Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
1714
- # Supplementary alignments are used in the representation of a chimeric
1715
- # alignment. In a chimeric alignment, a read is split into multiple linear
1716
- # alignments that map to different reference contigs. The first linear alignment
1717
- # in the read will be designated as the representative alignment; the remaining
1718
- # linear alignments will be designated as supplementary alignments. These
1719
- # alignments may have different mapping quality scores. In each linear alignment
1720
- # in a chimeric alignment, the read will be hard clipped. The alignedSequence
1721
- # and alignedQuality fields in the alignment record will only represent the
1722
- # bases for its respective linear alignment.
1723
- # Corresponds to the JSON property `supplementaryAlignment`
1724
- # @return [Boolean]
1725
- attr_accessor :supplementary_alignment
1726
- alias_method :supplementary_alignment?, :supplementary_alignment
1727
-
1728
- def initialize(**args)
1729
- update!(**args)
1730
- end
1731
-
1732
- # Update properties of this object
1733
- def update!(**args)
1734
- @aligned_quality = args[:aligned_quality] unless args[:aligned_quality].nil?
1735
- @aligned_sequence = args[:aligned_sequence] unless args[:aligned_sequence].nil?
1736
- @alignment = args[:alignment] unless args[:alignment].nil?
1737
- @duplicate_fragment = args[:duplicate_fragment] unless args[:duplicate_fragment].nil?
1738
- @failed_vendor_quality_checks = args[:failed_vendor_quality_checks] unless args[:failed_vendor_quality_checks].nil?
1739
- @fragment_length = args[:fragment_length] unless args[:fragment_length].nil?
1740
- @fragment_name = args[:fragment_name] unless args[:fragment_name].nil?
1741
- @id = args[:id] unless args[:id].nil?
1742
- @info = args[:info] unless args[:info].nil?
1743
- @next_mate_position = args[:next_mate_position] unless args[:next_mate_position].nil?
1744
- @number_reads = args[:number_reads] unless args[:number_reads].nil?
1745
- @proper_placement = args[:proper_placement] unless args[:proper_placement].nil?
1746
- @read_group_id = args[:read_group_id] unless args[:read_group_id].nil?
1747
- @read_group_set_id = args[:read_group_set_id] unless args[:read_group_set_id].nil?
1748
- @read_number = args[:read_number] unless args[:read_number].nil?
1749
- @secondary_alignment = args[:secondary_alignment] unless args[:secondary_alignment].nil?
1750
- @supplementary_alignment = args[:supplementary_alignment] unless args[:supplementary_alignment].nil?
1751
- end
1752
- end
1753
-
1754
- # A read group is all the data that's processed the same way by the sequencer.
1755
- class ReadGroup
1756
- include Google::Apis::Core::Hashable
1757
-
1758
- # The ID of the dataset this read group belongs to.
1759
- # Corresponds to the JSON property `datasetId`
1760
- # @return [String]
1761
- attr_accessor :dataset_id
1762
-
1763
- # A free-form text description of this read group.
1764
- # Corresponds to the JSON property `description`
1765
- # @return [String]
1766
- attr_accessor :description
1767
-
1768
- # The experiment used to generate this read group.
1769
- # Corresponds to the JSON property `experiment`
1770
- # @return [Google::Apis::GenomicsV1beta2::ReadGroupExperiment]
1771
- attr_accessor :experiment
1772
-
1773
- # The generated unique read group ID. Note: This is different than the @RG ID
1774
- # field in the SAM spec. For that value, see the name field.
1775
- # Corresponds to the JSON property `id`
1776
- # @return [String]
1777
- attr_accessor :id
1778
-
1779
- # A string which maps to an array of values.
1780
- # Corresponds to the JSON property `info`
1781
- # @return [Hash<String,Array<String>>]
1782
- attr_accessor :info
1783
-
1784
- # The read group name. This corresponds to the @RG ID field in the SAM spec.
1785
- # Corresponds to the JSON property `name`
1786
- # @return [String]
1787
- attr_accessor :name
1788
-
1789
- # The predicted insert size of this read group. The insert size is the length
1790
- # the sequenced DNA fragment from end-to-end, not including the adapters.
1791
- # Corresponds to the JSON property `predictedInsertSize`
1792
- # @return [Fixnum]
1793
- attr_accessor :predicted_insert_size
1794
-
1795
- # The programs used to generate this read group. Programs are always identical
1796
- # for all read groups within a read group set. For this reason, only the first
1797
- # read group in a returned set will have this field populated.
1798
- # Corresponds to the JSON property `programs`
1799
- # @return [Array<Google::Apis::GenomicsV1beta2::ReadGroupProgram>]
1800
- attr_accessor :programs
1801
-
1802
- # The reference set the reads in this read group are aligned to. Required if
1803
- # there are any read alignments.
1804
- # Corresponds to the JSON property `referenceSetId`
1805
- # @return [String]
1806
- attr_accessor :reference_set_id
1807
-
1808
- # The sample this read group's data was generated from. Note: This is not an
1809
- # actual ID within this repository, but rather an identifier for a sample which
1810
- # may be meaningful to some external system.
1811
- # Corresponds to the JSON property `sampleId`
1812
- # @return [String]
1813
- attr_accessor :sample_id
1814
-
1815
- def initialize(**args)
1816
- update!(**args)
1817
- end
1818
-
1819
- # Update properties of this object
1820
- def update!(**args)
1821
- @dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
1822
- @description = args[:description] unless args[:description].nil?
1823
- @experiment = args[:experiment] unless args[:experiment].nil?
1824
- @id = args[:id] unless args[:id].nil?
1825
- @info = args[:info] unless args[:info].nil?
1826
- @name = args[:name] unless args[:name].nil?
1827
- @predicted_insert_size = args[:predicted_insert_size] unless args[:predicted_insert_size].nil?
1828
- @programs = args[:programs] unless args[:programs].nil?
1829
- @reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
1830
- @sample_id = args[:sample_id] unless args[:sample_id].nil?
1831
- end
1832
- end
1833
-
1834
- #
1835
- class ReadGroupExperiment
1836
- include Google::Apis::Core::Hashable
1837
-
1838
- # The instrument model used as part of this experiment. This maps to sequencing
1839
- # technology in BAM.
1840
- # Corresponds to the JSON property `instrumentModel`
1841
- # @return [String]
1842
- attr_accessor :instrument_model
1843
-
1844
- # The library used as part of this experiment. Note: This is not an actual ID
1845
- # within this repository, but rather an identifier for a library which may be
1846
- # meaningful to some external system.
1847
- # Corresponds to the JSON property `libraryId`
1848
- # @return [String]
1849
- attr_accessor :library_id
1850
-
1851
- # The platform unit used as part of this experiment e.g. flowcell-barcode.lane
1852
- # for Illumina or slide for SOLiD. Corresponds to the
1853
- # Corresponds to the JSON property `platformUnit`
1854
- # @return [String]
1855
- attr_accessor :platform_unit
1856
-
1857
- # The sequencing center used as part of this experiment.
1858
- # Corresponds to the JSON property `sequencingCenter`
1859
- # @return [String]
1860
- attr_accessor :sequencing_center
1861
-
1862
- def initialize(**args)
1863
- update!(**args)
1864
- end
1865
-
1866
- # Update properties of this object
1867
- def update!(**args)
1868
- @instrument_model = args[:instrument_model] unless args[:instrument_model].nil?
1869
- @library_id = args[:library_id] unless args[:library_id].nil?
1870
- @platform_unit = args[:platform_unit] unless args[:platform_unit].nil?
1871
- @sequencing_center = args[:sequencing_center] unless args[:sequencing_center].nil?
1872
- end
1873
- end
1874
-
1875
- #
1876
- class ReadGroupProgram
1877
- include Google::Apis::Core::Hashable
1878
-
1879
- # The command line used to run this program.
1880
- # Corresponds to the JSON property `commandLine`
1881
- # @return [String]
1882
- attr_accessor :command_line
1883
-
1884
- # The user specified locally unique ID of the program. Used along with
1885
- # prevProgramId to define an ordering between programs.
1886
- # Corresponds to the JSON property `id`
1887
- # @return [String]
1888
- attr_accessor :id
1889
-
1890
- # The name of the program.
1891
- # Corresponds to the JSON property `name`
1892
- # @return [String]
1893
- attr_accessor :name
1894
-
1895
- # The ID of the program run before this one.
1896
- # Corresponds to the JSON property `prevProgramId`
1897
- # @return [String]
1898
- attr_accessor :prev_program_id
1899
-
1900
- # The version of the program run.
1901
- # Corresponds to the JSON property `version`
1902
- # @return [String]
1903
- attr_accessor :version
1904
-
1905
- def initialize(**args)
1906
- update!(**args)
1907
- end
1908
-
1909
- # Update properties of this object
1910
- def update!(**args)
1911
- @command_line = args[:command_line] unless args[:command_line].nil?
1912
- @id = args[:id] unless args[:id].nil?
1913
- @name = args[:name] unless args[:name].nil?
1914
- @prev_program_id = args[:prev_program_id] unless args[:prev_program_id].nil?
1915
- @version = args[:version] unless args[:version].nil?
1916
- end
1917
- end
1918
-
1919
- # A read group set is a logical collection of read groups, which are collections
1920
- # of reads produced by a sequencer. A read group set typically models reads
1921
- # corresponding to one sample, sequenced one way, and aligned one way.
1922
- # - A read group set belongs to one dataset.
1923
- # - A read group belongs to one read group set.
1924
- # - A read belongs to one read group.
1925
- class ReadGroupSet
1926
- include Google::Apis::Core::Hashable
1927
-
1928
- # The dataset ID.
1929
- # Corresponds to the JSON property `datasetId`
1930
- # @return [String]
1931
- attr_accessor :dataset_id
1932
-
1933
- # The filename of the original source file for this read group set, if any.
1934
- # Corresponds to the JSON property `filename`
1935
- # @return [String]
1936
- attr_accessor :filename
1937
-
1938
- # The read group set ID.
1939
- # Corresponds to the JSON property `id`
1940
- # @return [String]
1941
- attr_accessor :id
1942
-
1943
- # A string which maps to an array of values.
1944
- # Corresponds to the JSON property `info`
1945
- # @return [Hash<String,Array<String>>]
1946
- attr_accessor :info
1947
-
1948
- # The read group set name. By default this will be initialized to the sample
1949
- # name of the sequenced data contained in this set.
1950
- # Corresponds to the JSON property `name`
1951
- # @return [String]
1952
- attr_accessor :name
1953
-
1954
- # The read groups in this set. There are typically 1-10 read groups in a read
1955
- # group set.
1956
- # Corresponds to the JSON property `readGroups`
1957
- # @return [Array<Google::Apis::GenomicsV1beta2::ReadGroup>]
1958
- attr_accessor :read_groups
1959
-
1960
- # The reference set the reads in this read group set are aligned to.
1961
- # Corresponds to the JSON property `referenceSetId`
1962
- # @return [String]
1963
- attr_accessor :reference_set_id
1964
-
1965
- def initialize(**args)
1966
- update!(**args)
1967
- end
1968
-
1969
- # Update properties of this object
1970
- def update!(**args)
1971
- @dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
1972
- @filename = args[:filename] unless args[:filename].nil?
1973
- @id = args[:id] unless args[:id].nil?
1974
- @info = args[:info] unless args[:info].nil?
1975
- @name = args[:name] unless args[:name].nil?
1976
- @read_groups = args[:read_groups] unless args[:read_groups].nil?
1977
- @reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
1978
- end
1979
- end
1980
-
1981
- # A reference is a canonical assembled DNA sequence, intended to act as a
1982
- # reference coordinate space for other genomic annotations. A single reference
1983
- # might represent the human chromosome 1 or mitochandrial DNA, for instance. A
1984
- # reference belongs to one or more reference sets.
1985
- class Reference
1986
- include Google::Apis::Core::Hashable
1987
-
1988
- # The Google generated immutable ID of the reference.
1989
- # Corresponds to the JSON property `id`
1990
- # @return [String]
1991
- attr_accessor :id
1992
-
1993
- # The length of this reference's sequence.
1994
- # Corresponds to the JSON property `length`
1995
- # @return [String]
1996
- attr_accessor :length
1997
-
1998
- # MD5 of the upper-case sequence excluding all whitespace characters (this is
1999
- # equivalent to SQ:M5 in SAM). This value is represented in lower case
2000
- # hexadecimal format.
2001
- # Corresponds to the JSON property `md5checksum`
2002
- # @return [String]
2003
- attr_accessor :md5checksum
2004
-
2005
- # The name of this reference, for example 22.
2006
- # Corresponds to the JSON property `name`
2007
- # @return [String]
2008
- attr_accessor :name
2009
-
2010
- # ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not
2011
- # specified by the containing reference set.
2012
- # Corresponds to the JSON property `ncbiTaxonId`
2013
- # @return [Fixnum]
2014
- attr_accessor :ncbi_taxon_id
2015
-
2016
- # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with
2017
- # a version number, for example GCF_000001405.26.
2018
- # Corresponds to the JSON property `sourceAccessions`
2019
- # @return [Array<String>]
2020
- attr_accessor :source_accessions
2021
-
2022
- # The URI from which the sequence was obtained. Specifies a FASTA format file/
2023
- # string with one name, sequence pair.
2024
- # Corresponds to the JSON property `sourceURI`
2025
- # @return [String]
2026
- attr_accessor :source_uri
2027
-
2028
- def initialize(**args)
2029
- update!(**args)
2030
- end
2031
-
2032
- # Update properties of this object
2033
- def update!(**args)
2034
- @id = args[:id] unless args[:id].nil?
2035
- @length = args[:length] unless args[:length].nil?
2036
- @md5checksum = args[:md5checksum] unless args[:md5checksum].nil?
2037
- @name = args[:name] unless args[:name].nil?
2038
- @ncbi_taxon_id = args[:ncbi_taxon_id] unless args[:ncbi_taxon_id].nil?
2039
- @source_accessions = args[:source_accessions] unless args[:source_accessions].nil?
2040
- @source_uri = args[:source_uri] unless args[:source_uri].nil?
2041
- end
2042
- end
2043
-
2044
- # ReferenceBound records an upper bound for the starting coordinate of variants
2045
- # in a particular reference.
2046
- class ReferenceBound
2047
- include Google::Apis::Core::Hashable
2048
-
2049
- # The reference the bound is associate with.
2050
- # Corresponds to the JSON property `referenceName`
2051
- # @return [String]
2052
- attr_accessor :reference_name
2053
-
2054
- # An upper bound (inclusive) on the starting coordinate of any variant in the
2055
- # reference sequence.
2056
- # Corresponds to the JSON property `upperBound`
2057
- # @return [String]
2058
- attr_accessor :upper_bound
2059
-
2060
- def initialize(**args)
2061
- update!(**args)
2062
- end
2063
-
2064
- # Update properties of this object
2065
- def update!(**args)
2066
- @reference_name = args[:reference_name] unless args[:reference_name].nil?
2067
- @upper_bound = args[:upper_bound] unless args[:upper_bound].nil?
2068
- end
2069
- end
2070
-
2071
- # A reference set is a set of references which typically comprise a reference
2072
- # assembly for a species, such as GRCh38 which is representative of the human
2073
- # genome. A reference set defines a common coordinate space for comparing
2074
- # reference-aligned experimental data. A reference set contains 1 or more
2075
- # references.
2076
- class ReferenceSet
2077
- include Google::Apis::Core::Hashable
2078
-
2079
- # Public id of this reference set, such as GRCh37.
2080
- # Corresponds to the JSON property `assemblyId`
2081
- # @return [String]
2082
- attr_accessor :assembly_id
2083
-
2084
- # Free text description of this reference set.
2085
- # Corresponds to the JSON property `description`
2086
- # @return [String]
2087
- attr_accessor :description
2088
-
2089
- # The Google generated immutable ID of the reference set.
2090
- # Corresponds to the JSON property `id`
2091
- # @return [String]
2092
- attr_accessor :id
2093
-
2094
- # Order-independent MD5 checksum which identifies this reference set. The
2095
- # checksum is computed by sorting all lower case hexidecimal string reference.
2096
- # md5checksum (for all reference in this set) in ascending lexicographic order,
2097
- # concatenating, and taking the MD5 of that value. The resulting value is
2098
- # represented in lower case hexadecimal format.
2099
- # Corresponds to the JSON property `md5checksum`
2100
- # @return [String]
2101
- attr_accessor :md5checksum
2102
-
2103
- # ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating the
2104
- # species which this assembly is intended to model. Note that contained
2105
- # references may specify a different ncbiTaxonId, as assemblies may contain
2106
- # reference sequences which do not belong to the modeled species, e.g. EBV in a
2107
- # human reference genome.
2108
- # Corresponds to the JSON property `ncbiTaxonId`
2109
- # @return [Fixnum]
2110
- attr_accessor :ncbi_taxon_id
2111
-
2112
- # The IDs of the reference objects that are part of this set. Reference.
2113
- # md5checksum must be unique within this set.
2114
- # Corresponds to the JSON property `referenceIds`
2115
- # @return [Array<String>]
2116
- attr_accessor :reference_ids
2117
-
2118
- # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with
2119
- # a version number, for example NC_000001.11.
2120
- # Corresponds to the JSON property `sourceAccessions`
2121
- # @return [Array<String>]
2122
- attr_accessor :source_accessions
2123
-
2124
- # The URI from which the references were obtained.
2125
- # Corresponds to the JSON property `sourceURI`
2126
- # @return [String]
2127
- attr_accessor :source_uri
2128
-
2129
- def initialize(**args)
2130
- update!(**args)
2131
- end
2132
-
2133
- # Update properties of this object
2134
- def update!(**args)
2135
- @assembly_id = args[:assembly_id] unless args[:assembly_id].nil?
2136
- @description = args[:description] unless args[:description].nil?
2137
- @id = args[:id] unless args[:id].nil?
2138
- @md5checksum = args[:md5checksum] unless args[:md5checksum].nil?
2139
- @ncbi_taxon_id = args[:ncbi_taxon_id] unless args[:ncbi_taxon_id].nil?
2140
- @reference_ids = args[:reference_ids] unless args[:reference_ids].nil?
2141
- @source_accessions = args[:source_accessions] unless args[:source_accessions].nil?
2142
- @source_uri = args[:source_uri] unless args[:source_uri].nil?
2143
- end
2144
- end
2145
-
2146
- #
2147
- class SearchAnnotationSetsRequest
2148
- include Google::Apis::Core::Hashable
2149
-
2150
- # The dataset IDs to search within. Caller must have READ access to these
2151
- # datasets.
2152
- # Corresponds to the JSON property `datasetIds`
2153
- # @return [Array<String>]
2154
- attr_accessor :dataset_ids
2155
-
2156
- # Only return annotations sets for which a substring of the name matches this
2157
- # string (case insensitive).
2158
- # Corresponds to the JSON property `name`
2159
- # @return [String]
2160
- attr_accessor :name
2161
-
2162
- # Specifies number of results to return in a single page. If unspecified, it
2163
- # will default to 128. The maximum value is 1024.
2164
- # Corresponds to the JSON property `pageSize`
2165
- # @return [Fixnum]
2166
- attr_accessor :page_size
2167
-
2168
- # The continuation token, which is used to page through large result sets. To
2169
- # get the next page of results, set this parameter to the value of nextPageToken
2170
- # from the previous response.
2171
- # Corresponds to the JSON property `pageToken`
2172
- # @return [String]
2173
- attr_accessor :page_token
2174
-
2175
- # If specified, only annotation sets associated with the given reference set are
2176
- # returned.
2177
- # Corresponds to the JSON property `referenceSetId`
2178
- # @return [String]
2179
- attr_accessor :reference_set_id
2180
-
2181
- # If specified, only annotation sets that have any of these types are returned.
2182
- # Corresponds to the JSON property `types`
2183
- # @return [Array<String>]
2184
- attr_accessor :types
2185
-
2186
- def initialize(**args)
2187
- update!(**args)
2188
- end
2189
-
2190
- # Update properties of this object
2191
- def update!(**args)
2192
- @dataset_ids = args[:dataset_ids] unless args[:dataset_ids].nil?
2193
- @name = args[:name] unless args[:name].nil?
2194
- @page_size = args[:page_size] unless args[:page_size].nil?
2195
- @page_token = args[:page_token] unless args[:page_token].nil?
2196
- @reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
2197
- @types = args[:types] unless args[:types].nil?
2198
- end
2199
- end
2200
-
2201
- #
2202
- class SearchAnnotationSetsResponse
2203
- include Google::Apis::Core::Hashable
2204
-
2205
- # The matching annotation sets.
2206
- # Corresponds to the JSON property `annotationSets`
2207
- # @return [Array<Google::Apis::GenomicsV1beta2::AnnotationSet>]
2208
- attr_accessor :annotation_sets
2209
-
2210
- # The continuation token, which is used to page through large result sets.
2211
- # Provide this value in a subsequent request to return the next page of results.
2212
- # This field will be empty if there aren't any additional results.
2213
- # Corresponds to the JSON property `nextPageToken`
2214
- # @return [String]
2215
- attr_accessor :next_page_token
2216
-
2217
- def initialize(**args)
2218
- update!(**args)
2219
- end
2220
-
2221
- # Update properties of this object
2222
- def update!(**args)
2223
- @annotation_sets = args[:annotation_sets] unless args[:annotation_sets].nil?
2224
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
2225
- end
2226
- end
2227
-
2228
- #
2229
- class SearchAnnotationsRequest
2230
- include Google::Apis::Core::Hashable
2231
-
2232
- # The annotation sets to search within. The caller must have READ access to
2233
- # these annotation sets. Required. All queried annotation sets must have the
2234
- # same type.
2235
- # Corresponds to the JSON property `annotationSetIds`
2236
- # @return [Array<String>]
2237
- attr_accessor :annotation_set_ids
2238
-
2239
- # Specifies number of results to return in a single page. If unspecified, it
2240
- # will default to 256. The maximum value is 2048.
2241
- # Corresponds to the JSON property `pageSize`
2242
- # @return [Fixnum]
2243
- attr_accessor :page_size
2244
-
2245
- # The continuation token, which is used to page through large result sets. To
2246
- # get the next page of results, set this parameter to the value of nextPageToken
2247
- # from the previous response.
2248
- # Corresponds to the JSON property `pageToken`
2249
- # @return [String]
2250
- attr_accessor :page_token
2251
-
2252
- # A 0-based half-open genomic coordinate range for search requests.
2253
- # Corresponds to the JSON property `range`
2254
- # @return [Google::Apis::GenomicsV1beta2::QueryRange]
2255
- attr_accessor :range
2256
-
2257
- def initialize(**args)
2258
- update!(**args)
2259
- end
2260
-
2261
- # Update properties of this object
2262
- def update!(**args)
2263
- @annotation_set_ids = args[:annotation_set_ids] unless args[:annotation_set_ids].nil?
2264
- @page_size = args[:page_size] unless args[:page_size].nil?
2265
- @page_token = args[:page_token] unless args[:page_token].nil?
2266
- @range = args[:range] unless args[:range].nil?
2267
- end
2268
- end
2269
-
2270
- #
2271
- class SearchAnnotationsResponse
2272
- include Google::Apis::Core::Hashable
2273
-
2274
- # The matching annotations.
2275
- # Corresponds to the JSON property `annotations`
2276
- # @return [Array<Google::Apis::GenomicsV1beta2::Annotation>]
2277
- attr_accessor :annotations
2278
-
2279
- # The continuation token, which is used to page through large result sets.
2280
- # Provide this value in a subsequent request to return the next page of results.
2281
- # This field will be empty if there aren't any additional results.
2282
- # Corresponds to the JSON property `nextPageToken`
2283
- # @return [String]
2284
- attr_accessor :next_page_token
2285
-
2286
- def initialize(**args)
2287
- update!(**args)
2288
- end
2289
-
2290
- # Update properties of this object
2291
- def update!(**args)
2292
- @annotations = args[:annotations] unless args[:annotations].nil?
2293
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
2294
- end
2295
- end
2296
-
2297
- # The call set search request.
2298
- class SearchCallSetsRequest
2299
- include Google::Apis::Core::Hashable
2300
-
2301
- # Only return call sets for which a substring of the name matches this string.
2302
- # Corresponds to the JSON property `name`
2303
- # @return [String]
2304
- attr_accessor :name
2305
-
2306
- # The maximum number of call sets to return. If unspecified, defaults to 1000.
2307
- # Corresponds to the JSON property `pageSize`
2308
- # @return [Fixnum]
2309
- attr_accessor :page_size
2310
-
2311
- # The continuation token, which is used to page through large result sets. To
2312
- # get the next page of results, set this parameter to the value of nextPageToken
2313
- # from the previous response.
2314
- # Corresponds to the JSON property `pageToken`
2315
- # @return [String]
2316
- attr_accessor :page_token
2317
-
2318
- # Restrict the query to call sets within the given variant sets. At least one ID
2319
- # must be provided.
2320
- # Corresponds to the JSON property `variantSetIds`
2321
- # @return [Array<String>]
2322
- attr_accessor :variant_set_ids
2323
-
2324
- def initialize(**args)
2325
- update!(**args)
2326
- end
2327
-
2328
- # Update properties of this object
2329
- def update!(**args)
2330
- @name = args[:name] unless args[:name].nil?
2331
- @page_size = args[:page_size] unless args[:page_size].nil?
2332
- @page_token = args[:page_token] unless args[:page_token].nil?
2333
- @variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil?
2334
- end
2335
- end
2336
-
2337
- # The call set search response.
2338
- class SearchCallSetsResponse
2339
- include Google::Apis::Core::Hashable
2340
-
2341
- # The list of matching call sets.
2342
- # Corresponds to the JSON property `callSets`
2343
- # @return [Array<Google::Apis::GenomicsV1beta2::CallSet>]
2344
- attr_accessor :call_sets
2345
-
2346
- # The continuation token, which is used to page through large result sets.
2347
- # Provide this value in a subsequent request to return the next page of results.
2348
- # This field will be empty if there aren't any additional results.
2349
- # Corresponds to the JSON property `nextPageToken`
2350
- # @return [String]
2351
- attr_accessor :next_page_token
2352
-
2353
- def initialize(**args)
2354
- update!(**args)
2355
- end
2356
-
2357
- # Update properties of this object
2358
- def update!(**args)
2359
- @call_sets = args[:call_sets] unless args[:call_sets].nil?
2360
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
2361
- end
2362
- end
2363
-
2364
- # The jobs search request.
2365
- class SearchJobsRequest
2366
- include Google::Apis::Core::Hashable
2367
-
2368
- # If specified, only jobs created on or after this date, given in milliseconds
2369
- # since Unix epoch, will be returned.
2370
- # Corresponds to the JSON property `createdAfter`
2371
- # @return [String]
2372
- attr_accessor :created_after
2373
-
2374
- # If specified, only jobs created prior to this date, given in milliseconds
2375
- # since Unix epoch, will be returned.
2376
- # Corresponds to the JSON property `createdBefore`
2377
- # @return [String]
2378
- attr_accessor :created_before
2379
-
2380
- # Specifies the number of results to return in a single page. Defaults to 128.
2381
- # The maximum value is 256.
2382
- # Corresponds to the JSON property `pageSize`
2383
- # @return [Fixnum]
2384
- attr_accessor :page_size
2385
-
2386
- # The continuation token which is used to page through large result sets. To get
2387
- # the next page of results, set this parameter to the value of the nextPageToken
2388
- # from the previous response.
2389
- # Corresponds to the JSON property `pageToken`
2390
- # @return [String]
2391
- attr_accessor :page_token
2392
-
2393
- # Required. Only return jobs which belong to this Google Developers Console
2394
- # project.
2395
- # Corresponds to the JSON property `projectNumber`
2396
- # @return [String]
2397
- attr_accessor :project_number
2398
-
2399
- # Only return jobs which have a matching status.
2400
- # Corresponds to the JSON property `status`
2401
- # @return [Array<String>]
2402
- attr_accessor :status
2403
-
2404
- def initialize(**args)
2405
- update!(**args)
2406
- end
2407
-
2408
- # Update properties of this object
2409
- def update!(**args)
2410
- @created_after = args[:created_after] unless args[:created_after].nil?
2411
- @created_before = args[:created_before] unless args[:created_before].nil?
2412
- @page_size = args[:page_size] unless args[:page_size].nil?
2413
- @page_token = args[:page_token] unless args[:page_token].nil?
2414
- @project_number = args[:project_number] unless args[:project_number].nil?
2415
- @status = args[:status] unless args[:status].nil?
2416
- end
2417
- end
2418
-
2419
- # The job search response.
2420
- class SearchJobsResponse
2421
- include Google::Apis::Core::Hashable
2422
-
2423
- # The list of jobs results, ordered newest to oldest.
2424
- # Corresponds to the JSON property `jobs`
2425
- # @return [Array<Google::Apis::GenomicsV1beta2::Job>]
2426
- attr_accessor :jobs
2427
-
2428
- # The continuation token which is used to page through large result sets.
2429
- # Provide this value is a subsequent request to return the next page of results.
2430
- # This field will be empty if there are no more results.
2431
- # Corresponds to the JSON property `nextPageToken`
2432
- # @return [String]
2433
- attr_accessor :next_page_token
2434
-
2435
- def initialize(**args)
2436
- update!(**args)
2437
- end
2438
-
2439
- # Update properties of this object
2440
- def update!(**args)
2441
- @jobs = args[:jobs] unless args[:jobs].nil?
2442
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
2443
- end
2444
- end
2445
-
2446
- # The read group set search request.
2447
- class SearchReadGroupSetsRequest
2448
- include Google::Apis::Core::Hashable
2449
-
2450
- # Restricts this query to read group sets within the given datasets. At least
2451
- # one ID must be provided.
2452
- # Corresponds to the JSON property `datasetIds`
2453
- # @return [Array<String>]
2454
- attr_accessor :dataset_ids
2455
-
2456
- # Only return read group sets for which a substring of the name matches this
2457
- # string.
2458
- # Corresponds to the JSON property `name`
2459
- # @return [String]
2460
- attr_accessor :name
2461
-
2462
- # Specifies number of results to return in a single page. If unspecified, it
2463
- # will default to 256. The maximum value is 1024.
2464
- # Corresponds to the JSON property `pageSize`
2465
- # @return [Fixnum]
2466
- attr_accessor :page_size
2467
-
2468
- # The continuation token, which is used to page through large result sets. To
2469
- # get the next page of results, set this parameter to the value of nextPageToken
2470
- # from the previous response.
2471
- # Corresponds to the JSON property `pageToken`
2472
- # @return [String]
2473
- attr_accessor :page_token
2474
-
2475
- def initialize(**args)
2476
- update!(**args)
2477
- end
2478
-
2479
- # Update properties of this object
2480
- def update!(**args)
2481
- @dataset_ids = args[:dataset_ids] unless args[:dataset_ids].nil?
2482
- @name = args[:name] unless args[:name].nil?
2483
- @page_size = args[:page_size] unless args[:page_size].nil?
2484
- @page_token = args[:page_token] unless args[:page_token].nil?
2485
- end
2486
- end
2487
-
2488
- # The read group set search response.
2489
- class SearchReadGroupSetsResponse
2490
- include Google::Apis::Core::Hashable
2491
-
2492
- # The continuation token, which is used to page through large result sets.
2493
- # Provide this value in a subsequent request to return the next page of results.
2494
- # This field will be empty if there aren't any additional results.
2495
- # Corresponds to the JSON property `nextPageToken`
2496
- # @return [String]
2497
- attr_accessor :next_page_token
2498
-
2499
- # The list of matching read group sets.
2500
- # Corresponds to the JSON property `readGroupSets`
2501
- # @return [Array<Google::Apis::GenomicsV1beta2::ReadGroupSet>]
2502
- attr_accessor :read_group_sets
2503
-
2504
- def initialize(**args)
2505
- update!(**args)
2506
- end
2507
-
2508
- # Update properties of this object
2509
- def update!(**args)
2510
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
2511
- @read_group_sets = args[:read_group_sets] unless args[:read_group_sets].nil?
2512
- end
2513
- end
2514
-
2515
- # The read search request.
2516
- class SearchReadsRequest
2517
- include Google::Apis::Core::Hashable
2518
-
2519
- # The end position of the range on the reference, 0-based exclusive. If
2520
- # specified, referenceName must also be specified.
2521
- # Corresponds to the JSON property `end`
2522
- # @return [String]
2523
- attr_accessor :end
2524
-
2525
- # Specifies number of results to return in a single page. If unspecified, it
2526
- # will default to 256. The maximum value is 2048.
2527
- # Corresponds to the JSON property `pageSize`
2528
- # @return [Fixnum]
2529
- attr_accessor :page_size
2530
-
2531
- # The continuation token, which is used to page through large result sets. To
2532
- # get the next page of results, set this parameter to the value of nextPageToken
2533
- # from the previous response.
2534
- # Corresponds to the JSON property `pageToken`
2535
- # @return [String]
2536
- attr_accessor :page_token
2537
-
2538
- # The IDs of the read groups within which to search for reads. All specified
2539
- # read groups must belong to the same read group sets. Must specify one of
2540
- # readGroupSetIds or readGroupIds.
2541
- # Corresponds to the JSON property `readGroupIds`
2542
- # @return [Array<String>]
2543
- attr_accessor :read_group_ids
2544
-
2545
- # The IDs of the read groups sets within which to search for reads. All
2546
- # specified read group sets must be aligned against a common set of reference
2547
- # sequences; this defines the genomic coordinates for the query. Must specify
2548
- # one of readGroupSetIds or readGroupIds.
2549
- # Corresponds to the JSON property `readGroupSetIds`
2550
- # @return [Array<String>]
2551
- attr_accessor :read_group_set_ids
2552
-
2553
- # The reference sequence name, for example chr1, 1, or chrX. If set to *, only
2554
- # unmapped reads are returned.
2555
- # Corresponds to the JSON property `referenceName`
2556
- # @return [String]
2557
- attr_accessor :reference_name
2558
-
2559
- # The start position of the range on the reference, 0-based inclusive. If
2560
- # specified, referenceName must also be specified.
2561
- # Corresponds to the JSON property `start`
2562
- # @return [String]
2563
- attr_accessor :start
2564
-
2565
- def initialize(**args)
2566
- update!(**args)
2567
- end
2568
-
2569
- # Update properties of this object
2570
- def update!(**args)
2571
- @end = args[:end] unless args[:end].nil?
2572
- @page_size = args[:page_size] unless args[:page_size].nil?
2573
- @page_token = args[:page_token] unless args[:page_token].nil?
2574
- @read_group_ids = args[:read_group_ids] unless args[:read_group_ids].nil?
2575
- @read_group_set_ids = args[:read_group_set_ids] unless args[:read_group_set_ids].nil?
2576
- @reference_name = args[:reference_name] unless args[:reference_name].nil?
2577
- @start = args[:start] unless args[:start].nil?
2578
- end
2579
- end
2580
-
2581
- # The read search response.
2582
- class SearchReadsResponse
2583
- include Google::Apis::Core::Hashable
2584
-
2585
- # The list of matching alignments sorted by mapped genomic coordinate, if any,
2586
- # ascending in position within the same reference. Unmapped reads, which have no
2587
- # position, are returned last and are further sorted in ascending lexicographic
2588
- # order by fragment name.
2589
- # Corresponds to the JSON property `alignments`
2590
- # @return [Array<Google::Apis::GenomicsV1beta2::Read>]
2591
- attr_accessor :alignments
2592
-
2593
- # The continuation token, which is used to page through large result sets.
2594
- # Provide this value in a subsequent request to return the next page of results.
2595
- # This field will be empty if there aren't any additional results.
2596
- # Corresponds to the JSON property `nextPageToken`
2597
- # @return [String]
2598
- attr_accessor :next_page_token
2599
-
2600
- def initialize(**args)
2601
- update!(**args)
2602
- end
2603
-
2604
- # Update properties of this object
2605
- def update!(**args)
2606
- @alignments = args[:alignments] unless args[:alignments].nil?
2607
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
2608
- end
2609
- end
2610
-
2611
- #
2612
- class SearchReferenceSetsRequest
2613
- include Google::Apis::Core::Hashable
2614
-
2615
- # If present, return references for which the accession matches any of these
2616
- # strings. Best to give a version number, for example GCF_000001405.26. If only
2617
- # the main accession number is given then all records with that main accession
2618
- # will be returned, whichever version. Note that different versions will have
2619
- # different sequences.
2620
- # Corresponds to the JSON property `accessions`
2621
- # @return [Array<String>]
2622
- attr_accessor :accessions
2623
-
2624
- # If present, return reference sets for which a substring of their assemblyId
2625
- # matches this string (case insensitive).
2626
- # Corresponds to the JSON property `assemblyId`
2627
- # @return [String]
2628
- attr_accessor :assembly_id
2629
-
2630
- # If present, return references for which the md5checksum matches. See
2631
- # ReferenceSet.md5checksum for details.
2632
- # Corresponds to the JSON property `md5checksums`
2633
- # @return [Array<String>]
2634
- attr_accessor :md5checksums
2635
-
2636
- # Specifies the maximum number of results to return in a single page.
2637
- # Corresponds to the JSON property `pageSize`
2638
- # @return [Fixnum]
2639
- attr_accessor :page_size
2640
-
2641
- # The continuation token, which is used to page through large result sets. To
2642
- # get the next page of results, set this parameter to the value of nextPageToken
2643
- # from the previous response.
2644
- # Corresponds to the JSON property `pageToken`
2645
- # @return [String]
2646
- attr_accessor :page_token
2647
-
2648
- def initialize(**args)
2649
- update!(**args)
2650
- end
2651
-
2652
- # Update properties of this object
2653
- def update!(**args)
2654
- @accessions = args[:accessions] unless args[:accessions].nil?
2655
- @assembly_id = args[:assembly_id] unless args[:assembly_id].nil?
2656
- @md5checksums = args[:md5checksums] unless args[:md5checksums].nil?
2657
- @page_size = args[:page_size] unless args[:page_size].nil?
2658
- @page_token = args[:page_token] unless args[:page_token].nil?
2659
- end
2660
- end
2661
-
2662
- #
2663
- class SearchReferenceSetsResponse
2664
- include Google::Apis::Core::Hashable
2665
-
2666
- # The continuation token, which is used to page through large result sets.
2667
- # Provide this value in a subsequent request to return the next page of results.
2668
- # This field will be empty if there aren't any additional results.
2669
- # Corresponds to the JSON property `nextPageToken`
2670
- # @return [String]
2671
- attr_accessor :next_page_token
2672
-
2673
- # The matching references sets.
2674
- # Corresponds to the JSON property `referenceSets`
2675
- # @return [Array<Google::Apis::GenomicsV1beta2::ReferenceSet>]
2676
- attr_accessor :reference_sets
2677
-
2678
- def initialize(**args)
2679
- update!(**args)
2680
- end
2681
-
2682
- # Update properties of this object
2683
- def update!(**args)
2684
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
2685
- @reference_sets = args[:reference_sets] unless args[:reference_sets].nil?
2686
- end
2687
- end
2688
-
2689
- #
2690
- class SearchReferencesRequest
2691
- include Google::Apis::Core::Hashable
2692
-
2693
- # If present, return references for which the accession matches this string.
2694
- # Best to give a version number, for example GCF_000001405.26. If only the main
2695
- # accession number is given then all records with that main accession will be
2696
- # returned, whichever version. Note that different versions will have different
2697
- # sequences.
2698
- # Corresponds to the JSON property `accessions`
2699
- # @return [Array<String>]
2700
- attr_accessor :accessions
2701
-
2702
- # If present, return references for which the md5checksum matches. See Reference.
2703
- # md5checksum for construction details.
2704
- # Corresponds to the JSON property `md5checksums`
2705
- # @return [Array<String>]
2706
- attr_accessor :md5checksums
2707
-
2708
- # Specifies the maximum number of results to return in a single page.
2709
- # Corresponds to the JSON property `pageSize`
2710
- # @return [Fixnum]
2711
- attr_accessor :page_size
2712
-
2713
- # The continuation token, which is used to page through large result sets. To
2714
- # get the next page of results, set this parameter to the value of nextPageToken
2715
- # from the previous response.
2716
- # Corresponds to the JSON property `pageToken`
2717
- # @return [String]
2718
- attr_accessor :page_token
2719
-
2720
- # If present, return only references which belong to this reference set.
2721
- # Corresponds to the JSON property `referenceSetId`
2722
- # @return [String]
2723
- attr_accessor :reference_set_id
2724
-
2725
- def initialize(**args)
2726
- update!(**args)
2727
- end
2728
-
2729
- # Update properties of this object
2730
- def update!(**args)
2731
- @accessions = args[:accessions] unless args[:accessions].nil?
2732
- @md5checksums = args[:md5checksums] unless args[:md5checksums].nil?
2733
- @page_size = args[:page_size] unless args[:page_size].nil?
2734
- @page_token = args[:page_token] unless args[:page_token].nil?
2735
- @reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
2736
- end
2737
- end
2738
-
2739
- #
2740
- class SearchReferencesResponse
2741
- include Google::Apis::Core::Hashable
2742
-
2743
- # The continuation token, which is used to page through large result sets.
2744
- # Provide this value in a subsequent request to return the next page of results.
2745
- # This field will be empty if there aren't any additional results.
2746
- # Corresponds to the JSON property `nextPageToken`
2747
- # @return [String]
2748
- attr_accessor :next_page_token
2749
-
2750
- # The matching references.
2751
- # Corresponds to the JSON property `references`
2752
- # @return [Array<Google::Apis::GenomicsV1beta2::Reference>]
2753
- attr_accessor :references
2754
-
2755
- def initialize(**args)
2756
- update!(**args)
2757
- end
2758
-
2759
- # Update properties of this object
2760
- def update!(**args)
2761
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
2762
- @references = args[:references] unless args[:references].nil?
2763
- end
2764
- end
2765
-
2766
- # The search variant sets request.
2767
- class SearchVariantSetsRequest
2768
- include Google::Apis::Core::Hashable
2769
-
2770
- # Exactly one dataset ID must be provided here. Only variant sets which belong
2771
- # to this dataset will be returned.
2772
- # Corresponds to the JSON property `datasetIds`
2773
- # @return [Array<String>]
2774
- attr_accessor :dataset_ids
2775
-
2776
- # The maximum number of variant sets to return in a request.
2777
- # Corresponds to the JSON property `pageSize`
2778
- # @return [Fixnum]
2779
- attr_accessor :page_size
2780
-
2781
- # The continuation token, which is used to page through large result sets. To
2782
- # get the next page of results, set this parameter to the value of nextPageToken
2783
- # from the previous response.
2784
- # Corresponds to the JSON property `pageToken`
2785
- # @return [String]
2786
- attr_accessor :page_token
2787
-
2788
- def initialize(**args)
2789
- update!(**args)
2790
- end
2791
-
2792
- # Update properties of this object
2793
- def update!(**args)
2794
- @dataset_ids = args[:dataset_ids] unless args[:dataset_ids].nil?
2795
- @page_size = args[:page_size] unless args[:page_size].nil?
2796
- @page_token = args[:page_token] unless args[:page_token].nil?
2797
- end
2798
- end
2799
-
2800
- # The search variant sets response.
2801
- class SearchVariantSetsResponse
2802
- include Google::Apis::Core::Hashable
2803
-
2804
- # The continuation token, which is used to page through large result sets.
2805
- # Provide this value in a subsequent request to return the next page of results.
2806
- # This field will be empty if there aren't any additional results.
2807
- # Corresponds to the JSON property `nextPageToken`
2808
- # @return [String]
2809
- attr_accessor :next_page_token
2810
-
2811
- # The variant sets belonging to the requested dataset.
2812
- # Corresponds to the JSON property `variantSets`
2813
- # @return [Array<Google::Apis::GenomicsV1beta2::VariantSet>]
2814
- attr_accessor :variant_sets
2815
-
2816
- def initialize(**args)
2817
- update!(**args)
2818
- end
2819
-
2820
- # Update properties of this object
2821
- def update!(**args)
2822
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
2823
- @variant_sets = args[:variant_sets] unless args[:variant_sets].nil?
2824
- end
2825
- end
2826
-
2827
- # The variant search request.
2828
- class SearchVariantsRequest
2829
- include Google::Apis::Core::Hashable
2830
-
2831
- # Only return variant calls which belong to call sets with these ids. Leaving
2832
- # this blank returns all variant calls. If a variant has no calls belonging to
2833
- # any of these call sets, it won't be returned at all. Currently, variants with
2834
- # no calls from any call set will never be returned.
2835
- # Corresponds to the JSON property `callSetIds`
2836
- # @return [Array<String>]
2837
- attr_accessor :call_set_ids
2838
-
2839
- # The end of the window, 0-based exclusive. If unspecified or 0, defaults to the
2840
- # length of the reference.
2841
- # Corresponds to the JSON property `end`
2842
- # @return [String]
2843
- attr_accessor :end
2844
-
2845
- # The maximum number of calls to return. However, at least one variant will
2846
- # always be returned, even if it has more calls than this limit. If unspecified,
2847
- # defaults to 5000.
2848
- # Corresponds to the JSON property `maxCalls`
2849
- # @return [Fixnum]
2850
- attr_accessor :max_calls
2851
-
2852
- # The maximum number of variants to return. If unspecified, defaults to 5000.
2853
- # Corresponds to the JSON property `pageSize`
2854
- # @return [Fixnum]
2855
- attr_accessor :page_size
2856
-
2857
- # The continuation token, which is used to page through large result sets. To
2858
- # get the next page of results, set this parameter to the value of nextPageToken
2859
- # from the previous response.
2860
- # Corresponds to the JSON property `pageToken`
2861
- # @return [String]
2862
- attr_accessor :page_token
2863
-
2864
- # Required. Only return variants in this reference sequence.
2865
- # Corresponds to the JSON property `referenceName`
2866
- # @return [String]
2867
- attr_accessor :reference_name
2868
-
2869
- # The beginning of the window (0-based, inclusive) for which overlapping
2870
- # variants should be returned. If unspecified, defaults to 0.
2871
- # Corresponds to the JSON property `start`
2872
- # @return [String]
2873
- attr_accessor :start
2874
-
2875
- # Only return variants which have exactly this name.
2876
- # Corresponds to the JSON property `variantName`
2877
- # @return [String]
2878
- attr_accessor :variant_name
2879
-
2880
- # At most one variant set ID must be provided. Only variants from this variant
2881
- # set will be returned. If omitted, a call set id must be included in the
2882
- # request.
2883
- # Corresponds to the JSON property `variantSetIds`
2884
- # @return [Array<String>]
2885
- attr_accessor :variant_set_ids
2886
-
2887
- def initialize(**args)
2888
- update!(**args)
2889
- end
2890
-
2891
- # Update properties of this object
2892
- def update!(**args)
2893
- @call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil?
2894
- @end = args[:end] unless args[:end].nil?
2895
- @max_calls = args[:max_calls] unless args[:max_calls].nil?
2896
- @page_size = args[:page_size] unless args[:page_size].nil?
2897
- @page_token = args[:page_token] unless args[:page_token].nil?
2898
- @reference_name = args[:reference_name] unless args[:reference_name].nil?
2899
- @start = args[:start] unless args[:start].nil?
2900
- @variant_name = args[:variant_name] unless args[:variant_name].nil?
2901
- @variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil?
2902
- end
2903
- end
2904
-
2905
- # The variant search response.
2906
- class SearchVariantsResponse
2907
- include Google::Apis::Core::Hashable
2908
-
2909
- # The continuation token, which is used to page through large result sets.
2910
- # Provide this value in a subsequent request to return the next page of results.
2911
- # This field will be empty if there aren't any additional results.
2912
- # Corresponds to the JSON property `nextPageToken`
2913
- # @return [String]
2914
- attr_accessor :next_page_token
2915
-
2916
- # The list of matching Variants.
2917
- # Corresponds to the JSON property `variants`
2918
- # @return [Array<Google::Apis::GenomicsV1beta2::Variant>]
2919
- attr_accessor :variants
2920
-
2921
- def initialize(**args)
2922
- update!(**args)
2923
- end
2924
-
2925
- # Update properties of this object
2926
- def update!(**args)
2927
- @next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
2928
- @variants = args[:variants] unless args[:variants].nil?
2929
- end
2930
- end
2931
-
2932
- # A transcript represents the assertion that a particular region of the
2933
- # reference genome may be transcribed as RNA.
2934
- class Transcript
2935
- include Google::Apis::Core::Hashable
2936
-
2937
- # The range of the coding sequence for this transcript, if any. To determine the
2938
- # exact ranges of coding sequence, intersect this range with those of the exons,
2939
- # if any. If there are any exons, the codingSequence must start and end within
2940
- # them.
2941
- # Note that in some cases, the reference genome will not exactly match the
2942
- # observed mRNA transcript e.g. due to variance in the source genome from
2943
- # reference. In these cases, exon.frame will not necessarily match the expected
2944
- # reference reading frame and coding exon reference bases cannot necessarily be
2945
- # concatenated to produce the original transcript mRNA.
2946
- # Corresponds to the JSON property `codingSequence`
2947
- # @return [Google::Apis::GenomicsV1beta2::TranscriptCodingSequence]
2948
- attr_accessor :coding_sequence
2949
-
2950
- # The exons that compose this transcript. This field should be unset for genomes
2951
- # where transcript splicing does not occur, for example prokaryotes.
2952
- # Introns are regions of the transcript that are not included in the spliced RNA
2953
- # product. Though not explicitly modeled here, intron ranges can be deduced; all
2954
- # regions of this transcript that are not exons are introns.
2955
- # Exonic sequences do not necessarily code for a translational product (amino
2956
- # acids). Only the regions of exons bounded by the codingSequence correspond to
2957
- # coding DNA sequence.
2958
- # Exons are ordered by start position and may not overlap.
2959
- # Corresponds to the JSON property `exons`
2960
- # @return [Array<Google::Apis::GenomicsV1beta2::TranscriptExon>]
2961
- attr_accessor :exons
2962
-
2963
- # The annotation ID of the gene from which this transcript is transcribed.
2964
- # Corresponds to the JSON property `geneId`
2965
- # @return [String]
2966
- attr_accessor :gene_id
2967
-
2968
- def initialize(**args)
2969
- update!(**args)
2970
- end
2971
-
2972
- # Update properties of this object
2973
- def update!(**args)
2974
- @coding_sequence = args[:coding_sequence] unless args[:coding_sequence].nil?
2975
- @exons = args[:exons] unless args[:exons].nil?
2976
- @gene_id = args[:gene_id] unless args[:gene_id].nil?
2977
- end
2978
- end
2979
-
2980
- #
2981
- class TranscriptCodingSequence
2982
- include Google::Apis::Core::Hashable
2983
-
2984
- # The end of the coding sequence on this annotation's reference sequence, 0-
2985
- # based exclusive. Note that this position is relative to the reference start,
2986
- # and not the containing annotation start.
2987
- # Corresponds to the JSON property `end`
2988
- # @return [String]
2989
- attr_accessor :end
2990
-
2991
- # The start of the coding sequence on this annotation's reference sequence, 0-
2992
- # based inclusive. Note that this position is relative to the reference start,
2993
- # and not the containing annotation start.
2994
- # Corresponds to the JSON property `start`
2995
- # @return [String]
2996
- attr_accessor :start
2997
-
2998
- def initialize(**args)
2999
- update!(**args)
3000
- end
3001
-
3002
- # Update properties of this object
3003
- def update!(**args)
3004
- @end = args[:end] unless args[:end].nil?
3005
- @start = args[:start] unless args[:start].nil?
3006
- end
3007
- end
3008
-
3009
- #
3010
- class TranscriptExon
3011
- include Google::Apis::Core::Hashable
3012
-
3013
- # The end position of the exon on this annotation's reference sequence, 0-based
3014
- # exclusive. Note that this is relative to the reference start, and not the
3015
- # containing annotation start.
3016
- # Corresponds to the JSON property `end`
3017
- # @return [String]
3018
- attr_accessor :end
3019
-
3020
- # Wrapper message for `int32`.
3021
- # The JSON representation for `Int32Value` is JSON number.
3022
- # Corresponds to the JSON property `frame`
3023
- # @return [Google::Apis::GenomicsV1beta2::Int32Value]
3024
- attr_accessor :frame
3025
-
3026
- # The start position of the exon on this annotation's reference sequence, 0-
3027
- # based inclusive. Note that this is relative to the reference start, and not
3028
- # the containing annotation start.
3029
- # Corresponds to the JSON property `start`
3030
- # @return [String]
3031
- attr_accessor :start
3032
-
3033
- def initialize(**args)
3034
- update!(**args)
3035
- end
3036
-
3037
- # Update properties of this object
3038
- def update!(**args)
3039
- @end = args[:end] unless args[:end].nil?
3040
- @frame = args[:frame] unless args[:frame].nil?
3041
- @start = args[:start] unless args[:start].nil?
3042
- end
3043
- end
3044
-
3045
- # A variant represents a change in DNA sequence relative to a reference sequence.
3046
- # For example, a variant could represent a SNP or an insertion. Variants belong
3047
- # to a variant set. Each of the calls on a variant represent a determination of
3048
- # genotype with respect to that variant. For example, a call might assign
3049
- # probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named
3050
- # NA12345. A call belongs to a call set, which contains related calls typically
3051
- # from one sample.
3052
- class Variant
3053
- include Google::Apis::Core::Hashable
3054
-
3055
- # The bases that appear instead of the reference bases.
3056
- # Corresponds to the JSON property `alternateBases`
3057
- # @return [Array<String>]
3058
- attr_accessor :alternate_bases
3059
-
3060
- # The variant calls for this particular variant. Each one represents the
3061
- # determination of genotype with respect to this variant.
3062
- # Corresponds to the JSON property `calls`
3063
- # @return [Array<Google::Apis::GenomicsV1beta2::Call>]
3064
- attr_accessor :calls
3065
-
3066
- # The date this variant was created, in milliseconds from the epoch.
3067
- # Corresponds to the JSON property `created`
3068
- # @return [String]
3069
- attr_accessor :created
3070
-
3071
- # The end position (0-based) of this variant. This corresponds to the first base
3072
- # after the last base in the reference allele. So, the length of the reference
3073
- # allele is (end - start). This is useful for variants that don't explicitly
3074
- # give alternate bases, for example large deletions.
3075
- # Corresponds to the JSON property `end`
3076
- # @return [String]
3077
- attr_accessor :end
3078
-
3079
- # A list of filters (normally quality filters) this variant has failed. PASS
3080
- # indicates this variant has passed all filters.
3081
- # Corresponds to the JSON property `filter`
3082
- # @return [Array<String>]
3083
- attr_accessor :filter
3084
-
3085
- # The Google generated ID of the variant, immutable.
3086
- # Corresponds to the JSON property `id`
3087
- # @return [String]
3088
- attr_accessor :id
3089
-
3090
- # A string which maps to an array of values.
3091
- # Corresponds to the JSON property `info`
3092
- # @return [Hash<String,Array<String>>]
3093
- attr_accessor :info
3094
-
3095
- # Names for the variant, for example a RefSNP ID.
3096
- # Corresponds to the JSON property `names`
3097
- # @return [Array<String>]
3098
- attr_accessor :names
3099
-
3100
- # A measure of how likely this variant is to be real. A higher value is better.
3101
- # Corresponds to the JSON property `quality`
3102
- # @return [Float]
3103
- attr_accessor :quality
3104
-
3105
- # The reference bases for this variant. They start at the given position.
3106
- # Corresponds to the JSON property `referenceBases`
3107
- # @return [String]
3108
- attr_accessor :reference_bases
3109
-
3110
- # The reference on which this variant occurs. (such as chr20 or X)
3111
- # Corresponds to the JSON property `referenceName`
3112
- # @return [String]
3113
- attr_accessor :reference_name
3114
-
3115
- # The position at which this variant occurs (0-based). This corresponds to the
3116
- # first base of the string of reference bases.
3117
- # Corresponds to the JSON property `start`
3118
- # @return [String]
3119
- attr_accessor :start
3120
-
3121
- # The ID of the variant set this variant belongs to.
3122
- # Corresponds to the JSON property `variantSetId`
3123
- # @return [String]
3124
- attr_accessor :variant_set_id
3125
-
3126
- def initialize(**args)
3127
- update!(**args)
3128
- end
3129
-
3130
- # Update properties of this object
3131
- def update!(**args)
3132
- @alternate_bases = args[:alternate_bases] unless args[:alternate_bases].nil?
3133
- @calls = args[:calls] unless args[:calls].nil?
3134
- @created = args[:created] unless args[:created].nil?
3135
- @end = args[:end] unless args[:end].nil?
3136
- @filter = args[:filter] unless args[:filter].nil?
3137
- @id = args[:id] unless args[:id].nil?
3138
- @info = args[:info] unless args[:info].nil?
3139
- @names = args[:names] unless args[:names].nil?
3140
- @quality = args[:quality] unless args[:quality].nil?
3141
- @reference_bases = args[:reference_bases] unless args[:reference_bases].nil?
3142
- @reference_name = args[:reference_name] unless args[:reference_name].nil?
3143
- @start = args[:start] unless args[:start].nil?
3144
- @variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil?
3145
- end
3146
- end
3147
-
3148
- # A Variant annotation.
3149
- class VariantAnnotation
3150
- include Google::Apis::Core::Hashable
3151
-
3152
- # The alternate allele for this variant. If multiple alternate alleles exist at
3153
- # this location, create a separate variant for each one, as they may represent
3154
- # distinct conditions.
3155
- # Corresponds to the JSON property `alternateBases`
3156
- # @return [String]
3157
- attr_accessor :alternate_bases
3158
-
3159
- # Describes the clinical significance of a variant. It is adapted from the
3160
- # ClinVar controlled vocabulary for clinical significance described at: http://
3161
- # www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
3162
- # Corresponds to the JSON property `clinicalSignificance`
3163
- # @return [String]
3164
- attr_accessor :clinical_significance
3165
-
3166
- # The set of conditions associated with this variant. A condition describes the
3167
- # way a variant influences human health.
3168
- # Corresponds to the JSON property `conditions`
3169
- # @return [Array<Google::Apis::GenomicsV1beta2::VariantAnnotationCondition>]
3170
- attr_accessor :conditions
3171
-
3172
- # Effect of the variant on the coding sequence.
3173
- # Corresponds to the JSON property `effect`
3174
- # @return [String]
3175
- attr_accessor :effect
3176
-
3177
- # Google annotation ID of the gene affected by this variant. This should be
3178
- # provided when the variant is created.
3179
- # Corresponds to the JSON property `geneId`
3180
- # @return [String]
3181
- attr_accessor :gene_id
3182
-
3183
- # Google annotation IDs of the transcripts affected by this variant. These
3184
- # should be provided when the variant is created.
3185
- # Corresponds to the JSON property `transcriptIds`
3186
- # @return [Array<String>]
3187
- attr_accessor :transcript_ids
3188
-
3189
- # Type has been adapted from ClinVar's list of variant types.
3190
- # Corresponds to the JSON property `type`
3191
- # @return [String]
3192
- attr_accessor :type
3193
-
3194
- def initialize(**args)
3195
- update!(**args)
3196
- end
3197
-
3198
- # Update properties of this object
3199
- def update!(**args)
3200
- @alternate_bases = args[:alternate_bases] unless args[:alternate_bases].nil?
3201
- @clinical_significance = args[:clinical_significance] unless args[:clinical_significance].nil?
3202
- @conditions = args[:conditions] unless args[:conditions].nil?
3203
- @effect = args[:effect] unless args[:effect].nil?
3204
- @gene_id = args[:gene_id] unless args[:gene_id].nil?
3205
- @transcript_ids = args[:transcript_ids] unless args[:transcript_ids].nil?
3206
- @type = args[:type] unless args[:type].nil?
3207
- end
3208
- end
3209
-
3210
- #
3211
- class VariantAnnotationCondition
3212
- include Google::Apis::Core::Hashable
3213
-
3214
- # The MedGen concept id associated with this gene. Search for these IDs at http:/
3215
- # /www.ncbi.nlm.nih.gov/medgen/
3216
- # Corresponds to the JSON property `conceptId`
3217
- # @return [String]
3218
- attr_accessor :concept_id
3219
-
3220
- # The set of external IDs for this condition.
3221
- # Corresponds to the JSON property `externalIds`
3222
- # @return [Array<Google::Apis::GenomicsV1beta2::ExternalId>]
3223
- attr_accessor :external_ids
3224
-
3225
- # A set of names for the condition.
3226
- # Corresponds to the JSON property `names`
3227
- # @return [Array<String>]
3228
- attr_accessor :names
3229
-
3230
- # The OMIM id for this condition. Search for these IDs at http://omim.org/
3231
- # Corresponds to the JSON property `omimId`
3232
- # @return [String]
3233
- attr_accessor :omim_id
3234
-
3235
- def initialize(**args)
3236
- update!(**args)
3237
- end
3238
-
3239
- # Update properties of this object
3240
- def update!(**args)
3241
- @concept_id = args[:concept_id] unless args[:concept_id].nil?
3242
- @external_ids = args[:external_ids] unless args[:external_ids].nil?
3243
- @names = args[:names] unless args[:names].nil?
3244
- @omim_id = args[:omim_id] unless args[:omim_id].nil?
3245
- end
3246
- end
3247
-
3248
- # A variant set is a collection of call sets and variants. It contains summary
3249
- # statistics of those contents. A variant set belongs to a dataset.
3250
- class VariantSet
3251
- include Google::Apis::Core::Hashable
3252
-
3253
- # The dataset to which this variant set belongs. Immutable.
3254
- # Corresponds to the JSON property `datasetId`
3255
- # @return [String]
3256
- attr_accessor :dataset_id
3257
-
3258
- # The Google-generated ID of the variant set. Immutable.
3259
- # Corresponds to the JSON property `id`
3260
- # @return [String]
3261
- attr_accessor :id
3262
-
3263
- # The metadata associated with this variant set.
3264
- # Corresponds to the JSON property `metadata`
3265
- # @return [Array<Google::Apis::GenomicsV1beta2::Metadata>]
3266
- attr_accessor :metadata
3267
-
3268
- # A list of all references used by the variants in a variant set with associated
3269
- # coordinate upper bounds for each one.
3270
- # Corresponds to the JSON property `referenceBounds`
3271
- # @return [Array<Google::Apis::GenomicsV1beta2::ReferenceBound>]
3272
- attr_accessor :reference_bounds
3273
-
3274
- def initialize(**args)
3275
- update!(**args)
3276
- end
3277
-
3278
- # Update properties of this object
3279
- def update!(**args)
3280
- @dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
3281
- @id = args[:id] unless args[:id].nil?
3282
- @metadata = args[:metadata] unless args[:metadata].nil?
3283
- @reference_bounds = args[:reference_bounds] unless args[:reference_bounds].nil?
3284
- end
3285
- end
3286
- end
3287
- end
3288
- end