google-api-client 0.10.1 → 0.10.2

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Files changed (176) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +3 -0
  3. data/api_names.yaml +395 -0
  4. data/generated/google/apis/adexchangebuyer2_v2beta1.rb +1 -1
  5. data/generated/google/apis/adexchangebuyer2_v2beta1/classes.rb +254 -254
  6. data/generated/google/apis/adexchangebuyer2_v2beta1/representations.rb +65 -65
  7. data/generated/google/apis/adexchangebuyer2_v2beta1/service.rb +220 -220
  8. data/generated/google/apis/admin_directory_v1.rb +1 -1
  9. data/generated/google/apis/admin_directory_v1/classes.rb +106 -0
  10. data/generated/google/apis/admin_directory_v1/representations.rb +37 -0
  11. data/generated/google/apis/admin_reports_v1.rb +3 -3
  12. data/generated/google/apis/admin_reports_v1/service.rb +6 -6
  13. data/generated/google/apis/adsense_v1_4.rb +1 -1
  14. data/generated/google/apis/adsensehost_v4_1.rb +1 -1
  15. data/generated/google/apis/analytics_v3.rb +1 -1
  16. data/generated/google/apis/analytics_v3/service.rb +39 -0
  17. data/generated/google/apis/analyticsreporting_v4/classes.rb +920 -920
  18. data/generated/google/apis/analyticsreporting_v4/representations.rb +197 -197
  19. data/generated/google/apis/analyticsreporting_v4/service.rb +4 -4
  20. data/generated/google/apis/androidenterprise_v1.rb +1 -1
  21. data/generated/google/apis/androidenterprise_v1/classes.rb +8 -13
  22. data/generated/google/apis/androidenterprise_v1/service.rb +3 -3
  23. data/generated/google/apis/appengine_v1beta5.rb +1 -1
  24. data/generated/google/apis/appengine_v1beta5/classes.rb +115 -5
  25. data/generated/google/apis/appengine_v1beta5/representations.rb +37 -0
  26. data/generated/google/apis/appengine_v1beta5/service.rb +12 -9
  27. data/generated/google/apis/appstate_v1.rb +1 -1
  28. data/generated/google/apis/bigquery_v2.rb +1 -1
  29. data/generated/google/apis/bigquery_v2/classes.rb +32 -37
  30. data/generated/google/apis/bigquery_v2/service.rb +10 -2
  31. data/generated/google/apis/calendar_v3.rb +1 -1
  32. data/generated/google/apis/calendar_v3/classes.rb +205 -0
  33. data/generated/google/apis/calendar_v3/representations.rb +97 -0
  34. data/generated/google/apis/classroom_v1.rb +22 -25
  35. data/generated/google/apis/classroom_v1/classes.rb +998 -907
  36. data/generated/google/apis/classroom_v1/representations.rb +240 -240
  37. data/generated/google/apis/classroom_v1/service.rb +1269 -1061
  38. data/generated/google/apis/cloudbuild_v1.rb +1 -1
  39. data/generated/google/apis/cloudbuild_v1/classes.rb +164 -163
  40. data/generated/google/apis/cloudbuild_v1/representations.rb +31 -31
  41. data/generated/google/apis/cloudbuild_v1/service.rb +114 -114
  42. data/generated/google/apis/clouddebugger_v2.rb +1 -1
  43. data/generated/google/apis/clouddebugger_v2/classes.rb +687 -687
  44. data/generated/google/apis/clouddebugger_v2/representations.rb +147 -147
  45. data/generated/google/apis/clouddebugger_v2/service.rb +132 -132
  46. data/generated/google/apis/cloudkms_v1.rb +1 -1
  47. data/generated/google/apis/cloudkms_v1/classes.rb +231 -248
  48. data/generated/google/apis/cloudkms_v1/representations.rb +74 -74
  49. data/generated/google/apis/cloudkms_v1/service.rb +228 -228
  50. data/generated/google/apis/cloudmonitoring_v2beta2.rb +1 -1
  51. data/generated/google/apis/cloudresourcemanager_v1.rb +1 -1
  52. data/generated/google/apis/cloudresourcemanager_v1/classes.rb +738 -128
  53. data/generated/google/apis/cloudresourcemanager_v1/representations.rb +245 -23
  54. data/generated/google/apis/cloudresourcemanager_v1/service.rb +1293 -249
  55. data/generated/google/apis/cloudresourcemanager_v1beta1.rb +4 -4
  56. data/generated/google/apis/cloudresourcemanager_v1beta1/classes.rb +982 -372
  57. data/generated/google/apis/cloudresourcemanager_v1beta1/representations.rb +293 -71
  58. data/generated/google/apis/cloudresourcemanager_v1beta1/service.rb +626 -277
  59. data/generated/google/apis/cloudtrace_v1.rb +1 -1
  60. data/generated/google/apis/cloudtrace_v1/classes.rb +19 -19
  61. data/generated/google/apis/cloudtrace_v1/representations.rb +2 -2
  62. data/generated/google/apis/cloudtrace_v1/service.rb +30 -30
  63. data/generated/google/apis/compute_beta.rb +1 -1
  64. data/generated/google/apis/compute_beta/classes.rb +116 -0
  65. data/generated/google/apis/compute_beta/representations.rb +48 -0
  66. data/generated/google/apis/compute_beta/service.rb +46 -1
  67. data/generated/google/apis/compute_v1.rb +1 -1
  68. data/generated/google/apis/dataflow_v1b3.rb +1 -1
  69. data/generated/google/apis/dataflow_v1b3/classes.rb +3276 -3320
  70. data/generated/google/apis/dataflow_v1b3/representations.rb +779 -781
  71. data/generated/google/apis/dataflow_v1b3/service.rb +225 -225
  72. data/generated/google/apis/dataproc_v1.rb +1 -1
  73. data/generated/google/apis/dataproc_v1/classes.rb +1221 -1207
  74. data/generated/google/apis/dataproc_v1/representations.rb +255 -253
  75. data/generated/google/apis/dataproc_v1/service.rb +100 -100
  76. data/generated/google/apis/deploymentmanager_v2.rb +1 -1
  77. data/generated/google/apis/deploymentmanager_v2/classes.rb +5 -5
  78. data/generated/google/apis/dns_v1.rb +1 -1
  79. data/generated/google/apis/dns_v2beta1.rb +1 -1
  80. data/generated/google/apis/doubleclicksearch_v2.rb +1 -1
  81. data/generated/google/apis/drive_v2.rb +1 -1
  82. data/generated/google/apis/drive_v2/classes.rb +3 -1
  83. data/generated/google/apis/drive_v3.rb +1 -1
  84. data/generated/google/apis/drive_v3/classes.rb +3 -1
  85. data/generated/google/apis/fusiontables_v2.rb +1 -1
  86. data/generated/google/apis/games_configuration_v1configuration.rb +1 -1
  87. data/generated/google/apis/games_management_v1management.rb +1 -1
  88. data/generated/google/apis/games_v1.rb +1 -1
  89. data/generated/google/apis/genomics_v1.rb +7 -7
  90. data/generated/google/apis/genomics_v1/classes.rb +959 -959
  91. data/generated/google/apis/genomics_v1/representations.rb +238 -238
  92. data/generated/google/apis/genomics_v1/service.rb +996 -996
  93. data/generated/google/apis/iam_v1.rb +1 -1
  94. data/generated/google/apis/iam_v1/classes.rb +440 -440
  95. data/generated/google/apis/iam_v1/representations.rb +94 -94
  96. data/generated/google/apis/iam_v1/service.rb +170 -173
  97. data/generated/google/apis/identitytoolkit_v3.rb +1 -1
  98. data/generated/google/apis/identitytoolkit_v3/classes.rb +55 -0
  99. data/generated/google/apis/identitytoolkit_v3/representations.rb +8 -0
  100. data/generated/google/apis/kgsearch_v1/service.rb +4 -4
  101. data/generated/google/apis/language_v1beta1.rb +1 -1
  102. data/generated/google/apis/language_v1beta1/classes.rb +427 -427
  103. data/generated/google/apis/language_v1beta1/representations.rb +113 -113
  104. data/generated/google/apis/language_v1beta1/service.rb +25 -24
  105. data/generated/google/apis/licensing_v1.rb +2 -2
  106. data/generated/google/apis/licensing_v1/classes.rb +14 -2
  107. data/generated/google/apis/licensing_v1/representations.rb +2 -0
  108. data/generated/google/apis/licensing_v1/service.rb +1 -1
  109. data/generated/google/apis/logging_v2beta1.rb +1 -1
  110. data/generated/google/apis/logging_v2beta1/classes.rb +864 -864
  111. data/generated/google/apis/logging_v2beta1/representations.rb +168 -168
  112. data/generated/google/apis/logging_v2beta1/service.rb +261 -261
  113. data/generated/google/apis/manufacturers_v1.rb +1 -1
  114. data/generated/google/apis/manufacturers_v1/classes.rb +452 -105
  115. data/generated/google/apis/manufacturers_v1/representations.rb +138 -18
  116. data/generated/google/apis/manufacturers_v1/service.rb +11 -11
  117. data/generated/google/apis/mirror_v1.rb +1 -1
  118. data/generated/google/apis/monitoring_v3.rb +7 -7
  119. data/generated/google/apis/monitoring_v3/classes.rb +668 -670
  120. data/generated/google/apis/monitoring_v3/representations.rb +140 -140
  121. data/generated/google/apis/monitoring_v3/service.rb +208 -208
  122. data/generated/google/apis/partners_v2.rb +1 -1
  123. data/generated/google/apis/partners_v2/classes.rb +505 -505
  124. data/generated/google/apis/partners_v2/representations.rb +118 -118
  125. data/generated/google/apis/partners_v2/service.rb +275 -275
  126. data/generated/google/apis/people_v1.rb +1 -1
  127. data/generated/google/apis/people_v1/classes.rb +1037 -1031
  128. data/generated/google/apis/people_v1/representations.rb +247 -246
  129. data/generated/google/apis/people_v1/service.rb +20 -20
  130. data/generated/google/apis/plus_domains_v1.rb +1 -1
  131. data/generated/google/apis/plus_v1.rb +1 -1
  132. data/generated/google/apis/proximitybeacon_v1beta1.rb +1 -1
  133. data/generated/google/apis/proximitybeacon_v1beta1/classes.rb +392 -392
  134. data/generated/google/apis/proximitybeacon_v1beta1/representations.rb +93 -93
  135. data/generated/google/apis/proximitybeacon_v1beta1/service.rb +381 -381
  136. data/generated/google/apis/pubsub_v1.rb +4 -4
  137. data/generated/google/apis/pubsub_v1/classes.rb +131 -132
  138. data/generated/google/apis/pubsub_v1/representations.rb +35 -35
  139. data/generated/google/apis/pubsub_v1/service.rb +399 -408
  140. data/generated/google/apis/reseller_v1.rb +1 -1
  141. data/generated/google/apis/reseller_v1/classes.rb +9 -0
  142. data/generated/google/apis/reseller_v1/representations.rb +1 -0
  143. data/generated/google/apis/script_v1.rb +9 -9
  144. data/generated/google/apis/script_v1/classes.rb +110 -110
  145. data/generated/google/apis/script_v1/representations.rb +26 -26
  146. data/generated/google/apis/sheets_v4.rb +4 -4
  147. data/generated/google/apis/sheets_v4/classes.rb +4329 -4329
  148. data/generated/google/apis/sheets_v4/representations.rb +856 -856
  149. data/generated/google/apis/sheets_v4/service.rb +106 -106
  150. data/generated/google/apis/slides_v1.rb +4 -4
  151. data/generated/google/apis/slides_v1/classes.rb +2923 -2841
  152. data/generated/google/apis/slides_v1/representations.rb +722 -691
  153. data/generated/google/apis/slides_v1/service.rb +58 -15
  154. data/generated/google/apis/speech_v1beta1.rb +1 -1
  155. data/generated/google/apis/speech_v1beta1/classes.rb +191 -191
  156. data/generated/google/apis/speech_v1beta1/representations.rb +57 -57
  157. data/generated/google/apis/speech_v1beta1/service.rb +70 -70
  158. data/generated/google/apis/storage_v1.rb +1 -1
  159. data/generated/google/apis/storage_v1/classes.rb +151 -0
  160. data/generated/google/apis/storage_v1/representations.rb +45 -0
  161. data/generated/google/apis/storage_v1/service.rb +248 -0
  162. data/generated/google/apis/vision_v1.rb +1 -1
  163. data/generated/google/apis/vision_v1/classes.rb +1227 -1221
  164. data/generated/google/apis/vision_v1/representations.rb +217 -215
  165. data/generated/google/apis/webmasters_v3.rb +1 -1
  166. data/generated/google/apis/youtube_analytics_v1.rb +1 -1
  167. data/generated/google/apis/youtube_partner_v1.rb +1 -1
  168. data/generated/google/apis/youtube_partner_v1/classes.rb +78 -0
  169. data/generated/google/apis/youtube_partner_v1/representations.rb +34 -0
  170. data/generated/google/apis/youtube_partner_v1/service.rb +40 -0
  171. data/generated/google/apis/youtubereporting_v1.rb +4 -4
  172. data/generated/google/apis/youtubereporting_v1/classes.rb +65 -65
  173. data/generated/google/apis/youtubereporting_v1/representations.rb +18 -18
  174. data/generated/google/apis/youtubereporting_v1/service.rb +111 -111
  175. data/lib/google/apis/version.rb +1 -1
  176. metadata +2 -2
@@ -25,7 +25,7 @@ module Google
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  # @see https://developers.google.com/cloud-dns
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  module DnsV1
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  VERSION = 'V1'
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- REVISION = '20170221'
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+ REVISION = '20170322'
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29
 
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  # View and manage your data across Google Cloud Platform services
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  AUTH_CLOUD_PLATFORM = 'https://www.googleapis.com/auth/cloud-platform'
@@ -25,7 +25,7 @@ module Google
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  # @see https://developers.google.com/cloud-dns
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  module DnsV2beta1
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  VERSION = 'V2beta1'
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- REVISION = '20170221'
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+ REVISION = '20170322'
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29
 
30
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  # View and manage your data across Google Cloud Platform services
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  AUTH_CLOUD_PLATFORM = 'https://www.googleapis.com/auth/cloud-platform'
@@ -26,7 +26,7 @@ module Google
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  # @see https://developers.google.com/doubleclick-search/
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  module DoubleclicksearchV2
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  VERSION = 'V2'
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- REVISION = '20170228'
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+ REVISION = '20170314'
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  # View and manage your advertising data in DoubleClick Search
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  AUTH_DOUBLECLICKSEARCH = 'https://www.googleapis.com/auth/doubleclicksearch'
@@ -26,7 +26,7 @@ module Google
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  # @see https://developers.google.com/drive/
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  module DriveV2
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  VERSION = 'V2'
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- REVISION = '20170228'
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+ REVISION = '20170320'
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  # View and manage the files in your Google Drive
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  AUTH_DRIVE = 'https://www.googleapis.com/auth/drive'
@@ -1571,7 +1571,9 @@ module Google
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  # @return [String]
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  attr_accessor :thumbnail_version
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- # The title of this file.
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+ # The title of this file. Note that for immutable items such as the top level
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+ # folders of Team Drives, My Drive root folder, and Application Data folder the
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+ # title is constant.
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  # Corresponds to the JSON property `title`
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  # @return [String]
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  attr_accessor :title
@@ -26,7 +26,7 @@ module Google
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  # @see https://developers.google.com/drive/
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  module DriveV3
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  VERSION = 'V3'
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- REVISION = '20170228'
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+ REVISION = '20170320'
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  # View and manage the files in your Google Drive
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  AUTH_DRIVE = 'https://www.googleapis.com/auth/drive'
@@ -618,7 +618,9 @@ module Google
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  # @return [DateTime]
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  attr_accessor :modified_time
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- # The name of the file. This is not necessarily unique within a folder.
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+ # The name of the file. This is not necessarily unique within a folder. Note
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+ # that for immutable items such as the top level folders of Team Drives, My
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+ # Drive root folder, and Application Data folder the name is constant.
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  # Corresponds to the JSON property `name`
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  # @return [String]
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  attr_accessor :name
@@ -25,7 +25,7 @@ module Google
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  # @see https://developers.google.com/fusiontables
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  module FusiontablesV2
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  VERSION = 'V2'
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- REVISION = '20160526'
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+ REVISION = '20170321'
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  # Manage your Fusion Tables
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  AUTH_FUSIONTABLES = 'https://www.googleapis.com/auth/fusiontables'
@@ -25,7 +25,7 @@ module Google
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  # @see https://developers.google.com/games/services
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  module GamesConfigurationV1configuration
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  VERSION = 'V1configuration'
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- REVISION = '20170302'
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+ REVISION = '20170323'
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  # View and manage your Google Play Developer account
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  AUTH_ANDROIDPUBLISHER = 'https://www.googleapis.com/auth/androidpublisher'
@@ -25,7 +25,7 @@ module Google
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  # @see https://developers.google.com/games/services
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  module GamesManagementV1management
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  VERSION = 'V1management'
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- REVISION = '20170302'
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+ REVISION = '20170323'
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  # Share your Google+ profile information and view and manage your game activity
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  AUTH_GAMES = 'https://www.googleapis.com/auth/games'
@@ -25,7 +25,7 @@ module Google
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  # @see https://developers.google.com/games/services/
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  module GamesV1
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  VERSION = 'V1'
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- REVISION = '20170302'
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+ REVISION = '20170323'
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  # View and manage its own configuration data in your Google Drive
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  AUTH_DRIVE_APPDATA = 'https://www.googleapis.com/auth/drive.appdata'
@@ -25,7 +25,13 @@ module Google
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  # @see https://cloud.google.com/genomics
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  module GenomicsV1
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  VERSION = 'V1'
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- REVISION = '20170309'
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+ REVISION = '20170322'
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+
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+ # View and manage your data across Google Cloud Platform services
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+ AUTH_CLOUD_PLATFORM = 'https://www.googleapis.com/auth/cloud-platform'
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+
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+ # View Genomics data
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+ AUTH_GENOMICS_READONLY = 'https://www.googleapis.com/auth/genomics.readonly'
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  # View and manage Genomics data
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  AUTH_GENOMICS = 'https://www.googleapis.com/auth/genomics'
@@ -35,12 +41,6 @@ module Google
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  # Manage your data in Google Cloud Storage
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  AUTH_DEVSTORAGE_READ_WRITE = 'https://www.googleapis.com/auth/devstorage.read_write'
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-
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- # View and manage your data across Google Cloud Platform services
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- AUTH_CLOUD_PLATFORM = 'https://www.googleapis.com/auth/cloud-platform'
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-
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- # View Genomics data
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- AUTH_GENOMICS_READONLY = 'https://www.googleapis.com/auth/genomics.readonly'
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  end
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  end
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  end
@@ -22,238 +22,6 @@ module Google
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  module Apis
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  module GenomicsV1
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- # Response message for `TestIamPermissions` method.
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- class TestIamPermissionsResponse
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- include Google::Apis::Core::Hashable
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-
29
- # A subset of `TestPermissionsRequest.permissions` that the caller is
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- # allowed.
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- # Corresponds to the JSON property `permissions`
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- # @return [Array<String>]
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- attr_accessor :permissions
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-
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- def initialize(**args)
36
- update!(**args)
37
- end
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-
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- # Update properties of this object
40
- def update!(**args)
41
- @permissions = args[:permissions] if args.key?(:permissions)
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- end
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- end
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-
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- # Request message for `GetIamPolicy` method.
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- class GetIamPolicyRequest
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- include Google::Apis::Core::Hashable
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-
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- def initialize(**args)
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- update!(**args)
51
- end
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-
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- # Update properties of this object
54
- def update!(**args)
55
- end
56
- end
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-
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- #
59
- class SearchReferencesResponse
60
- include Google::Apis::Core::Hashable
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-
62
- # The matching references.
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- # Corresponds to the JSON property `references`
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- # @return [Array<Google::Apis::GenomicsV1::Reference>]
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- attr_accessor :references
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-
67
- # The continuation token, which is used to page through large result sets.
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- # Provide this value in a subsequent request to return the next page of
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- # results. This field will be empty if there aren't any additional results.
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- # Corresponds to the JSON property `nextPageToken`
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- # @return [String]
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- attr_accessor :next_page_token
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-
74
- def initialize(**args)
75
- update!(**args)
76
- end
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-
78
- # Update properties of this object
79
- def update!(**args)
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- @references = args[:references] if args.key?(:references)
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- @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
82
- end
83
- end
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-
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- #
86
- class SearchAnnotationSetsRequest
87
- include Google::Apis::Core::Hashable
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-
89
- # Only return annotations sets for which a substring of the name matches this
90
- # string (case insensitive).
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- # Corresponds to the JSON property `name`
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- # @return [String]
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- attr_accessor :name
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-
95
- # If specified, only annotation sets associated with the given reference set
96
- # are returned.
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- # Corresponds to the JSON property `referenceSetId`
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- # @return [String]
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- attr_accessor :reference_set_id
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-
101
- # The continuation token, which is used to page through large result sets.
102
- # To get the next page of results, set this parameter to the value of
103
- # `nextPageToken` from the previous response.
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- # Corresponds to the JSON property `pageToken`
105
- # @return [String]
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- attr_accessor :page_token
107
-
108
- # The maximum number of results to return in a single page. If unspecified,
109
- # defaults to 128. The maximum value is 1024.
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- # Corresponds to the JSON property `pageSize`
111
- # @return [Fixnum]
112
- attr_accessor :page_size
113
-
114
- # Required. The dataset IDs to search within. Caller must have `READ` access
115
- # to these datasets.
116
- # Corresponds to the JSON property `datasetIds`
117
- # @return [Array<String>]
118
- attr_accessor :dataset_ids
119
-
120
- # If specified, only annotation sets that have any of these types are
121
- # returned.
122
- # Corresponds to the JSON property `types`
123
- # @return [Array<String>]
124
- attr_accessor :types
125
-
126
- def initialize(**args)
127
- update!(**args)
128
- end
129
-
130
- # Update properties of this object
131
- def update!(**args)
132
- @name = args[:name] if args.key?(:name)
133
- @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
134
- @page_token = args[:page_token] if args.key?(:page_token)
135
- @page_size = args[:page_size] if args.key?(:page_size)
136
- @dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
137
- @types = args[:types] if args.key?(:types)
138
- end
139
- end
140
-
141
- # The read group set search response.
142
- class SearchReadGroupSetsResponse
143
- include Google::Apis::Core::Hashable
144
-
145
- # The list of matching read group sets.
146
- # Corresponds to the JSON property `readGroupSets`
147
- # @return [Array<Google::Apis::GenomicsV1::ReadGroupSet>]
148
- attr_accessor :read_group_sets
149
-
150
- # The continuation token, which is used to page through large result sets.
151
- # Provide this value in a subsequent request to return the next page of
152
- # results. This field will be empty if there aren't any additional results.
153
- # Corresponds to the JSON property `nextPageToken`
154
- # @return [String]
155
- attr_accessor :next_page_token
156
-
157
- def initialize(**args)
158
- update!(**args)
159
- end
160
-
161
- # Update properties of this object
162
- def update!(**args)
163
- @read_group_sets = args[:read_group_sets] if args.key?(:read_group_sets)
164
- @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
165
- end
166
- end
167
-
168
- #
169
- class SearchReferencesRequest
170
- include Google::Apis::Core::Hashable
171
-
172
- # If present, return references for which the
173
- # md5checksum matches exactly.
174
- # Corresponds to the JSON property `md5checksums`
175
- # @return [Array<String>]
176
- attr_accessor :md5checksums
177
-
178
- # If present, return references for which a prefix of any of
179
- # sourceAccessions match
180
- # any of these strings. Accession numbers typically have a main number and a
181
- # version, for example `GCF_000001405.26`.
182
- # Corresponds to the JSON property `accessions`
183
- # @return [Array<String>]
184
- attr_accessor :accessions
185
-
186
- # The continuation token, which is used to page through large result sets.
187
- # To get the next page of results, set this parameter to the value of
188
- # `nextPageToken` from the previous response.
189
- # Corresponds to the JSON property `pageToken`
190
- # @return [String]
191
- attr_accessor :page_token
192
-
193
- # If present, return only references which belong to this reference set.
194
- # Corresponds to the JSON property `referenceSetId`
195
- # @return [String]
196
- attr_accessor :reference_set_id
197
-
198
- # The maximum number of results to return in a single page. If unspecified,
199
- # defaults to 1024. The maximum value is 4096.
200
- # Corresponds to the JSON property `pageSize`
201
- # @return [Fixnum]
202
- attr_accessor :page_size
203
-
204
- def initialize(**args)
205
- update!(**args)
206
- end
207
-
208
- # Update properties of this object
209
- def update!(**args)
210
- @md5checksums = args[:md5checksums] if args.key?(:md5checksums)
211
- @accessions = args[:accessions] if args.key?(:accessions)
212
- @page_token = args[:page_token] if args.key?(:page_token)
213
- @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
214
- @page_size = args[:page_size] if args.key?(:page_size)
215
- end
216
- end
217
-
218
- # A linear alignment can be represented by one CIGAR string. Describes the
219
- # mapped position and local alignment of the read to the reference.
220
- class LinearAlignment
221
- include Google::Apis::Core::Hashable
222
-
223
- # An abstraction for referring to a genomic position, in relation to some
224
- # already known reference. For now, represents a genomic position as a
225
- # reference name, a base number on that reference (0-based), and a
226
- # determination of forward or reverse strand.
227
- # Corresponds to the JSON property `position`
228
- # @return [Google::Apis::GenomicsV1::Position]
229
- attr_accessor :position
230
-
231
- # Represents the local alignment of this sequence (alignment matches, indels,
232
- # etc) against the reference.
233
- # Corresponds to the JSON property `cigar`
234
- # @return [Array<Google::Apis::GenomicsV1::CigarUnit>]
235
- attr_accessor :cigar
236
-
237
- # The mapping quality of this alignment. Represents how likely
238
- # the read maps to this position as opposed to other locations.
239
- # Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
240
- # the nearest integer.
241
- # Corresponds to the JSON property `mappingQuality`
242
- # @return [Fixnum]
243
- attr_accessor :mapping_quality
244
-
245
- def initialize(**args)
246
- update!(**args)
247
- end
248
-
249
- # Update properties of this object
250
- def update!(**args)
251
- @position = args[:position] if args.key?(:position)
252
- @cigar = args[:cigar] if args.key?(:cigar)
253
- @mapping_quality = args[:mapping_quality] if args.key?(:mapping_quality)
254
- end
255
- end
256
-
257
25
  # A Dataset is a collection of genomic data.
258
26
  # For more genomics resource definitions, see [Fundamentals of Google
259
27
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
@@ -339,12 +107,6 @@ module Google
339
107
  # @return [String]
340
108
  attr_accessor :id
341
109
 
342
- # The predicted insert size of this read group. The insert size is the length
343
- # the sequenced DNA fragment from end-to-end, not including the adapters.
344
- # Corresponds to the JSON property `predictedInsertSize`
345
- # @return [Fixnum]
346
- attr_accessor :predicted_insert_size
347
-
348
110
  # The programs used to generate this read group. Programs are always
349
111
  # identical for all read groups within a read group set. For this reason,
350
112
  # only the first read group in a returned set will have this field
@@ -353,6 +115,12 @@ module Google
353
115
  # @return [Array<Google::Apis::GenomicsV1::Program>]
354
116
  attr_accessor :programs
355
117
 
118
+ # The predicted insert size of this read group. The insert size is the length
119
+ # the sequenced DNA fragment from end-to-end, not including the adapters.
120
+ # Corresponds to the JSON property `predictedInsertSize`
121
+ # @return [Fixnum]
122
+ attr_accessor :predicted_insert_size
123
+
356
124
  # A free-form text description of this read group.
357
125
  # Corresponds to the JSON property `description`
358
126
  # @return [String]
@@ -383,8 +151,8 @@ module Google
383
151
  @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
384
152
  @info = args[:info] if args.key?(:info)
385
153
  @id = args[:id] if args.key?(:id)
386
- @predicted_insert_size = args[:predicted_insert_size] if args.key?(:predicted_insert_size)
387
154
  @programs = args[:programs] if args.key?(:programs)
155
+ @predicted_insert_size = args[:predicted_insert_size] if args.key?(:predicted_insert_size)
388
156
  @description = args[:description] if args.key?(:description)
389
157
  @sample_id = args[:sample_id] if args.key?(:sample_id)
390
158
  @dataset_id = args[:dataset_id] if args.key?(:dataset_id)
@@ -404,27 +172,17 @@ module Google
404
172
  class ReadGroupSet
405
173
  include Google::Apis::Core::Hashable
406
174
 
407
- # The server-generated read group set ID, unique for all read group sets.
408
- # Corresponds to the JSON property `id`
409
- # @return [String]
410
- attr_accessor :id
411
-
412
- # The dataset to which this read group set belongs.
413
- # Corresponds to the JSON property `datasetId`
414
- # @return [String]
415
- attr_accessor :dataset_id
175
+ # The read groups in this set. There are typically 1-10 read groups in a read
176
+ # group set.
177
+ # Corresponds to the JSON property `readGroups`
178
+ # @return [Array<Google::Apis::GenomicsV1::ReadGroup>]
179
+ attr_accessor :read_groups
416
180
 
417
181
  # The filename of the original source file for this read group set, if any.
418
182
  # Corresponds to the JSON property `filename`
419
183
  # @return [String]
420
184
  attr_accessor :filename
421
185
 
422
- # The read groups in this set. There are typically 1-10 read groups in a read
423
- # group set.
424
- # Corresponds to the JSON property `readGroups`
425
- # @return [Array<Google::Apis::GenomicsV1::ReadGroup>]
426
- attr_accessor :read_groups
427
-
428
186
  # The read group set name. By default this will be initialized to the sample
429
187
  # name of the sequenced data contained in this set.
430
188
  # Corresponds to the JSON property `name`
@@ -441,19 +199,29 @@ module Google
441
199
  # @return [Hash<String,Array<Object>>]
442
200
  attr_accessor :info
443
201
 
202
+ # The server-generated read group set ID, unique for all read group sets.
203
+ # Corresponds to the JSON property `id`
204
+ # @return [String]
205
+ attr_accessor :id
206
+
207
+ # The dataset to which this read group set belongs.
208
+ # Corresponds to the JSON property `datasetId`
209
+ # @return [String]
210
+ attr_accessor :dataset_id
211
+
444
212
  def initialize(**args)
445
213
  update!(**args)
446
214
  end
447
215
 
448
216
  # Update properties of this object
449
217
  def update!(**args)
450
- @id = args[:id] if args.key?(:id)
451
- @dataset_id = args[:dataset_id] if args.key?(:dataset_id)
452
- @filename = args[:filename] if args.key?(:filename)
453
218
  @read_groups = args[:read_groups] if args.key?(:read_groups)
219
+ @filename = args[:filename] if args.key?(:filename)
454
220
  @name = args[:name] if args.key?(:name)
455
221
  @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
456
222
  @info = args[:info] if args.key?(:info)
223
+ @id = args[:id] if args.key?(:id)
224
+ @dataset_id = args[:dataset_id] if args.key?(:dataset_id)
457
225
  end
458
226
  end
459
227
 
@@ -461,11 +229,6 @@ module Google
461
229
  class SearchVariantSetsResponse
462
230
  include Google::Apis::Core::Hashable
463
231
 
464
- # The variant sets belonging to the requested dataset.
465
- # Corresponds to the JSON property `variantSets`
466
- # @return [Array<Google::Apis::GenomicsV1::VariantSet>]
467
- attr_accessor :variant_sets
468
-
469
232
  # The continuation token, which is used to page through large result sets.
470
233
  # Provide this value in a subsequent request to return the next page of
471
234
  # results. This field will be empty if there aren't any additional results.
@@ -473,14 +236,19 @@ module Google
473
236
  # @return [String]
474
237
  attr_accessor :next_page_token
475
238
 
239
+ # The variant sets belonging to the requested dataset.
240
+ # Corresponds to the JSON property `variantSets`
241
+ # @return [Array<Google::Apis::GenomicsV1::VariantSet>]
242
+ attr_accessor :variant_sets
243
+
476
244
  def initialize(**args)
477
245
  update!(**args)
478
246
  end
479
247
 
480
248
  # Update properties of this object
481
249
  def update!(**args)
482
- @variant_sets = args[:variant_sets] if args.key?(:variant_sets)
483
250
  @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
251
+ @variant_sets = args[:variant_sets] if args.key?(:variant_sets)
484
252
  end
485
253
  end
486
254
 
@@ -578,13 +346,6 @@ module Google
578
346
  class Position
579
347
  include Google::Apis::Core::Hashable
580
348
 
581
- # Whether this position is on the reverse strand, as opposed to the forward
582
- # strand.
583
- # Corresponds to the JSON property `reverseStrand`
584
- # @return [Boolean]
585
- attr_accessor :reverse_strand
586
- alias_method :reverse_strand?, :reverse_strand
587
-
588
349
  # The 0-based offset from the start of the forward strand for that reference.
589
350
  # Corresponds to the JSON property `position`
590
351
  # @return [String]
@@ -595,15 +356,22 @@ module Google
595
356
  # @return [String]
596
357
  attr_accessor :reference_name
597
358
 
359
+ # Whether this position is on the reverse strand, as opposed to the forward
360
+ # strand.
361
+ # Corresponds to the JSON property `reverseStrand`
362
+ # @return [Boolean]
363
+ attr_accessor :reverse_strand
364
+ alias_method :reverse_strand?, :reverse_strand
365
+
598
366
  def initialize(**args)
599
367
  update!(**args)
600
368
  end
601
369
 
602
370
  # Update properties of this object
603
371
  def update!(**args)
604
- @reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
605
372
  @position = args[:position] if args.key?(:position)
606
373
  @reference_name = args[:reference_name] if args.key?(:reference_name)
374
+ @reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
607
375
  end
608
376
  end
609
377
 
@@ -638,6 +406,12 @@ module Google
638
406
  class SearchCallSetsRequest
639
407
  include Google::Apis::Core::Hashable
640
408
 
409
+ # Restrict the query to call sets within the given variant sets. At least one
410
+ # ID must be provided.
411
+ # Corresponds to the JSON property `variantSetIds`
412
+ # @return [Array<String>]
413
+ attr_accessor :variant_set_ids
414
+
641
415
  # Only return call sets for which a substring of the name matches this
642
416
  # string.
643
417
  # Corresponds to the JSON property `name`
@@ -657,22 +431,16 @@ module Google
657
431
  # @return [Fixnum]
658
432
  attr_accessor :page_size
659
433
 
660
- # Restrict the query to call sets within the given variant sets. At least one
661
- # ID must be provided.
662
- # Corresponds to the JSON property `variantSetIds`
663
- # @return [Array<String>]
664
- attr_accessor :variant_set_ids
665
-
666
434
  def initialize(**args)
667
435
  update!(**args)
668
436
  end
669
437
 
670
438
  # Update properties of this object
671
439
  def update!(**args)
440
+ @variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
672
441
  @name = args[:name] if args.key?(:name)
673
442
  @page_token = args[:page_token] if args.key?(:page_token)
674
443
  @page_size = args[:page_size] if args.key?(:page_size)
675
- @variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
676
444
  end
677
445
  end
678
446
 
@@ -796,14 +564,6 @@ module Google
796
564
  class SearchReadsRequest
797
565
  include Google::Apis::Core::Hashable
798
566
 
799
- # The IDs of the read groups sets within which to search for reads. All
800
- # specified read group sets must be aligned against a common set of reference
801
- # sequences; this defines the genomic coordinates for the query. Must specify
802
- # one of `readGroupSetIds` or `readGroupIds`.
803
- # Corresponds to the JSON property `readGroupSetIds`
804
- # @return [Array<String>]
805
- attr_accessor :read_group_set_ids
806
-
807
567
  # The IDs of the read groups within which to search for reads. All specified
808
568
  # read groups must belong to the same read group sets. Must specify one of
809
569
  # `readGroupSetIds` or `readGroupIds`.
@@ -843,19 +603,40 @@ module Google
843
603
  # @return [String]
844
604
  attr_accessor :reference_name
845
605
 
606
+ # The IDs of the read groups sets within which to search for reads. All
607
+ # specified read group sets must be aligned against a common set of reference
608
+ # sequences; this defines the genomic coordinates for the query. Must specify
609
+ # one of `readGroupSetIds` or `readGroupIds`.
610
+ # Corresponds to the JSON property `readGroupSetIds`
611
+ # @return [Array<String>]
612
+ attr_accessor :read_group_set_ids
613
+
846
614
  def initialize(**args)
847
615
  update!(**args)
848
616
  end
849
617
 
850
618
  # Update properties of this object
851
619
  def update!(**args)
852
- @read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids)
853
620
  @read_group_ids = args[:read_group_ids] if args.key?(:read_group_ids)
854
621
  @end = args[:end] if args.key?(:end)
855
622
  @page_token = args[:page_token] if args.key?(:page_token)
856
623
  @page_size = args[:page_size] if args.key?(:page_size)
857
624
  @start = args[:start] if args.key?(:start)
858
625
  @reference_name = args[:reference_name] if args.key?(:reference_name)
626
+ @read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids)
627
+ end
628
+ end
629
+
630
+ # The request message for Operations.CancelOperation.
631
+ class CancelOperationRequest
632
+ include Google::Apis::Core::Hashable
633
+
634
+ def initialize(**args)
635
+ update!(**args)
636
+ end
637
+
638
+ # Update properties of this object
639
+ def update!(**args)
859
640
  end
860
641
  end
861
642
 
@@ -868,24 +649,32 @@ module Google
868
649
  class Annotation
869
650
  include Google::Apis::Core::Hashable
870
651
 
652
+ # Whether this range refers to the reverse strand, as opposed to the forward
653
+ # strand. Note that regardless of this field, the start/end position of the
654
+ # range always refer to the forward strand.
655
+ # Corresponds to the JSON property `reverseStrand`
656
+ # @return [Boolean]
657
+ attr_accessor :reverse_strand
658
+ alias_method :reverse_strand?, :reverse_strand
659
+
871
660
  # The display name corresponding to the reference specified by
872
661
  # `referenceId`, for example `chr1`, `1`, or `chrX`.
873
662
  # Corresponds to the JSON property `referenceName`
874
663
  # @return [String]
875
664
  attr_accessor :reference_name
876
665
 
877
- # The data type for this annotation. Must match the containing annotation
878
- # set's type.
879
- # Corresponds to the JSON property `type`
880
- # @return [String]
881
- attr_accessor :type
882
-
883
666
  # A map of additional read alignment information. This must be of the form
884
667
  # map<string, string[]> (string key mapping to a list of string values).
885
668
  # Corresponds to the JSON property `info`
886
669
  # @return [Hash<String,Array<Object>>]
887
670
  attr_accessor :info
888
671
 
672
+ # The data type for this annotation. Must match the containing annotation
673
+ # set's type.
674
+ # Corresponds to the JSON property `type`
675
+ # @return [String]
676
+ attr_accessor :type
677
+
889
678
  # The end position of the range on the reference, 0-based exclusive.
890
679
  # Corresponds to the JSON property `end`
891
680
  # @return [String]
@@ -920,23 +709,15 @@ module Google
920
709
  # @return [Google::Apis::GenomicsV1::VariantAnnotation]
921
710
  attr_accessor :variant
922
711
 
923
- # The server-generated annotation ID, unique across all annotations.
924
- # Corresponds to the JSON property `id`
925
- # @return [String]
926
- attr_accessor :id
927
-
928
712
  # The ID of the Google Genomics reference associated with this range.
929
713
  # Corresponds to the JSON property `referenceId`
930
714
  # @return [String]
931
715
  attr_accessor :reference_id
932
716
 
933
- # Whether this range refers to the reverse strand, as opposed to the forward
934
- # strand. Note that regardless of this field, the start/end position of the
935
- # range always refer to the forward strand.
936
- # Corresponds to the JSON property `reverseStrand`
937
- # @return [Boolean]
938
- attr_accessor :reverse_strand
939
- alias_method :reverse_strand?, :reverse_strand
717
+ # The server-generated annotation ID, unique across all annotations.
718
+ # Corresponds to the JSON property `id`
719
+ # @return [String]
720
+ attr_accessor :id
940
721
 
941
722
  def initialize(**args)
942
723
  update!(**args)
@@ -944,53 +725,18 @@ module Google
944
725
 
945
726
  # Update properties of this object
946
727
  def update!(**args)
728
+ @reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
947
729
  @reference_name = args[:reference_name] if args.key?(:reference_name)
948
- @type = args[:type] if args.key?(:type)
949
730
  @info = args[:info] if args.key?(:info)
731
+ @type = args[:type] if args.key?(:type)
950
732
  @end = args[:end] if args.key?(:end)
951
733
  @transcript = args[:transcript] if args.key?(:transcript)
952
734
  @start = args[:start] if args.key?(:start)
953
735
  @annotation_set_id = args[:annotation_set_id] if args.key?(:annotation_set_id)
954
736
  @name = args[:name] if args.key?(:name)
955
737
  @variant = args[:variant] if args.key?(:variant)
956
- @id = args[:id] if args.key?(:id)
957
738
  @reference_id = args[:reference_id] if args.key?(:reference_id)
958
- @reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
959
- end
960
- end
961
-
962
- # The request message for Operations.CancelOperation.
963
- class CancelOperationRequest
964
- include Google::Apis::Core::Hashable
965
-
966
- def initialize(**args)
967
- update!(**args)
968
- end
969
-
970
- # Update properties of this object
971
- def update!(**args)
972
- end
973
- end
974
-
975
- # Runtime metadata that will be populated in the
976
- # runtimeMetadata
977
- # field of the Operation associated with a RunPipeline execution.
978
- class RuntimeMetadata
979
- include Google::Apis::Core::Hashable
980
-
981
- # Describes a Compute Engine resource that is being managed by a running
982
- # pipeline.
983
- # Corresponds to the JSON property `computeEngine`
984
- # @return [Google::Apis::GenomicsV1::ComputeEngine]
985
- attr_accessor :compute_engine
986
-
987
- def initialize(**args)
988
- update!(**args)
989
- end
990
-
991
- # Update properties of this object
992
- def update!(**args)
993
- @compute_engine = args[:compute_engine] if args.key?(:compute_engine)
739
+ @id = args[:id] if args.key?(:id)
994
740
  end
995
741
  end
996
742
 
@@ -999,14 +745,6 @@ module Google
999
745
  class Operation
1000
746
  include Google::Apis::Core::Hashable
1001
747
 
1002
- # If the value is `false`, it means the operation is still in progress.
1003
- # If true, the operation is completed, and either `error` or `response` is
1004
- # available.
1005
- # Corresponds to the JSON property `done`
1006
- # @return [Boolean]
1007
- attr_accessor :done
1008
- alias_method :done?, :done
1009
-
1010
748
  # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If
1011
749
  # importing Variants, an ImportVariantsResponse is returned. For pipelines and
1012
750
  # exports, an empty response is returned.
@@ -1069,17 +807,47 @@ module Google
1069
807
  # @return [Hash<String,Object>]
1070
808
  attr_accessor :metadata
1071
809
 
810
+ # If the value is `false`, it means the operation is still in progress.
811
+ # If true, the operation is completed, and either `error` or `response` is
812
+ # available.
813
+ # Corresponds to the JSON property `done`
814
+ # @return [Boolean]
815
+ attr_accessor :done
816
+ alias_method :done?, :done
817
+
1072
818
  def initialize(**args)
1073
819
  update!(**args)
1074
820
  end
1075
821
 
1076
822
  # Update properties of this object
1077
823
  def update!(**args)
1078
- @done = args[:done] if args.key?(:done)
1079
824
  @response = args[:response] if args.key?(:response)
1080
825
  @name = args[:name] if args.key?(:name)
1081
826
  @error = args[:error] if args.key?(:error)
1082
827
  @metadata = args[:metadata] if args.key?(:metadata)
828
+ @done = args[:done] if args.key?(:done)
829
+ end
830
+ end
831
+
832
+ # Runtime metadata that will be populated in the
833
+ # runtimeMetadata
834
+ # field of the Operation associated with a RunPipeline execution.
835
+ class RuntimeMetadata
836
+ include Google::Apis::Core::Hashable
837
+
838
+ # Describes a Compute Engine resource that is being managed by a running
839
+ # pipeline.
840
+ # Corresponds to the JSON property `computeEngine`
841
+ # @return [Google::Apis::GenomicsV1::ComputeEngine]
842
+ attr_accessor :compute_engine
843
+
844
+ def initialize(**args)
845
+ update!(**args)
846
+ end
847
+
848
+ # Update properties of this object
849
+ def update!(**args)
850
+ @compute_engine = args[:compute_engine] if args.key?(:compute_engine)
1083
851
  end
1084
852
  end
1085
853
 
@@ -1109,6 +877,26 @@ module Google
1109
877
  class VariantCall
1110
878
  include Google::Apis::Core::Hashable
1111
879
 
880
+ # The name of the call set this variant call belongs to.
881
+ # Corresponds to the JSON property `callSetName`
882
+ # @return [String]
883
+ attr_accessor :call_set_name
884
+
885
+ # The genotype likelihoods for this variant call. Each array entry
886
+ # represents how likely a specific genotype is for this call. The value
887
+ # ordering is defined by the GL tag in the VCF spec.
888
+ # If Phred-scaled genotype likelihood scores (PL) are available and
889
+ # log10(P) genotype likelihood scores (GL) are not, PL scores are converted
890
+ # to GL scores. If both are available, PL scores are stored in `info`.
891
+ # Corresponds to the JSON property `genotypeLikelihood`
892
+ # @return [Array<Float>]
893
+ attr_accessor :genotype_likelihood
894
+
895
+ # The ID of the call set this variant call belongs to.
896
+ # Corresponds to the JSON property `callSetId`
897
+ # @return [String]
898
+ attr_accessor :call_set_id
899
+
1112
900
  # The genotype of this variant call. Each value represents either the value
1113
901
  # of the `referenceBases` field or a 1-based index into
1114
902
  # `alternateBases`. If a variant had a `referenceBases`
@@ -1140,38 +928,18 @@ module Google
1140
928
  # @return [Hash<String,Array<Object>>]
1141
929
  attr_accessor :info
1142
930
 
1143
- # The name of the call set this variant call belongs to.
1144
- # Corresponds to the JSON property `callSetName`
1145
- # @return [String]
1146
- attr_accessor :call_set_name
1147
-
1148
- # The genotype likelihoods for this variant call. Each array entry
1149
- # represents how likely a specific genotype is for this call. The value
1150
- # ordering is defined by the GL tag in the VCF spec.
1151
- # If Phred-scaled genotype likelihood scores (PL) are available and
1152
- # log10(P) genotype likelihood scores (GL) are not, PL scores are converted
1153
- # to GL scores. If both are available, PL scores are stored in `info`.
1154
- # Corresponds to the JSON property `genotypeLikelihood`
1155
- # @return [Array<Float>]
1156
- attr_accessor :genotype_likelihood
1157
-
1158
- # The ID of the call set this variant call belongs to.
1159
- # Corresponds to the JSON property `callSetId`
1160
- # @return [String]
1161
- attr_accessor :call_set_id
1162
-
1163
931
  def initialize(**args)
1164
932
  update!(**args)
1165
933
  end
1166
934
 
1167
935
  # Update properties of this object
1168
936
  def update!(**args)
1169
- @genotype = args[:genotype] if args.key?(:genotype)
1170
- @phaseset = args[:phaseset] if args.key?(:phaseset)
1171
- @info = args[:info] if args.key?(:info)
1172
937
  @call_set_name = args[:call_set_name] if args.key?(:call_set_name)
1173
938
  @genotype_likelihood = args[:genotype_likelihood] if args.key?(:genotype_likelihood)
1174
939
  @call_set_id = args[:call_set_id] if args.key?(:call_set_id)
940
+ @genotype = args[:genotype] if args.key?(:genotype)
941
+ @phaseset = args[:phaseset] if args.key?(:phaseset)
942
+ @info = args[:info] if args.key?(:info)
1175
943
  end
1176
944
  end
1177
945
 
@@ -1206,13 +974,6 @@ module Google
1206
974
  class ListBasesResponse
1207
975
  include Google::Apis::Core::Hashable
1208
976
 
1209
- # The offset position (0-based) of the given `sequence` from the
1210
- # start of this `Reference`. This value will differ for each page
1211
- # in a paginated request.
1212
- # Corresponds to the JSON property `offset`
1213
- # @return [String]
1214
- attr_accessor :offset
1215
-
1216
977
  # The continuation token, which is used to page through large result sets.
1217
978
  # Provide this value in a subsequent request to return the next page of
1218
979
  # results. This field will be empty if there aren't any additional results.
@@ -1225,15 +986,22 @@ module Google
1225
986
  # @return [String]
1226
987
  attr_accessor :sequence
1227
988
 
989
+ # The offset position (0-based) of the given `sequence` from the
990
+ # start of this `Reference`. This value will differ for each page
991
+ # in a paginated request.
992
+ # Corresponds to the JSON property `offset`
993
+ # @return [String]
994
+ attr_accessor :offset
995
+
1228
996
  def initialize(**args)
1229
997
  update!(**args)
1230
998
  end
1231
999
 
1232
1000
  # Update properties of this object
1233
1001
  def update!(**args)
1234
- @offset = args[:offset] if args.key?(:offset)
1235
1002
  @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
1236
1003
  @sequence = args[:sequence] if args.key?(:sequence)
1004
+ @offset = args[:offset] if args.key?(:offset)
1237
1005
  end
1238
1006
  end
1239
1007
 
@@ -1309,19 +1077,6 @@ module Google
1309
1077
  end
1310
1078
  end
1311
1079
 
1312
- #
1313
- class UndeleteDatasetRequest
1314
- include Google::Apis::Core::Hashable
1315
-
1316
- def initialize(**args)
1317
- update!(**args)
1318
- end
1319
-
1320
- # Update properties of this object
1321
- def update!(**args)
1322
- end
1323
- end
1324
-
1325
1080
  # Associates `members` with a `role`.
1326
1081
  class Binding
1327
1082
  include Google::Apis::Core::Hashable
@@ -1362,10 +1117,29 @@ module Google
1362
1117
  end
1363
1118
  end
1364
1119
 
1120
+ #
1121
+ class UndeleteDatasetRequest
1122
+ include Google::Apis::Core::Hashable
1123
+
1124
+ def initialize(**args)
1125
+ update!(**args)
1126
+ end
1127
+
1128
+ # Update properties of this object
1129
+ def update!(**args)
1130
+ end
1131
+ end
1132
+
1365
1133
  # A 0-based half-open genomic coordinate range for search requests.
1366
1134
  class Range
1367
1135
  include Google::Apis::Core::Hashable
1368
1136
 
1137
+ # The reference sequence name, for example `chr1`,
1138
+ # `1`, or `chrX`.
1139
+ # Corresponds to the JSON property `referenceName`
1140
+ # @return [String]
1141
+ attr_accessor :reference_name
1142
+
1369
1143
  # The start position of the range on the reference, 0-based inclusive.
1370
1144
  # Corresponds to the JSON property `start`
1371
1145
  # @return [String]
@@ -1376,21 +1150,15 @@ module Google
1376
1150
  # @return [String]
1377
1151
  attr_accessor :end
1378
1152
 
1379
- # The reference sequence name, for example `chr1`,
1380
- # `1`, or `chrX`.
1381
- # Corresponds to the JSON property `referenceName`
1382
- # @return [String]
1383
- attr_accessor :reference_name
1384
-
1385
1153
  def initialize(**args)
1386
1154
  update!(**args)
1387
1155
  end
1388
1156
 
1389
1157
  # Update properties of this object
1390
1158
  def update!(**args)
1159
+ @reference_name = args[:reference_name] if args.key?(:reference_name)
1391
1160
  @start = args[:start] if args.key?(:start)
1392
1161
  @end = args[:end] if args.key?(:end)
1393
- @reference_name = args[:reference_name] if args.key?(:reference_name)
1394
1162
  end
1395
1163
  end
1396
1164
 
@@ -1512,11 +1280,6 @@ module Google
1512
1280
  class SearchCallSetsResponse
1513
1281
  include Google::Apis::Core::Hashable
1514
1282
 
1515
- # The list of matching call sets.
1516
- # Corresponds to the JSON property `callSets`
1517
- # @return [Array<Google::Apis::GenomicsV1::CallSet>]
1518
- attr_accessor :call_sets
1519
-
1520
1283
  # The continuation token, which is used to page through large result sets.
1521
1284
  # Provide this value in a subsequent request to return the next page of
1522
1285
  # results. This field will be empty if there aren't any additional results.
@@ -1524,14 +1287,19 @@ module Google
1524
1287
  # @return [String]
1525
1288
  attr_accessor :next_page_token
1526
1289
 
1290
+ # The list of matching call sets.
1291
+ # Corresponds to the JSON property `callSets`
1292
+ # @return [Array<Google::Apis::GenomicsV1::CallSet>]
1293
+ attr_accessor :call_sets
1294
+
1527
1295
  def initialize(**args)
1528
1296
  update!(**args)
1529
1297
  end
1530
1298
 
1531
1299
  # Update properties of this object
1532
1300
  def update!(**args)
1533
- @call_sets = args[:call_sets] if args.key?(:call_sets)
1534
1301
  @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
1302
+ @call_sets = args[:call_sets] if args.key?(:call_sets)
1535
1303
  end
1536
1304
  end
1537
1305
 
@@ -1548,6 +1316,12 @@ module Google
1548
1316
  class Variant
1549
1317
  include Google::Apis::Core::Hashable
1550
1318
 
1319
+ # The reference on which this variant occurs.
1320
+ # (such as `chr20` or `X`)
1321
+ # Corresponds to the JSON property `referenceName`
1322
+ # @return [String]
1323
+ attr_accessor :reference_name
1324
+
1551
1325
  # A map of additional variant information. This must be of the form
1552
1326
  # map<string, string[]> (string key mapping to a list of string values).
1553
1327
  # Corresponds to the JSON property `info`
@@ -1560,15 +1334,21 @@ module Google
1560
1334
  # @return [String]
1561
1335
  attr_accessor :reference_bases
1562
1336
 
1337
+ # The bases that appear instead of the reference bases.
1338
+ # Corresponds to the JSON property `alternateBases`
1339
+ # @return [Array<String>]
1340
+ attr_accessor :alternate_bases
1341
+
1563
1342
  # Names for the variant, for example a RefSNP ID.
1564
1343
  # Corresponds to the JSON property `names`
1565
1344
  # @return [Array<String>]
1566
1345
  attr_accessor :names
1567
1346
 
1568
- # The bases that appear instead of the reference bases.
1569
- # Corresponds to the JSON property `alternateBases`
1347
+ # A list of filters (normally quality filters) this variant has failed.
1348
+ # `PASS` indicates this variant has passed all filters.
1349
+ # Corresponds to the JSON property `filter`
1570
1350
  # @return [Array<String>]
1571
- attr_accessor :alternate_bases
1351
+ attr_accessor :filter
1572
1352
 
1573
1353
  # The end position (0-based) of this variant. This corresponds to the first
1574
1354
  # base after the last base in the reference allele. So, the length of
@@ -1578,12 +1358,6 @@ module Google
1578
1358
  # @return [String]
1579
1359
  attr_accessor :end
1580
1360
 
1581
- # A list of filters (normally quality filters) this variant has failed.
1582
- # `PASS` indicates this variant has passed all filters.
1583
- # Corresponds to the JSON property `filter`
1584
- # @return [Array<String>]
1585
- attr_accessor :filter
1586
-
1587
1361
  # The variant calls for this particular variant. Each one represents the
1588
1362
  # determination of genotype with respect to this variant.
1589
1363
  # Corresponds to the JSON property `calls`
@@ -1617,31 +1391,25 @@ module Google
1617
1391
  # @return [String]
1618
1392
  attr_accessor :variant_set_id
1619
1393
 
1620
- # The reference on which this variant occurs.
1621
- # (such as `chr20` or `X`)
1622
- # Corresponds to the JSON property `referenceName`
1623
- # @return [String]
1624
- attr_accessor :reference_name
1625
-
1626
1394
  def initialize(**args)
1627
1395
  update!(**args)
1628
1396
  end
1629
1397
 
1630
1398
  # Update properties of this object
1631
1399
  def update!(**args)
1400
+ @reference_name = args[:reference_name] if args.key?(:reference_name)
1632
1401
  @info = args[:info] if args.key?(:info)
1633
1402
  @reference_bases = args[:reference_bases] if args.key?(:reference_bases)
1634
- @names = args[:names] if args.key?(:names)
1635
1403
  @alternate_bases = args[:alternate_bases] if args.key?(:alternate_bases)
1636
- @end = args[:end] if args.key?(:end)
1404
+ @names = args[:names] if args.key?(:names)
1637
1405
  @filter = args[:filter] if args.key?(:filter)
1406
+ @end = args[:end] if args.key?(:end)
1638
1407
  @calls = args[:calls] if args.key?(:calls)
1639
1408
  @created = args[:created] if args.key?(:created)
1640
1409
  @start = args[:start] if args.key?(:start)
1641
1410
  @quality = args[:quality] if args.key?(:quality)
1642
1411
  @id = args[:id] if args.key?(:id)
1643
1412
  @variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
1644
- @reference_name = args[:reference_name] if args.key?(:reference_name)
1645
1413
  end
1646
1414
  end
1647
1415
 
@@ -1649,87 +1417,15 @@ module Google
1649
1417
  class ListOperationsResponse
1650
1418
  include Google::Apis::Core::Hashable
1651
1419
 
1652
- # A list of operations that matches the specified filter in the request.
1653
- # Corresponds to the JSON property `operations`
1654
- # @return [Array<Google::Apis::GenomicsV1::Operation>]
1655
- attr_accessor :operations
1656
-
1657
1420
  # The standard List next-page token.
1658
1421
  # Corresponds to the JSON property `nextPageToken`
1659
1422
  # @return [String]
1660
1423
  attr_accessor :next_page_token
1661
1424
 
1662
- def initialize(**args)
1663
- update!(**args)
1664
- end
1665
-
1666
- # Update properties of this object
1667
- def update!(**args)
1668
- @operations = args[:operations] if args.key?(:operations)
1669
- @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
1670
- end
1671
- end
1672
-
1673
- # The variant search request.
1674
- class SearchVariantsRequest
1675
- include Google::Apis::Core::Hashable
1676
-
1677
- # At most one variant set ID must be provided. Only variants from this
1678
- # variant set will be returned. If omitted, a call set id must be included in
1679
- # the request.
1680
- # Corresponds to the JSON property `variantSetIds`
1681
- # @return [Array<String>]
1682
- attr_accessor :variant_set_ids
1683
-
1684
- # The end of the window, 0-based exclusive. If unspecified or 0, defaults to
1685
- # the length of the reference.
1686
- # Corresponds to the JSON property `end`
1687
- # @return [String]
1688
- attr_accessor :end
1689
-
1690
- # The maximum number of calls to return in a single page. Note that this
1691
- # limit may be exceeded in the event that a matching variant contains more
1692
- # calls than the requested maximum. If unspecified, defaults to 5000. The
1693
- # maximum value is 10000.
1694
- # Corresponds to the JSON property `maxCalls`
1695
- # @return [Fixnum]
1696
- attr_accessor :max_calls
1697
-
1698
- # The continuation token, which is used to page through large result sets.
1699
- # To get the next page of results, set this parameter to the value of
1700
- # `nextPageToken` from the previous response.
1701
- # Corresponds to the JSON property `pageToken`
1702
- # @return [String]
1703
- attr_accessor :page_token
1704
-
1705
- # The maximum number of variants to return in a single page. If unspecified,
1706
- # defaults to 5000. The maximum value is 10000.
1707
- # Corresponds to the JSON property `pageSize`
1708
- # @return [Fixnum]
1709
- attr_accessor :page_size
1710
-
1711
- # Only return variant calls which belong to call sets with these ids.
1712
- # Leaving this blank returns all variant calls. If a variant has no
1713
- # calls belonging to any of these call sets, it won't be returned at all.
1714
- # Corresponds to the JSON property `callSetIds`
1715
- # @return [Array<String>]
1716
- attr_accessor :call_set_ids
1717
-
1718
- # The beginning of the window (0-based, inclusive) for which
1719
- # overlapping variants should be returned. If unspecified, defaults to 0.
1720
- # Corresponds to the JSON property `start`
1721
- # @return [String]
1722
- attr_accessor :start
1723
-
1724
- # Only return variants which have exactly this name.
1725
- # Corresponds to the JSON property `variantName`
1726
- # @return [String]
1727
- attr_accessor :variant_name
1728
-
1729
- # Required. Only return variants in this reference sequence.
1730
- # Corresponds to the JSON property `referenceName`
1731
- # @return [String]
1732
- attr_accessor :reference_name
1425
+ # A list of operations that matches the specified filter in the request.
1426
+ # Corresponds to the JSON property `operations`
1427
+ # @return [Array<Google::Apis::GenomicsV1::Operation>]
1428
+ attr_accessor :operations
1733
1429
 
1734
1430
  def initialize(**args)
1735
1431
  update!(**args)
@@ -1737,15 +1433,8 @@ module Google
1737
1433
 
1738
1434
  # Update properties of this object
1739
1435
  def update!(**args)
1740
- @variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
1741
- @end = args[:end] if args.key?(:end)
1742
- @max_calls = args[:max_calls] if args.key?(:max_calls)
1743
- @page_token = args[:page_token] if args.key?(:page_token)
1744
- @page_size = args[:page_size] if args.key?(:page_size)
1745
- @call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
1746
- @start = args[:start] if args.key?(:start)
1747
- @variant_name = args[:variant_name] if args.key?(:variant_name)
1748
- @reference_name = args[:reference_name] if args.key?(:reference_name)
1436
+ @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
1437
+ @operations = args[:operations] if args.key?(:operations)
1749
1438
  end
1750
1439
  end
1751
1440
 
@@ -1822,15 +1511,22 @@ module Google
1822
1511
  end
1823
1512
  end
1824
1513
 
1825
- # The read group set search request.
1826
- class SearchReadGroupSetsRequest
1514
+ # The variant search request.
1515
+ class SearchVariantsRequest
1827
1516
  include Google::Apis::Core::Hashable
1828
1517
 
1829
- # Only return read group sets for which a substring of the name matches this
1830
- # string.
1831
- # Corresponds to the JSON property `name`
1518
+ # At most one variant set ID must be provided. Only variants from this
1519
+ # variant set will be returned. If omitted, a call set id must be included in
1520
+ # the request.
1521
+ # Corresponds to the JSON property `variantSetIds`
1522
+ # @return [Array<String>]
1523
+ attr_accessor :variant_set_ids
1524
+
1525
+ # The end of the window, 0-based exclusive. If unspecified or 0, defaults to
1526
+ # the length of the reference.
1527
+ # Corresponds to the JSON property `end`
1832
1528
  # @return [String]
1833
- attr_accessor :name
1529
+ attr_accessor :end
1834
1530
 
1835
1531
  # The continuation token, which is used to page through large result sets.
1836
1532
  # To get the next page of results, set this parameter to the value of
@@ -1839,30 +1535,102 @@ module Google
1839
1535
  # @return [String]
1840
1536
  attr_accessor :page_token
1841
1537
 
1842
- # The maximum number of results to return in a single page. If unspecified,
1843
- # defaults to 256. The maximum value is 1024.
1538
+ # The maximum number of calls to return in a single page. Note that this
1539
+ # limit may be exceeded in the event that a matching variant contains more
1540
+ # calls than the requested maximum. If unspecified, defaults to 5000. The
1541
+ # maximum value is 10000.
1542
+ # Corresponds to the JSON property `maxCalls`
1543
+ # @return [Fixnum]
1544
+ attr_accessor :max_calls
1545
+
1546
+ # The maximum number of variants to return in a single page. If unspecified,
1547
+ # defaults to 5000. The maximum value is 10000.
1844
1548
  # Corresponds to the JSON property `pageSize`
1845
1549
  # @return [Fixnum]
1846
1550
  attr_accessor :page_size
1847
1551
 
1848
- # Restricts this query to read group sets within the given datasets. At least
1849
- # one ID must be provided.
1850
- # Corresponds to the JSON property `datasetIds`
1552
+ # Only return variant calls which belong to call sets with these ids.
1553
+ # Leaving this blank returns all variant calls. If a variant has no
1554
+ # calls belonging to any of these call sets, it won't be returned at all.
1555
+ # Corresponds to the JSON property `callSetIds`
1851
1556
  # @return [Array<String>]
1852
- attr_accessor :dataset_ids
1557
+ attr_accessor :call_set_ids
1853
1558
 
1854
- def initialize(**args)
1855
- update!(**args)
1856
- end
1559
+ # Only return variants which have exactly this name.
1560
+ # Corresponds to the JSON property `variantName`
1561
+ # @return [String]
1562
+ attr_accessor :variant_name
1857
1563
 
1858
- # Update properties of this object
1859
- def update!(**args)
1860
- @name = args[:name] if args.key?(:name)
1861
- @page_token = args[:page_token] if args.key?(:page_token)
1862
- @page_size = args[:page_size] if args.key?(:page_size)
1863
- @dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
1864
- end
1865
- end
1564
+ # The beginning of the window (0-based, inclusive) for which
1565
+ # overlapping variants should be returned. If unspecified, defaults to 0.
1566
+ # Corresponds to the JSON property `start`
1567
+ # @return [String]
1568
+ attr_accessor :start
1569
+
1570
+ # Required. Only return variants in this reference sequence.
1571
+ # Corresponds to the JSON property `referenceName`
1572
+ # @return [String]
1573
+ attr_accessor :reference_name
1574
+
1575
+ def initialize(**args)
1576
+ update!(**args)
1577
+ end
1578
+
1579
+ # Update properties of this object
1580
+ def update!(**args)
1581
+ @variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
1582
+ @end = args[:end] if args.key?(:end)
1583
+ @page_token = args[:page_token] if args.key?(:page_token)
1584
+ @max_calls = args[:max_calls] if args.key?(:max_calls)
1585
+ @page_size = args[:page_size] if args.key?(:page_size)
1586
+ @call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
1587
+ @variant_name = args[:variant_name] if args.key?(:variant_name)
1588
+ @start = args[:start] if args.key?(:start)
1589
+ @reference_name = args[:reference_name] if args.key?(:reference_name)
1590
+ end
1591
+ end
1592
+
1593
+ # The read group set search request.
1594
+ class SearchReadGroupSetsRequest
1595
+ include Google::Apis::Core::Hashable
1596
+
1597
+ # Restricts this query to read group sets within the given datasets. At least
1598
+ # one ID must be provided.
1599
+ # Corresponds to the JSON property `datasetIds`
1600
+ # @return [Array<String>]
1601
+ attr_accessor :dataset_ids
1602
+
1603
+ # Only return read group sets for which a substring of the name matches this
1604
+ # string.
1605
+ # Corresponds to the JSON property `name`
1606
+ # @return [String]
1607
+ attr_accessor :name
1608
+
1609
+ # The continuation token, which is used to page through large result sets.
1610
+ # To get the next page of results, set this parameter to the value of
1611
+ # `nextPageToken` from the previous response.
1612
+ # Corresponds to the JSON property `pageToken`
1613
+ # @return [String]
1614
+ attr_accessor :page_token
1615
+
1616
+ # The maximum number of results to return in a single page. If unspecified,
1617
+ # defaults to 256. The maximum value is 1024.
1618
+ # Corresponds to the JSON property `pageSize`
1619
+ # @return [Fixnum]
1620
+ attr_accessor :page_size
1621
+
1622
+ def initialize(**args)
1623
+ update!(**args)
1624
+ end
1625
+
1626
+ # Update properties of this object
1627
+ def update!(**args)
1628
+ @dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
1629
+ @name = args[:name] if args.key?(:name)
1630
+ @page_token = args[:page_token] if args.key?(:page_token)
1631
+ @page_size = args[:page_size] if args.key?(:page_size)
1632
+ end
1633
+ end
1866
1634
 
1867
1635
  #
1868
1636
  class SearchAnnotationsResponse
@@ -1895,6 +1663,13 @@ module Google
1895
1663
  class SearchReadsResponse
1896
1664
  include Google::Apis::Core::Hashable
1897
1665
 
1666
+ # The continuation token, which is used to page through large result sets.
1667
+ # Provide this value in a subsequent request to return the next page of
1668
+ # results. This field will be empty if there aren't any additional results.
1669
+ # Corresponds to the JSON property `nextPageToken`
1670
+ # @return [String]
1671
+ attr_accessor :next_page_token
1672
+
1898
1673
  # The list of matching alignments sorted by mapped genomic coordinate,
1899
1674
  # if any, ascending in position within the same reference. Unmapped reads,
1900
1675
  # which have no position, are returned contiguously and are sorted in
@@ -1903,21 +1678,14 @@ module Google
1903
1678
  # @return [Array<Google::Apis::GenomicsV1::Read>]
1904
1679
  attr_accessor :alignments
1905
1680
 
1906
- # The continuation token, which is used to page through large result sets.
1907
- # Provide this value in a subsequent request to return the next page of
1908
- # results. This field will be empty if there aren't any additional results.
1909
- # Corresponds to the JSON property `nextPageToken`
1910
- # @return [String]
1911
- attr_accessor :next_page_token
1912
-
1913
1681
  def initialize(**args)
1914
1682
  update!(**args)
1915
1683
  end
1916
1684
 
1917
1685
  # Update properties of this object
1918
1686
  def update!(**args)
1919
- @alignments = args[:alignments] if args.key?(:alignments)
1920
1687
  @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
1688
+ @alignments = args[:alignments] if args.key?(:alignments)
1921
1689
  end
1922
1690
  end
1923
1691
 
@@ -1925,6 +1693,12 @@ module Google
1925
1693
  class ClinicalCondition
1926
1694
  include Google::Apis::Core::Hashable
1927
1695
 
1696
+ # The MedGen concept id associated with this gene.
1697
+ # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
1698
+ # Corresponds to the JSON property `conceptId`
1699
+ # @return [String]
1700
+ attr_accessor :concept_id
1701
+
1928
1702
  # A set of names for the condition.
1929
1703
  # Corresponds to the JSON property `names`
1930
1704
  # @return [Array<String>]
@@ -1941,22 +1715,16 @@ module Google
1941
1715
  # @return [Array<Google::Apis::GenomicsV1::ExternalId>]
1942
1716
  attr_accessor :external_ids
1943
1717
 
1944
- # The MedGen concept id associated with this gene.
1945
- # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
1946
- # Corresponds to the JSON property `conceptId`
1947
- # @return [String]
1948
- attr_accessor :concept_id
1949
-
1950
1718
  def initialize(**args)
1951
1719
  update!(**args)
1952
1720
  end
1953
1721
 
1954
1722
  # Update properties of this object
1955
1723
  def update!(**args)
1724
+ @concept_id = args[:concept_id] if args.key?(:concept_id)
1956
1725
  @names = args[:names] if args.key?(:names)
1957
1726
  @omim_id = args[:omim_id] if args.key?(:omim_id)
1958
1727
  @external_ids = args[:external_ids] if args.key?(:external_ids)
1959
- @concept_id = args[:concept_id] if args.key?(:concept_id)
1960
1728
  end
1961
1729
  end
1962
1730
 
@@ -1964,6 +1732,16 @@ module Google
1964
1732
  class Program
1965
1733
  include Google::Apis::Core::Hashable
1966
1734
 
1735
+ # The command line used to run this program.
1736
+ # Corresponds to the JSON property `commandLine`
1737
+ # @return [String]
1738
+ attr_accessor :command_line
1739
+
1740
+ # The ID of the program run before this one.
1741
+ # Corresponds to the JSON property `prevProgramId`
1742
+ # @return [String]
1743
+ attr_accessor :prev_program_id
1744
+
1967
1745
  # The user specified locally unique ID of the program. Used along with
1968
1746
  # `prevProgramId` to define an ordering between programs.
1969
1747
  # Corresponds to the JSON property `id`
@@ -1981,15 +1759,44 @@ module Google
1981
1759
  # @return [String]
1982
1760
  attr_accessor :name
1983
1761
 
1984
- # The command line used to run this program.
1985
- # Corresponds to the JSON property `commandLine`
1762
+ def initialize(**args)
1763
+ update!(**args)
1764
+ end
1765
+
1766
+ # Update properties of this object
1767
+ def update!(**args)
1768
+ @command_line = args[:command_line] if args.key?(:command_line)
1769
+ @prev_program_id = args[:prev_program_id] if args.key?(:prev_program_id)
1770
+ @id = args[:id] if args.key?(:id)
1771
+ @version = args[:version] if args.key?(:version)
1772
+ @name = args[:name] if args.key?(:name)
1773
+ end
1774
+ end
1775
+
1776
+ # Describes a Compute Engine resource that is being managed by a running
1777
+ # pipeline.
1778
+ class ComputeEngine
1779
+ include Google::Apis::Core::Hashable
1780
+
1781
+ # The machine type of the instance.
1782
+ # Corresponds to the JSON property `machineType`
1986
1783
  # @return [String]
1987
- attr_accessor :command_line
1784
+ attr_accessor :machine_type
1988
1785
 
1989
- # The ID of the program run before this one.
1990
- # Corresponds to the JSON property `prevProgramId`
1786
+ # The names of the disks that were created for this pipeline.
1787
+ # Corresponds to the JSON property `diskNames`
1788
+ # @return [Array<String>]
1789
+ attr_accessor :disk_names
1790
+
1791
+ # The instance on which the operation is running.
1792
+ # Corresponds to the JSON property `instanceName`
1991
1793
  # @return [String]
1992
- attr_accessor :prev_program_id
1794
+ attr_accessor :instance_name
1795
+
1796
+ # The availability zone in which the instance resides.
1797
+ # Corresponds to the JSON property `zone`
1798
+ # @return [String]
1799
+ attr_accessor :zone
1993
1800
 
1994
1801
  def initialize(**args)
1995
1802
  update!(**args)
@@ -1997,11 +1804,10 @@ module Google
1997
1804
 
1998
1805
  # Update properties of this object
1999
1806
  def update!(**args)
2000
- @id = args[:id] if args.key?(:id)
2001
- @version = args[:version] if args.key?(:version)
2002
- @name = args[:name] if args.key?(:name)
2003
- @command_line = args[:command_line] if args.key?(:command_line)
2004
- @prev_program_id = args[:prev_program_id] if args.key?(:prev_program_id)
1807
+ @machine_type = args[:machine_type] if args.key?(:machine_type)
1808
+ @disk_names = args[:disk_names] if args.key?(:disk_names)
1809
+ @instance_name = args[:instance_name] if args.key?(:instance_name)
1810
+ @zone = args[:zone] if args.key?(:zone)
2005
1811
  end
2006
1812
  end
2007
1813
 
@@ -2032,66 +1838,28 @@ module Google
2032
1838
  end
2033
1839
  end
2034
1840
 
2035
- # Describes a Compute Engine resource that is being managed by a running
2036
- # pipeline.
2037
- class ComputeEngine
2038
- include Google::Apis::Core::Hashable
2039
-
2040
- # The instance on which the operation is running.
2041
- # Corresponds to the JSON property `instanceName`
2042
- # @return [String]
2043
- attr_accessor :instance_name
2044
-
2045
- # The availability zone in which the instance resides.
2046
- # Corresponds to the JSON property `zone`
2047
- # @return [String]
2048
- attr_accessor :zone
2049
-
2050
- # The machine type of the instance.
2051
- # Corresponds to the JSON property `machineType`
2052
- # @return [String]
2053
- attr_accessor :machine_type
2054
-
2055
- # The names of the disks that were created for this pipeline.
2056
- # Corresponds to the JSON property `diskNames`
2057
- # @return [Array<String>]
2058
- attr_accessor :disk_names
2059
-
2060
- def initialize(**args)
2061
- update!(**args)
2062
- end
2063
-
2064
- # Update properties of this object
2065
- def update!(**args)
2066
- @instance_name = args[:instance_name] if args.key?(:instance_name)
2067
- @zone = args[:zone] if args.key?(:zone)
2068
- @machine_type = args[:machine_type] if args.key?(:machine_type)
2069
- @disk_names = args[:disk_names] if args.key?(:disk_names)
2070
- end
2071
- end
2072
-
2073
1841
  #
2074
1842
  class ExternalId
2075
1843
  include Google::Apis::Core::Hashable
2076
1844
 
2077
- # The id used by the source of this data.
2078
- # Corresponds to the JSON property `id`
2079
- # @return [String]
2080
- attr_accessor :id
2081
-
2082
1845
  # The name of the source of this data.
2083
1846
  # Corresponds to the JSON property `sourceName`
2084
1847
  # @return [String]
2085
1848
  attr_accessor :source_name
2086
1849
 
1850
+ # The id used by the source of this data.
1851
+ # Corresponds to the JSON property `id`
1852
+ # @return [String]
1853
+ attr_accessor :id
1854
+
2087
1855
  def initialize(**args)
2088
1856
  update!(**args)
2089
1857
  end
2090
1858
 
2091
1859
  # Update properties of this object
2092
1860
  def update!(**args)
2093
- @id = args[:id] if args.key?(:id)
2094
1861
  @source_name = args[:source_name] if args.key?(:source_name)
1862
+ @id = args[:id] if args.key?(:id)
2095
1863
  end
2096
1864
  end
2097
1865
 
@@ -2137,18 +1905,6 @@ module Google
2137
1905
  class VariantSetMetadata
2138
1906
  include Google::Apis::Core::Hashable
2139
1907
 
2140
- # The type of data. Possible types include: Integer, Float,
2141
- # Flag, Character, and String.
2142
- # Corresponds to the JSON property `type`
2143
- # @return [String]
2144
- attr_accessor :type
2145
-
2146
- # Remaining structured metadata key-value pairs. This must be of the form
2147
- # map<string, string[]> (string key mapping to a list of string values).
2148
- # Corresponds to the JSON property `info`
2149
- # @return [Hash<String,Array<Object>>]
2150
- attr_accessor :info
2151
-
2152
1908
  # The number of values that can be included in a field described by this
2153
1909
  # metadata.
2154
1910
  # Corresponds to the JSON property `number`
@@ -2177,19 +1933,31 @@ module Google
2177
1933
  # @return [String]
2178
1934
  attr_accessor :description
2179
1935
 
1936
+ # Remaining structured metadata key-value pairs. This must be of the form
1937
+ # map<string, string[]> (string key mapping to a list of string values).
1938
+ # Corresponds to the JSON property `info`
1939
+ # @return [Hash<String,Array<Object>>]
1940
+ attr_accessor :info
1941
+
1942
+ # The type of data. Possible types include: Integer, Float,
1943
+ # Flag, Character, and String.
1944
+ # Corresponds to the JSON property `type`
1945
+ # @return [String]
1946
+ attr_accessor :type
1947
+
2180
1948
  def initialize(**args)
2181
1949
  update!(**args)
2182
1950
  end
2183
1951
 
2184
1952
  # Update properties of this object
2185
1953
  def update!(**args)
2186
- @type = args[:type] if args.key?(:type)
2187
- @info = args[:info] if args.key?(:info)
2188
1954
  @number = args[:number] if args.key?(:number)
2189
1955
  @id = args[:id] if args.key?(:id)
2190
1956
  @value = args[:value] if args.key?(:value)
2191
1957
  @key = args[:key] if args.key?(:key)
2192
1958
  @description = args[:description] if args.key?(:description)
1959
+ @info = args[:info] if args.key?(:info)
1960
+ @type = args[:type] if args.key?(:type)
2193
1961
  end
2194
1962
  end
2195
1963
 
@@ -2202,26 +1970,36 @@ module Google
2202
1970
  class Reference
2203
1971
  include Google::Apis::Core::Hashable
2204
1972
 
1973
+ # The server-generated reference ID, unique across all references.
1974
+ # Corresponds to the JSON property `id`
1975
+ # @return [String]
1976
+ attr_accessor :id
1977
+
1978
+ # The length of this reference's sequence.
1979
+ # Corresponds to the JSON property `length`
1980
+ # @return [String]
1981
+ attr_accessor :length
1982
+
2205
1983
  # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
2206
1984
  # with a version number, for example `GCF_000001405.26`.
2207
1985
  # Corresponds to the JSON property `sourceAccessions`
2208
1986
  # @return [Array<String>]
2209
1987
  attr_accessor :source_accessions
2210
1988
 
2211
- # ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
2212
- # Corresponds to the JSON property `ncbiTaxonId`
2213
- # @return [Fixnum]
2214
- attr_accessor :ncbi_taxon_id
2215
-
2216
1989
  # The URI from which the sequence was obtained. Typically specifies a FASTA
2217
1990
  # format file.
2218
1991
  # Corresponds to the JSON property `sourceUri`
2219
1992
  # @return [String]
2220
1993
  attr_accessor :source_uri
2221
1994
 
2222
- # The name of this reference, for example `22`.
2223
- # Corresponds to the JSON property `name`
2224
- # @return [String]
1995
+ # ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
1996
+ # Corresponds to the JSON property `ncbiTaxonId`
1997
+ # @return [Fixnum]
1998
+ attr_accessor :ncbi_taxon_id
1999
+
2000
+ # The name of this reference, for example `22`.
2001
+ # Corresponds to the JSON property `name`
2002
+ # @return [String]
2225
2003
  attr_accessor :name
2226
2004
 
2227
2005
  # MD5 of the upper-case sequence excluding all whitespace characters (this
@@ -2231,29 +2009,19 @@ module Google
2231
2009
  # @return [String]
2232
2010
  attr_accessor :md5checksum
2233
2011
 
2234
- # The server-generated reference ID, unique across all references.
2235
- # Corresponds to the JSON property `id`
2236
- # @return [String]
2237
- attr_accessor :id
2238
-
2239
- # The length of this reference's sequence.
2240
- # Corresponds to the JSON property `length`
2241
- # @return [String]
2242
- attr_accessor :length
2243
-
2244
2012
  def initialize(**args)
2245
2013
  update!(**args)
2246
2014
  end
2247
2015
 
2248
2016
  # Update properties of this object
2249
2017
  def update!(**args)
2018
+ @id = args[:id] if args.key?(:id)
2019
+ @length = args[:length] if args.key?(:length)
2250
2020
  @source_accessions = args[:source_accessions] if args.key?(:source_accessions)
2251
- @ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
2252
2021
  @source_uri = args[:source_uri] if args.key?(:source_uri)
2022
+ @ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
2253
2023
  @name = args[:name] if args.key?(:name)
2254
2024
  @md5checksum = args[:md5checksum] if args.key?(:md5checksum)
2255
- @id = args[:id] if args.key?(:id)
2256
- @length = args[:length] if args.key?(:length)
2257
2025
  end
2258
2026
  end
2259
2027
 
@@ -2261,6 +2029,12 @@ module Google
2261
2029
  class SearchReferenceSetsRequest
2262
2030
  include Google::Apis::Core::Hashable
2263
2031
 
2032
+ # If present, return reference sets for which the
2033
+ # md5checksum matches exactly.
2034
+ # Corresponds to the JSON property `md5checksums`
2035
+ # @return [Array<String>]
2036
+ attr_accessor :md5checksums
2037
+
2264
2038
  # If present, return reference sets for which a prefix of any of
2265
2039
  # sourceAccessions
2266
2040
  # match any of these strings. Accession numbers typically have a main number
@@ -2288,23 +2062,17 @@ module Google
2288
2062
  # @return [String]
2289
2063
  attr_accessor :assembly_id
2290
2064
 
2291
- # If present, return reference sets for which the
2292
- # md5checksum matches exactly.
2293
- # Corresponds to the JSON property `md5checksums`
2294
- # @return [Array<String>]
2295
- attr_accessor :md5checksums
2296
-
2297
2065
  def initialize(**args)
2298
2066
  update!(**args)
2299
2067
  end
2300
2068
 
2301
2069
  # Update properties of this object
2302
2070
  def update!(**args)
2071
+ @md5checksums = args[:md5checksums] if args.key?(:md5checksums)
2303
2072
  @accessions = args[:accessions] if args.key?(:accessions)
2304
2073
  @page_token = args[:page_token] if args.key?(:page_token)
2305
2074
  @page_size = args[:page_size] if args.key?(:page_size)
2306
2075
  @assembly_id = args[:assembly_id] if args.key?(:assembly_id)
2307
- @md5checksums = args[:md5checksums] if args.key?(:md5checksums)
2308
2076
  end
2309
2077
  end
2310
2078
 
@@ -2384,38 +2152,6 @@ module Google
2384
2152
  end
2385
2153
  end
2386
2154
 
2387
- #
2388
- class BatchCreateAnnotationsRequest
2389
- include Google::Apis::Core::Hashable
2390
-
2391
- # The annotations to be created. At most 4096 can be specified in a single
2392
- # request.
2393
- # Corresponds to the JSON property `annotations`
2394
- # @return [Array<Google::Apis::GenomicsV1::Annotation>]
2395
- attr_accessor :annotations
2396
-
2397
- # A unique request ID which enables the server to detect duplicated requests.
2398
- # If provided, duplicated requests will result in the same response; if not
2399
- # provided, duplicated requests may result in duplicated data. For a given
2400
- # annotation set, callers should not reuse `request_id`s when writing
2401
- # different batches of annotations - behavior in this case is undefined.
2402
- # A common approach is to use a UUID. For batch jobs where worker crashes are
2403
- # a possibility, consider using some unique variant of a worker or run ID.
2404
- # Corresponds to the JSON property `requestId`
2405
- # @return [String]
2406
- attr_accessor :request_id
2407
-
2408
- def initialize(**args)
2409
- update!(**args)
2410
- end
2411
-
2412
- # Update properties of this object
2413
- def update!(**args)
2414
- @annotations = args[:annotations] if args.key?(:annotations)
2415
- @request_id = args[:request_id] if args.key?(:request_id)
2416
- end
2417
- end
2418
-
2419
2155
  # A read alignment describes a linear alignment of a string of DNA to a
2420
2156
  # reference sequence, in addition to metadata
2421
2157
  # about the fragment (the molecule of DNA sequenced) and the read (the bases
@@ -2491,6 +2227,39 @@ module Google
2491
2227
  class Read
2492
2228
  include Google::Apis::Core::Hashable
2493
2229
 
2230
+ # A linear alignment can be represented by one CIGAR string. Describes the
2231
+ # mapped position and local alignment of the read to the reference.
2232
+ # Corresponds to the JSON property `alignment`
2233
+ # @return [Google::Apis::GenomicsV1::LinearAlignment]
2234
+ attr_accessor :alignment
2235
+
2236
+ # The server-generated read ID, unique across all reads. This is different
2237
+ # from the `fragmentName`.
2238
+ # Corresponds to the JSON property `id`
2239
+ # @return [String]
2240
+ attr_accessor :id
2241
+
2242
+ # The number of reads in the fragment (extension to SAM flag 0x1).
2243
+ # Corresponds to the JSON property `numberReads`
2244
+ # @return [Fixnum]
2245
+ attr_accessor :number_reads
2246
+
2247
+ # Whether this alignment is secondary. Equivalent to SAM flag 0x100.
2248
+ # A secondary alignment represents an alternative to the primary alignment
2249
+ # for this read. Aligners may return secondary alignments if a read can map
2250
+ # ambiguously to multiple coordinates in the genome. By convention, each read
2251
+ # has one and only one alignment where both `secondaryAlignment`
2252
+ # and `supplementaryAlignment` are false.
2253
+ # Corresponds to the JSON property `secondaryAlignment`
2254
+ # @return [Boolean]
2255
+ attr_accessor :secondary_alignment
2256
+ alias_method :secondary_alignment?, :secondary_alignment
2257
+
2258
+ # The fragment name. Equivalent to QNAME (query template name) in SAM.
2259
+ # Corresponds to the JSON property `fragmentName`
2260
+ # @return [String]
2261
+ attr_accessor :fragment_name
2262
+
2494
2263
  # The ID of the read group set this read belongs to. A read belongs to
2495
2264
  # exactly one read group set.
2496
2265
  # Corresponds to the JSON property `readGroupSetId`
@@ -2509,6 +2278,14 @@ module Google
2509
2278
  # @return [Fixnum]
2510
2279
  attr_accessor :read_number
2511
2280
 
2281
+ # The ID of the read group this read belongs to. A read belongs to exactly
2282
+ # one read group. This is a server-generated ID which is distinct from SAM's
2283
+ # RG tag (for that value, see
2284
+ # ReadGroup.name).
2285
+ # Corresponds to the JSON property `readGroupId`
2286
+ # @return [String]
2287
+ attr_accessor :read_group_id
2288
+
2512
2289
  # The bases of the read sequence contained in this alignment record,
2513
2290
  # **without CIGAR operations applied** (equivalent to SEQ in SAM).
2514
2291
  # `alignedSequence` and `alignedQuality` may be
@@ -2520,14 +2297,6 @@ module Google
2520
2297
  # @return [String]
2521
2298
  attr_accessor :aligned_sequence
2522
2299
 
2523
- # The ID of the read group this read belongs to. A read belongs to exactly
2524
- # one read group. This is a server-generated ID which is distinct from SAM's
2525
- # RG tag (for that value, see
2526
- # ReadGroup.name).
2527
- # Corresponds to the JSON property `readGroupId`
2528
- # @return [String]
2529
- attr_accessor :read_group_id
2530
-
2531
2300
  # An abstraction for referring to a genomic position, in relation to some
2532
2301
  # already known reference. For now, represents a genomic position as a
2533
2302
  # reference name, a base number on that reference (0-based), and a
@@ -2588,50 +2357,22 @@ module Google
2588
2357
  # @return [Array<Fixnum>]
2589
2358
  attr_accessor :aligned_quality
2590
2359
 
2591
- # A linear alignment can be represented by one CIGAR string. Describes the
2592
- # mapped position and local alignment of the read to the reference.
2593
- # Corresponds to the JSON property `alignment`
2594
- # @return [Google::Apis::GenomicsV1::LinearAlignment]
2595
- attr_accessor :alignment
2596
-
2597
- # The number of reads in the fragment (extension to SAM flag 0x1).
2598
- # Corresponds to the JSON property `numberReads`
2599
- # @return [Fixnum]
2600
- attr_accessor :number_reads
2601
-
2602
- # The server-generated read ID, unique across all reads. This is different
2603
- # from the `fragmentName`.
2604
- # Corresponds to the JSON property `id`
2605
- # @return [String]
2606
- attr_accessor :id
2607
-
2608
- # Whether this alignment is secondary. Equivalent to SAM flag 0x100.
2609
- # A secondary alignment represents an alternative to the primary alignment
2610
- # for this read. Aligners may return secondary alignments if a read can map
2611
- # ambiguously to multiple coordinates in the genome. By convention, each read
2612
- # has one and only one alignment where both `secondaryAlignment`
2613
- # and `supplementaryAlignment` are false.
2614
- # Corresponds to the JSON property `secondaryAlignment`
2615
- # @return [Boolean]
2616
- attr_accessor :secondary_alignment
2617
- alias_method :secondary_alignment?, :secondary_alignment
2618
-
2619
- # The fragment name. Equivalent to QNAME (query template name) in SAM.
2620
- # Corresponds to the JSON property `fragmentName`
2621
- # @return [String]
2622
- attr_accessor :fragment_name
2623
-
2624
2360
  def initialize(**args)
2625
2361
  update!(**args)
2626
2362
  end
2627
2363
 
2628
2364
  # Update properties of this object
2629
2365
  def update!(**args)
2366
+ @alignment = args[:alignment] if args.key?(:alignment)
2367
+ @id = args[:id] if args.key?(:id)
2368
+ @number_reads = args[:number_reads] if args.key?(:number_reads)
2369
+ @secondary_alignment = args[:secondary_alignment] if args.key?(:secondary_alignment)
2370
+ @fragment_name = args[:fragment_name] if args.key?(:fragment_name)
2630
2371
  @read_group_set_id = args[:read_group_set_id] if args.key?(:read_group_set_id)
2631
2372
  @duplicate_fragment = args[:duplicate_fragment] if args.key?(:duplicate_fragment)
2632
2373
  @read_number = args[:read_number] if args.key?(:read_number)
2633
- @aligned_sequence = args[:aligned_sequence] if args.key?(:aligned_sequence)
2634
2374
  @read_group_id = args[:read_group_id] if args.key?(:read_group_id)
2375
+ @aligned_sequence = args[:aligned_sequence] if args.key?(:aligned_sequence)
2635
2376
  @next_mate_position = args[:next_mate_position] if args.key?(:next_mate_position)
2636
2377
  @info = args[:info] if args.key?(:info)
2637
2378
  @proper_placement = args[:proper_placement] if args.key?(:proper_placement)
@@ -2639,73 +2380,29 @@ module Google
2639
2380
  @fragment_length = args[:fragment_length] if args.key?(:fragment_length)
2640
2381
  @failed_vendor_quality_checks = args[:failed_vendor_quality_checks] if args.key?(:failed_vendor_quality_checks)
2641
2382
  @aligned_quality = args[:aligned_quality] if args.key?(:aligned_quality)
2642
- @alignment = args[:alignment] if args.key?(:alignment)
2643
- @number_reads = args[:number_reads] if args.key?(:number_reads)
2644
- @id = args[:id] if args.key?(:id)
2645
- @secondary_alignment = args[:secondary_alignment] if args.key?(:secondary_alignment)
2646
- @fragment_name = args[:fragment_name] if args.key?(:fragment_name)
2647
2383
  end
2648
2384
  end
2649
2385
 
2650
- # A reference set is a set of references which typically comprise a reference
2651
- # assembly for a species, such as `GRCh38` which is representative
2652
- # of the human genome. A reference set defines a common coordinate space for
2653
- # comparing reference-aligned experimental data. A reference set contains 1 or
2654
- # more references.
2655
- # For more genomics resource definitions, see [Fundamentals of Google
2656
- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
2657
- class ReferenceSet
2386
+ #
2387
+ class BatchCreateAnnotationsRequest
2658
2388
  include Google::Apis::Core::Hashable
2659
2389
 
2660
- # The IDs of the reference objects that are part of this set.
2661
- # `Reference.md5checksum` must be unique within this set.
2662
- # Corresponds to the JSON property `referenceIds`
2663
- # @return [Array<String>]
2664
- attr_accessor :reference_ids
2665
-
2666
- # Order-independent MD5 checksum which identifies this reference set. The
2667
- # checksum is computed by sorting all lower case hexidecimal string
2668
- # `reference.md5checksum` (for all reference in this set) in
2669
- # ascending lexicographic order, concatenating, and taking the MD5 of that
2670
- # value. The resulting value is represented in lower case hexadecimal format.
2671
- # Corresponds to the JSON property `md5checksum`
2672
- # @return [String]
2673
- attr_accessor :md5checksum
2674
-
2675
- # Public id of this reference set, such as `GRCh37`.
2676
- # Corresponds to the JSON property `assemblyId`
2677
- # @return [String]
2678
- attr_accessor :assembly_id
2679
-
2680
- # The server-generated reference set ID, unique across all reference sets.
2681
- # Corresponds to the JSON property `id`
2682
- # @return [String]
2683
- attr_accessor :id
2684
-
2685
- # Free text description of this reference set.
2686
- # Corresponds to the JSON property `description`
2687
- # @return [String]
2688
- attr_accessor :description
2689
-
2690
- # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
2691
- # with a version number, for example `NC_000001.11`.
2692
- # Corresponds to the JSON property `sourceAccessions`
2693
- # @return [Array<String>]
2694
- attr_accessor :source_accessions
2695
-
2696
- # The URI from which the references were obtained.
2697
- # Corresponds to the JSON property `sourceUri`
2390
+ # A unique request ID which enables the server to detect duplicated requests.
2391
+ # If provided, duplicated requests will result in the same response; if not
2392
+ # provided, duplicated requests may result in duplicated data. For a given
2393
+ # annotation set, callers should not reuse `request_id`s when writing
2394
+ # different batches of annotations - behavior in this case is undefined.
2395
+ # A common approach is to use a UUID. For batch jobs where worker crashes are
2396
+ # a possibility, consider using some unique variant of a worker or run ID.
2397
+ # Corresponds to the JSON property `requestId`
2698
2398
  # @return [String]
2699
- attr_accessor :source_uri
2399
+ attr_accessor :request_id
2700
2400
 
2701
- # ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
2702
- # indicating the species which this reference set is intended to model. Note
2703
- # that contained references may specify a different `ncbiTaxonId`, as
2704
- # assemblies may contain reference sequences which do not belong to the
2705
- # modeled species, for example EBV in a human reference genome.
2706
- # Corresponds to the JSON property `ncbiTaxonId`
2707
- # @return [Fixnum]
2708
- attr_accessor :ncbi_taxon_id
2401
+ # The annotations to be created. At most 4096 can be specified in a single
2402
+ # request.
2403
+ # Corresponds to the JSON property `annotations`
2404
+ # @return [Array<Google::Apis::GenomicsV1::Annotation>]
2405
+ attr_accessor :annotations
2709
2406
 
2710
2407
  def initialize(**args)
2711
2408
  update!(**args)
@@ -2713,14 +2410,8 @@ module Google
2713
2410
 
2714
2411
  # Update properties of this object
2715
2412
  def update!(**args)
2716
- @reference_ids = args[:reference_ids] if args.key?(:reference_ids)
2717
- @md5checksum = args[:md5checksum] if args.key?(:md5checksum)
2718
- @assembly_id = args[:assembly_id] if args.key?(:assembly_id)
2719
- @id = args[:id] if args.key?(:id)
2720
- @description = args[:description] if args.key?(:description)
2721
- @source_accessions = args[:source_accessions] if args.key?(:source_accessions)
2722
- @source_uri = args[:source_uri] if args.key?(:source_uri)
2723
- @ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
2413
+ @request_id = args[:request_id] if args.key?(:request_id)
2414
+ @annotations = args[:annotations] if args.key?(:annotations)
2724
2415
  end
2725
2416
  end
2726
2417
 
@@ -2758,49 +2449,65 @@ module Google
2758
2449
  end
2759
2450
  end
2760
2451
 
2761
- # An annotation set is a logical grouping of annotations that share consistent
2762
- # type information and provenance. Examples of annotation sets include 'all
2763
- # genes from refseq', and 'all variant annotations from ClinVar'.
2764
- class AnnotationSet
2765
- include Google::Apis::Core::Hashable
2766
-
2767
- # The server-generated annotation set ID, unique across all annotation sets.
2768
- # Corresponds to the JSON property `id`
2769
- # @return [String]
2770
- attr_accessor :id
2771
-
2772
- # The dataset to which this annotation set belongs.
2773
- # Corresponds to the JSON property `datasetId`
2774
- # @return [String]
2775
- attr_accessor :dataset_id
2452
+ # A reference set is a set of references which typically comprise a reference
2453
+ # assembly for a species, such as `GRCh38` which is representative
2454
+ # of the human genome. A reference set defines a common coordinate space for
2455
+ # comparing reference-aligned experimental data. A reference set contains 1 or
2456
+ # more references.
2457
+ # For more genomics resource definitions, see [Fundamentals of Google
2458
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
2459
+ class ReferenceSet
2460
+ include Google::Apis::Core::Hashable
2776
2461
 
2777
- # The source URI describing the file from which this annotation set was
2778
- # generated, if any.
2462
+ # ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
2463
+ # indicating the species which this reference set is intended to model. Note
2464
+ # that contained references may specify a different `ncbiTaxonId`, as
2465
+ # assemblies may contain reference sequences which do not belong to the
2466
+ # modeled species, for example EBV in a human reference genome.
2467
+ # Corresponds to the JSON property `ncbiTaxonId`
2468
+ # @return [Fixnum]
2469
+ attr_accessor :ncbi_taxon_id
2470
+
2471
+ # The URI from which the references were obtained.
2779
2472
  # Corresponds to the JSON property `sourceUri`
2780
2473
  # @return [String]
2781
2474
  attr_accessor :source_uri
2782
2475
 
2783
- # The display name for this annotation set.
2784
- # Corresponds to the JSON property `name`
2476
+ # The IDs of the reference objects that are part of this set.
2477
+ # `Reference.md5checksum` must be unique within this set.
2478
+ # Corresponds to the JSON property `referenceIds`
2479
+ # @return [Array<String>]
2480
+ attr_accessor :reference_ids
2481
+
2482
+ # Order-independent MD5 checksum which identifies this reference set. The
2483
+ # checksum is computed by sorting all lower case hexidecimal string
2484
+ # `reference.md5checksum` (for all reference in this set) in
2485
+ # ascending lexicographic order, concatenating, and taking the MD5 of that
2486
+ # value. The resulting value is represented in lower case hexadecimal format.
2487
+ # Corresponds to the JSON property `md5checksum`
2785
2488
  # @return [String]
2786
- attr_accessor :name
2489
+ attr_accessor :md5checksum
2787
2490
 
2788
- # The ID of the reference set that defines the coordinate space for this
2789
- # set's annotations.
2790
- # Corresponds to the JSON property `referenceSetId`
2491
+ # Public id of this reference set, such as `GRCh37`.
2492
+ # Corresponds to the JSON property `assemblyId`
2791
2493
  # @return [String]
2792
- attr_accessor :reference_set_id
2494
+ attr_accessor :assembly_id
2793
2495
 
2794
- # A map of additional read alignment information. This must be of the form
2795
- # map<string, string[]> (string key mapping to a list of string values).
2796
- # Corresponds to the JSON property `info`
2797
- # @return [Hash<String,Array<Object>>]
2798
- attr_accessor :info
2496
+ # The server-generated reference set ID, unique across all reference sets.
2497
+ # Corresponds to the JSON property `id`
2498
+ # @return [String]
2499
+ attr_accessor :id
2799
2500
 
2800
- # The type of annotations contained within this set.
2801
- # Corresponds to the JSON property `type`
2501
+ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
2502
+ # with a version number, for example `NC_000001.11`.
2503
+ # Corresponds to the JSON property `sourceAccessions`
2504
+ # @return [Array<String>]
2505
+ attr_accessor :source_accessions
2506
+
2507
+ # Free text description of this reference set.
2508
+ # Corresponds to the JSON property `description`
2802
2509
  # @return [String]
2803
- attr_accessor :type
2510
+ attr_accessor :description
2804
2511
 
2805
2512
  def initialize(**args)
2806
2513
  update!(**args)
@@ -2808,13 +2515,14 @@ module Google
2808
2515
 
2809
2516
  # Update properties of this object
2810
2517
  def update!(**args)
2811
- @id = args[:id] if args.key?(:id)
2812
- @dataset_id = args[:dataset_id] if args.key?(:dataset_id)
2518
+ @ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
2813
2519
  @source_uri = args[:source_uri] if args.key?(:source_uri)
2814
- @name = args[:name] if args.key?(:name)
2815
- @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
2816
- @info = args[:info] if args.key?(:info)
2817
- @type = args[:type] if args.key?(:type)
2520
+ @reference_ids = args[:reference_ids] if args.key?(:reference_ids)
2521
+ @md5checksum = args[:md5checksum] if args.key?(:md5checksum)
2522
+ @assembly_id = args[:assembly_id] if args.key?(:assembly_id)
2523
+ @id = args[:id] if args.key?(:id)
2524
+ @source_accessions = args[:source_accessions] if args.key?(:source_accessions)
2525
+ @description = args[:description] if args.key?(:description)
2818
2526
  end
2819
2527
  end
2820
2528
 
@@ -2823,6 +2531,22 @@ module Google
2823
2531
  class Transcript
2824
2532
  include Google::Apis::Core::Hashable
2825
2533
 
2534
+ # The range of the coding sequence for this transcript, if any. To determine
2535
+ # the exact ranges of coding sequence, intersect this range with those of the
2536
+ # exons, if any. If there are any
2537
+ # exons, the
2538
+ # codingSequence must start
2539
+ # and end within them.
2540
+ # Note that in some cases, the reference genome will not exactly match the
2541
+ # observed mRNA transcript e.g. due to variance in the source genome from
2542
+ # reference. In these cases,
2543
+ # exon.frame will not necessarily
2544
+ # match the expected reference reading frame and coding exon reference bases
2545
+ # cannot necessarily be concatenated to produce the original transcript mRNA.
2546
+ # Corresponds to the JSON property `codingSequence`
2547
+ # @return [Google::Apis::GenomicsV1::CodingSequence]
2548
+ attr_accessor :coding_sequence
2549
+
2826
2550
  # The annotation ID of the gene from which this transcript is transcribed.
2827
2551
  # Corresponds to the JSON property `geneId`
2828
2552
  # @return [String]
@@ -2843,49 +2567,81 @@ module Google
2843
2567
  # @return [Array<Google::Apis::GenomicsV1::Exon>]
2844
2568
  attr_accessor :exons
2845
2569
 
2846
- # The range of the coding sequence for this transcript, if any. To determine
2847
- # the exact ranges of coding sequence, intersect this range with those of the
2848
- # exons, if any. If there are any
2849
- # exons, the
2850
- # codingSequence must start
2851
- # and end within them.
2852
- # Note that in some cases, the reference genome will not exactly match the
2853
- # observed mRNA transcript e.g. due to variance in the source genome from
2854
- # reference. In these cases,
2855
- # exon.frame will not necessarily
2856
- # match the expected reference reading frame and coding exon reference bases
2857
- # cannot necessarily be concatenated to produce the original transcript mRNA.
2858
- # Corresponds to the JSON property `codingSequence`
2859
- # @return [Google::Apis::GenomicsV1::CodingSequence]
2860
- attr_accessor :coding_sequence
2861
-
2862
2570
  def initialize(**args)
2863
2571
  update!(**args)
2864
2572
  end
2865
2573
 
2866
2574
  # Update properties of this object
2867
2575
  def update!(**args)
2576
+ @coding_sequence = args[:coding_sequence] if args.key?(:coding_sequence)
2868
2577
  @gene_id = args[:gene_id] if args.key?(:gene_id)
2869
2578
  @exons = args[:exons] if args.key?(:exons)
2870
- @coding_sequence = args[:coding_sequence] if args.key?(:coding_sequence)
2871
2579
  end
2872
2580
  end
2873
2581
 
2874
- #
2875
- class Experiment
2582
+ # An annotation set is a logical grouping of annotations that share consistent
2583
+ # type information and provenance. Examples of annotation sets include 'all
2584
+ # genes from refseq', and 'all variant annotations from ClinVar'.
2585
+ class AnnotationSet
2876
2586
  include Google::Apis::Core::Hashable
2877
2587
 
2878
- # The sequencing center used as part of this experiment.
2879
- # Corresponds to the JSON property `sequencingCenter`
2588
+ # The source URI describing the file from which this annotation set was
2589
+ # generated, if any.
2590
+ # Corresponds to the JSON property `sourceUri`
2880
2591
  # @return [String]
2881
- attr_accessor :sequencing_center
2592
+ attr_accessor :source_uri
2882
2593
 
2883
- # The platform unit used as part of this experiment, for example
2884
- # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
2885
- # @RG PU field in the SAM spec.
2886
- # Corresponds to the JSON property `platformUnit`
2594
+ # The dataset to which this annotation set belongs.
2595
+ # Corresponds to the JSON property `datasetId`
2887
2596
  # @return [String]
2888
- attr_accessor :platform_unit
2597
+ attr_accessor :dataset_id
2598
+
2599
+ # The display name for this annotation set.
2600
+ # Corresponds to the JSON property `name`
2601
+ # @return [String]
2602
+ attr_accessor :name
2603
+
2604
+ # The ID of the reference set that defines the coordinate space for this
2605
+ # set's annotations.
2606
+ # Corresponds to the JSON property `referenceSetId`
2607
+ # @return [String]
2608
+ attr_accessor :reference_set_id
2609
+
2610
+ # A map of additional read alignment information. This must be of the form
2611
+ # map<string, string[]> (string key mapping to a list of string values).
2612
+ # Corresponds to the JSON property `info`
2613
+ # @return [Hash<String,Array<Object>>]
2614
+ attr_accessor :info
2615
+
2616
+ # The type of annotations contained within this set.
2617
+ # Corresponds to the JSON property `type`
2618
+ # @return [String]
2619
+ attr_accessor :type
2620
+
2621
+ # The server-generated annotation set ID, unique across all annotation sets.
2622
+ # Corresponds to the JSON property `id`
2623
+ # @return [String]
2624
+ attr_accessor :id
2625
+
2626
+ def initialize(**args)
2627
+ update!(**args)
2628
+ end
2629
+
2630
+ # Update properties of this object
2631
+ def update!(**args)
2632
+ @source_uri = args[:source_uri] if args.key?(:source_uri)
2633
+ @dataset_id = args[:dataset_id] if args.key?(:dataset_id)
2634
+ @name = args[:name] if args.key?(:name)
2635
+ @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
2636
+ @info = args[:info] if args.key?(:info)
2637
+ @type = args[:type] if args.key?(:type)
2638
+ @id = args[:id] if args.key?(:id)
2639
+ end
2640
+ end
2641
+
2642
+ #
2643
+ class Experiment
2644
+ include Google::Apis::Core::Hashable
2889
2645
 
2890
2646
  # A client-supplied library identifier; a library is a collection of DNA
2891
2647
  # fragments which have been prepared for sequencing from a sample. This
@@ -2901,16 +2657,28 @@ module Google
2901
2657
  # @return [String]
2902
2658
  attr_accessor :instrument_model
2903
2659
 
2660
+ # The sequencing center used as part of this experiment.
2661
+ # Corresponds to the JSON property `sequencingCenter`
2662
+ # @return [String]
2663
+ attr_accessor :sequencing_center
2664
+
2665
+ # The platform unit used as part of this experiment, for example
2666
+ # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
2667
+ # @RG PU field in the SAM spec.
2668
+ # Corresponds to the JSON property `platformUnit`
2669
+ # @return [String]
2670
+ attr_accessor :platform_unit
2671
+
2904
2672
  def initialize(**args)
2905
2673
  update!(**args)
2906
2674
  end
2907
2675
 
2908
2676
  # Update properties of this object
2909
2677
  def update!(**args)
2910
- @sequencing_center = args[:sequencing_center] if args.key?(:sequencing_center)
2911
- @platform_unit = args[:platform_unit] if args.key?(:platform_unit)
2912
2678
  @library_id = args[:library_id] if args.key?(:library_id)
2913
2679
  @instrument_model = args[:instrument_model] if args.key?(:instrument_model)
2680
+ @sequencing_center = args[:sequencing_center] if args.key?(:sequencing_center)
2681
+ @platform_unit = args[:platform_unit] if args.key?(:platform_unit)
2914
2682
  end
2915
2683
  end
2916
2684
 
@@ -3058,6 +2826,16 @@ module Google
3058
2826
  class CallSet
3059
2827
  include Google::Apis::Core::Hashable
3060
2828
 
2829
+ # The date this call set was created in milliseconds from the epoch.
2830
+ # Corresponds to the JSON property `created`
2831
+ # @return [String]
2832
+ attr_accessor :created
2833
+
2834
+ # The sample ID this call set corresponds to.
2835
+ # Corresponds to the JSON property `sampleId`
2836
+ # @return [String]
2837
+ attr_accessor :sample_id
2838
+
3061
2839
  # The call set name.
3062
2840
  # Corresponds to the JSON property `name`
3063
2841
  # @return [String]
@@ -3084,28 +2862,18 @@ module Google
3084
2862
  # @return [String]
3085
2863
  attr_accessor :id
3086
2864
 
3087
- # The date this call set was created in milliseconds from the epoch.
3088
- # Corresponds to the JSON property `created`
3089
- # @return [String]
3090
- attr_accessor :created
3091
-
3092
- # The sample ID this call set corresponds to.
3093
- # Corresponds to the JSON property `sampleId`
3094
- # @return [String]
3095
- attr_accessor :sample_id
3096
-
3097
2865
  def initialize(**args)
3098
2866
  update!(**args)
3099
2867
  end
3100
2868
 
3101
2869
  # Update properties of this object
3102
2870
  def update!(**args)
2871
+ @created = args[:created] if args.key?(:created)
2872
+ @sample_id = args[:sample_id] if args.key?(:sample_id)
3103
2873
  @name = args[:name] if args.key?(:name)
3104
2874
  @info = args[:info] if args.key?(:info)
3105
2875
  @variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
3106
2876
  @id = args[:id] if args.key?(:id)
3107
- @created = args[:created] if args.key?(:created)
3108
- @sample_id = args[:sample_id] if args.key?(:sample_id)
3109
2877
  end
3110
2878
  end
3111
2879
 
@@ -3113,11 +2881,6 @@ module Google
3113
2881
  class SearchAnnotationSetsResponse
3114
2882
  include Google::Apis::Core::Hashable
3115
2883
 
3116
- # The matching annotation sets.
3117
- # Corresponds to the JSON property `annotationSets`
3118
- # @return [Array<Google::Apis::GenomicsV1::AnnotationSet>]
3119
- attr_accessor :annotation_sets
3120
-
3121
2884
  # The continuation token, which is used to page through large result sets.
3122
2885
  # Provide this value in a subsequent request to return the next page of
3123
2886
  # results. This field will be empty if there aren't any additional results.
@@ -3125,14 +2888,19 @@ module Google
3125
2888
  # @return [String]
3126
2889
  attr_accessor :next_page_token
3127
2890
 
2891
+ # The matching annotation sets.
2892
+ # Corresponds to the JSON property `annotationSets`
2893
+ # @return [Array<Google::Apis::GenomicsV1::AnnotationSet>]
2894
+ attr_accessor :annotation_sets
2895
+
3128
2896
  def initialize(**args)
3129
2897
  update!(**args)
3130
2898
  end
3131
2899
 
3132
2900
  # Update properties of this object
3133
2901
  def update!(**args)
3134
- @annotation_sets = args[:annotation_sets] if args.key?(:annotation_sets)
3135
2902
  @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
2903
+ @annotation_sets = args[:annotation_sets] if args.key?(:annotation_sets)
3136
2904
  end
3137
2905
  end
3138
2906
 
@@ -3140,6 +2908,19 @@ module Google
3140
2908
  class ImportVariantsRequest
3141
2909
  include Google::Apis::Core::Hashable
3142
2910
 
2911
+ # Convert reference names to the canonical representation.
2912
+ # hg19 haploytypes (those reference names containing "_hap")
2913
+ # are not modified in any way.
2914
+ # All other reference names are modified according to the following rules:
2915
+ # The reference name is capitalized.
2916
+ # The "chr" prefix is dropped for all autosomes and sex chromsomes.
2917
+ # For example "chr17" becomes "17" and "chrX" becomes "X".
2918
+ # All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
2919
+ # Corresponds to the JSON property `normalizeReferenceNames`
2920
+ # @return [Boolean]
2921
+ attr_accessor :normalize_reference_names
2922
+ alias_method :normalize_reference_names?, :normalize_reference_names
2923
+
3143
2924
  # The format of the variant data being imported. If unspecified, defaults to
3144
2925
  # to `VCF`.
3145
2926
  # Corresponds to the JSON property `format`
@@ -3166,30 +2947,56 @@ module Google
3166
2947
  # @return [Array<String>]
3167
2948
  attr_accessor :source_uris
3168
2949
 
3169
- # Convert reference names to the canonical representation.
3170
- # hg19 haploytypes (those reference names containing "_hap")
3171
- # are not modified in any way.
3172
- # All other reference names are modified according to the following rules:
3173
- # The reference name is capitalized.
3174
- # The "chr" prefix is dropped for all autosomes and sex chromsomes.
3175
- # For example "chr17" becomes "17" and "chrX" becomes "X".
3176
- # All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
3177
- # Corresponds to the JSON property `normalizeReferenceNames`
3178
- # @return [Boolean]
3179
- attr_accessor :normalize_reference_names
3180
- alias_method :normalize_reference_names?, :normalize_reference_names
3181
-
3182
2950
  def initialize(**args)
3183
2951
  update!(**args)
3184
2952
  end
3185
2953
 
3186
2954
  # Update properties of this object
3187
2955
  def update!(**args)
2956
+ @normalize_reference_names = args[:normalize_reference_names] if args.key?(:normalize_reference_names)
3188
2957
  @format = args[:format] if args.key?(:format)
3189
2958
  @info_merge_config = args[:info_merge_config] if args.key?(:info_merge_config)
3190
2959
  @variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
3191
2960
  @source_uris = args[:source_uris] if args.key?(:source_uris)
3192
- @normalize_reference_names = args[:normalize_reference_names] if args.key?(:normalize_reference_names)
2961
+ end
2962
+ end
2963
+
2964
+ #
2965
+ class ListCoverageBucketsResponse
2966
+ include Google::Apis::Core::Hashable
2967
+
2968
+ # The continuation token, which is used to page through large result sets.
2969
+ # Provide this value in a subsequent request to return the next page of
2970
+ # results. This field will be empty if there aren't any additional results.
2971
+ # Corresponds to the JSON property `nextPageToken`
2972
+ # @return [String]
2973
+ attr_accessor :next_page_token
2974
+
2975
+ # The length of each coverage bucket in base pairs. Note that buckets at the
2976
+ # end of a reference sequence may be shorter. This value is omitted if the
2977
+ # bucket width is infinity (the default behaviour, with no range or
2978
+ # `targetBucketWidth`).
2979
+ # Corresponds to the JSON property `bucketWidth`
2980
+ # @return [String]
2981
+ attr_accessor :bucket_width
2982
+
2983
+ # The coverage buckets. The list of buckets is sparse; a bucket with 0
2984
+ # overlapping reads is not returned. A bucket never crosses more than one
2985
+ # reference sequence. Each bucket has width `bucketWidth`, unless
2986
+ # its end is the end of the reference sequence.
2987
+ # Corresponds to the JSON property `coverageBuckets`
2988
+ # @return [Array<Google::Apis::GenomicsV1::CoverageBucket>]
2989
+ attr_accessor :coverage_buckets
2990
+
2991
+ def initialize(**args)
2992
+ update!(**args)
2993
+ end
2994
+
2995
+ # Update properties of this object
2996
+ def update!(**args)
2997
+ @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
2998
+ @bucket_width = args[:bucket_width] if args.key?(:bucket_width)
2999
+ @coverage_buckets = args[:coverage_buckets] if args.key?(:coverage_buckets)
3193
3000
  end
3194
3001
  end
3195
3002
 
@@ -3256,45 +3063,6 @@ module Google
3256
3063
  end
3257
3064
  end
3258
3065
 
3259
- #
3260
- class ListCoverageBucketsResponse
3261
- include Google::Apis::Core::Hashable
3262
-
3263
- # The continuation token, which is used to page through large result sets.
3264
- # Provide this value in a subsequent request to return the next page of
3265
- # results. This field will be empty if there aren't any additional results.
3266
- # Corresponds to the JSON property `nextPageToken`
3267
- # @return [String]
3268
- attr_accessor :next_page_token
3269
-
3270
- # The length of each coverage bucket in base pairs. Note that buckets at the
3271
- # end of a reference sequence may be shorter. This value is omitted if the
3272
- # bucket width is infinity (the default behaviour, with no range or
3273
- # `targetBucketWidth`).
3274
- # Corresponds to the JSON property `bucketWidth`
3275
- # @return [String]
3276
- attr_accessor :bucket_width
3277
-
3278
- # The coverage buckets. The list of buckets is sparse; a bucket with 0
3279
- # overlapping reads is not returned. A bucket never crosses more than one
3280
- # reference sequence. Each bucket has width `bucketWidth`, unless
3281
- # its end is the end of the reference sequence.
3282
- # Corresponds to the JSON property `coverageBuckets`
3283
- # @return [Array<Google::Apis::GenomicsV1::CoverageBucket>]
3284
- attr_accessor :coverage_buckets
3285
-
3286
- def initialize(**args)
3287
- update!(**args)
3288
- end
3289
-
3290
- # Update properties of this object
3291
- def update!(**args)
3292
- @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
3293
- @bucket_width = args[:bucket_width] if args.key?(:bucket_width)
3294
- @coverage_buckets = args[:coverage_buckets] if args.key?(:coverage_buckets)
3295
- end
3296
- end
3297
-
3298
3066
  # The variant data export request.
3299
3067
  class ExportVariantSetRequest
3300
3068
  include Google::Apis::Core::Hashable
@@ -3348,6 +3116,28 @@ module Google
3348
3116
  class SearchAnnotationsRequest
3349
3117
  include Google::Apis::Core::Hashable
3350
3118
 
3119
+ # The start position of the range on the reference, 0-based inclusive. If
3120
+ # specified,
3121
+ # referenceId or
3122
+ # referenceName
3123
+ # must be specified. Defaults to 0.
3124
+ # Corresponds to the JSON property `start`
3125
+ # @return [String]
3126
+ attr_accessor :start
3127
+
3128
+ # Required. The annotation sets to search within. The caller must have
3129
+ # `READ` access to these annotation sets.
3130
+ # All queried annotation sets must have the same type.
3131
+ # Corresponds to the JSON property `annotationSetIds`
3132
+ # @return [Array<String>]
3133
+ attr_accessor :annotation_set_ids
3134
+
3135
+ # The name of the reference to query, within the reference set associated
3136
+ # with this query.
3137
+ # Corresponds to the JSON property `referenceName`
3138
+ # @return [String]
3139
+ attr_accessor :reference_name
3140
+
3351
3141
  # The ID of the reference to query.
3352
3142
  # Corresponds to the JSON property `referenceId`
3353
3143
  # @return [String]
@@ -3374,41 +3164,19 @@ module Google
3374
3164
  # @return [Fixnum]
3375
3165
  attr_accessor :page_size
3376
3166
 
3377
- # The start position of the range on the reference, 0-based inclusive. If
3378
- # specified,
3379
- # referenceId or
3380
- # referenceName
3381
- # must be specified. Defaults to 0.
3382
- # Corresponds to the JSON property `start`
3383
- # @return [String]
3384
- attr_accessor :start
3385
-
3386
- # Required. The annotation sets to search within. The caller must have
3387
- # `READ` access to these annotation sets.
3388
- # All queried annotation sets must have the same type.
3389
- # Corresponds to the JSON property `annotationSetIds`
3390
- # @return [Array<String>]
3391
- attr_accessor :annotation_set_ids
3392
-
3393
- # The name of the reference to query, within the reference set associated
3394
- # with this query.
3395
- # Corresponds to the JSON property `referenceName`
3396
- # @return [String]
3397
- attr_accessor :reference_name
3398
-
3399
3167
  def initialize(**args)
3400
3168
  update!(**args)
3401
3169
  end
3402
3170
 
3403
3171
  # Update properties of this object
3404
3172
  def update!(**args)
3173
+ @start = args[:start] if args.key?(:start)
3174
+ @annotation_set_ids = args[:annotation_set_ids] if args.key?(:annotation_set_ids)
3175
+ @reference_name = args[:reference_name] if args.key?(:reference_name)
3405
3176
  @reference_id = args[:reference_id] if args.key?(:reference_id)
3406
3177
  @end = args[:end] if args.key?(:end)
3407
3178
  @page_token = args[:page_token] if args.key?(:page_token)
3408
3179
  @page_size = args[:page_size] if args.key?(:page_size)
3409
- @start = args[:start] if args.key?(:start)
3410
- @annotation_set_ids = args[:annotation_set_ids] if args.key?(:annotation_set_ids)
3411
- @reference_name = args[:reference_name] if args.key?(:reference_name)
3412
3180
  end
3413
3181
  end
3414
3182
 
@@ -3416,6 +3184,12 @@ module Google
3416
3184
  class OperationEvent
3417
3185
  include Google::Apis::Core::Hashable
3418
3186
 
3187
+ # Optional time of when event finished. An event can have a start time and no
3188
+ # finish time. If an event has a finish time, there must be a start time.
3189
+ # Corresponds to the JSON property `endTime`
3190
+ # @return [String]
3191
+ attr_accessor :end_time
3192
+
3419
3193
  # Optional time of when event started.
3420
3194
  # Corresponds to the JSON property `startTime`
3421
3195
  # @return [String]
@@ -3426,21 +3200,15 @@ module Google
3426
3200
  # @return [String]
3427
3201
  attr_accessor :description
3428
3202
 
3429
- # Optional time of when event finished. An event can have a start time and no
3430
- # finish time. If an event has a finish time, there must be a start time.
3431
- # Corresponds to the JSON property `endTime`
3432
- # @return [String]
3433
- attr_accessor :end_time
3434
-
3435
3203
  def initialize(**args)
3436
3204
  update!(**args)
3437
3205
  end
3438
3206
 
3439
3207
  # Update properties of this object
3440
3208
  def update!(**args)
3209
+ @end_time = args[:end_time] if args.key?(:end_time)
3441
3210
  @start_time = args[:start_time] if args.key?(:start_time)
3442
3211
  @description = args[:description] if args.key?(:description)
3443
- @end_time = args[:end_time] if args.key?(:end_time)
3444
3212
  end
3445
3213
  end
3446
3214
 
@@ -3472,6 +3240,238 @@ module Google
3472
3240
  @end = args[:end] if args.key?(:end)
3473
3241
  end
3474
3242
  end
3243
+
3244
+ # Request message for `GetIamPolicy` method.
3245
+ class GetIamPolicyRequest
3246
+ include Google::Apis::Core::Hashable
3247
+
3248
+ def initialize(**args)
3249
+ update!(**args)
3250
+ end
3251
+
3252
+ # Update properties of this object
3253
+ def update!(**args)
3254
+ end
3255
+ end
3256
+
3257
+ # Response message for `TestIamPermissions` method.
3258
+ class TestIamPermissionsResponse
3259
+ include Google::Apis::Core::Hashable
3260
+
3261
+ # A subset of `TestPermissionsRequest.permissions` that the caller is
3262
+ # allowed.
3263
+ # Corresponds to the JSON property `permissions`
3264
+ # @return [Array<String>]
3265
+ attr_accessor :permissions
3266
+
3267
+ def initialize(**args)
3268
+ update!(**args)
3269
+ end
3270
+
3271
+ # Update properties of this object
3272
+ def update!(**args)
3273
+ @permissions = args[:permissions] if args.key?(:permissions)
3274
+ end
3275
+ end
3276
+
3277
+ #
3278
+ class SearchReferencesResponse
3279
+ include Google::Apis::Core::Hashable
3280
+
3281
+ # The matching references.
3282
+ # Corresponds to the JSON property `references`
3283
+ # @return [Array<Google::Apis::GenomicsV1::Reference>]
3284
+ attr_accessor :references
3285
+
3286
+ # The continuation token, which is used to page through large result sets.
3287
+ # Provide this value in a subsequent request to return the next page of
3288
+ # results. This field will be empty if there aren't any additional results.
3289
+ # Corresponds to the JSON property `nextPageToken`
3290
+ # @return [String]
3291
+ attr_accessor :next_page_token
3292
+
3293
+ def initialize(**args)
3294
+ update!(**args)
3295
+ end
3296
+
3297
+ # Update properties of this object
3298
+ def update!(**args)
3299
+ @references = args[:references] if args.key?(:references)
3300
+ @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
3301
+ end
3302
+ end
3303
+
3304
+ #
3305
+ class SearchAnnotationSetsRequest
3306
+ include Google::Apis::Core::Hashable
3307
+
3308
+ # The continuation token, which is used to page through large result sets.
3309
+ # To get the next page of results, set this parameter to the value of
3310
+ # `nextPageToken` from the previous response.
3311
+ # Corresponds to the JSON property `pageToken`
3312
+ # @return [String]
3313
+ attr_accessor :page_token
3314
+
3315
+ # The maximum number of results to return in a single page. If unspecified,
3316
+ # defaults to 128. The maximum value is 1024.
3317
+ # Corresponds to the JSON property `pageSize`
3318
+ # @return [Fixnum]
3319
+ attr_accessor :page_size
3320
+
3321
+ # Required. The dataset IDs to search within. Caller must have `READ` access
3322
+ # to these datasets.
3323
+ # Corresponds to the JSON property `datasetIds`
3324
+ # @return [Array<String>]
3325
+ attr_accessor :dataset_ids
3326
+
3327
+ # If specified, only annotation sets that have any of these types are
3328
+ # returned.
3329
+ # Corresponds to the JSON property `types`
3330
+ # @return [Array<String>]
3331
+ attr_accessor :types
3332
+
3333
+ # Only return annotations sets for which a substring of the name matches this
3334
+ # string (case insensitive).
3335
+ # Corresponds to the JSON property `name`
3336
+ # @return [String]
3337
+ attr_accessor :name
3338
+
3339
+ # If specified, only annotation sets associated with the given reference set
3340
+ # are returned.
3341
+ # Corresponds to the JSON property `referenceSetId`
3342
+ # @return [String]
3343
+ attr_accessor :reference_set_id
3344
+
3345
+ def initialize(**args)
3346
+ update!(**args)
3347
+ end
3348
+
3349
+ # Update properties of this object
3350
+ def update!(**args)
3351
+ @page_token = args[:page_token] if args.key?(:page_token)
3352
+ @page_size = args[:page_size] if args.key?(:page_size)
3353
+ @dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
3354
+ @types = args[:types] if args.key?(:types)
3355
+ @name = args[:name] if args.key?(:name)
3356
+ @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
3357
+ end
3358
+ end
3359
+
3360
+ # The read group set search response.
3361
+ class SearchReadGroupSetsResponse
3362
+ include Google::Apis::Core::Hashable
3363
+
3364
+ # The continuation token, which is used to page through large result sets.
3365
+ # Provide this value in a subsequent request to return the next page of
3366
+ # results. This field will be empty if there aren't any additional results.
3367
+ # Corresponds to the JSON property `nextPageToken`
3368
+ # @return [String]
3369
+ attr_accessor :next_page_token
3370
+
3371
+ # The list of matching read group sets.
3372
+ # Corresponds to the JSON property `readGroupSets`
3373
+ # @return [Array<Google::Apis::GenomicsV1::ReadGroupSet>]
3374
+ attr_accessor :read_group_sets
3375
+
3376
+ def initialize(**args)
3377
+ update!(**args)
3378
+ end
3379
+
3380
+ # Update properties of this object
3381
+ def update!(**args)
3382
+ @next_page_token = args[:next_page_token] if args.key?(:next_page_token)
3383
+ @read_group_sets = args[:read_group_sets] if args.key?(:read_group_sets)
3384
+ end
3385
+ end
3386
+
3387
+ # A linear alignment can be represented by one CIGAR string. Describes the
3388
+ # mapped position and local alignment of the read to the reference.
3389
+ class LinearAlignment
3390
+ include Google::Apis::Core::Hashable
3391
+
3392
+ # An abstraction for referring to a genomic position, in relation to some
3393
+ # already known reference. For now, represents a genomic position as a
3394
+ # reference name, a base number on that reference (0-based), and a
3395
+ # determination of forward or reverse strand.
3396
+ # Corresponds to the JSON property `position`
3397
+ # @return [Google::Apis::GenomicsV1::Position]
3398
+ attr_accessor :position
3399
+
3400
+ # Represents the local alignment of this sequence (alignment matches, indels,
3401
+ # etc) against the reference.
3402
+ # Corresponds to the JSON property `cigar`
3403
+ # @return [Array<Google::Apis::GenomicsV1::CigarUnit>]
3404
+ attr_accessor :cigar
3405
+
3406
+ # The mapping quality of this alignment. Represents how likely
3407
+ # the read maps to this position as opposed to other locations.
3408
+ # Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
3409
+ # the nearest integer.
3410
+ # Corresponds to the JSON property `mappingQuality`
3411
+ # @return [Fixnum]
3412
+ attr_accessor :mapping_quality
3413
+
3414
+ def initialize(**args)
3415
+ update!(**args)
3416
+ end
3417
+
3418
+ # Update properties of this object
3419
+ def update!(**args)
3420
+ @position = args[:position] if args.key?(:position)
3421
+ @cigar = args[:cigar] if args.key?(:cigar)
3422
+ @mapping_quality = args[:mapping_quality] if args.key?(:mapping_quality)
3423
+ end
3424
+ end
3425
+
3426
+ #
3427
+ class SearchReferencesRequest
3428
+ include Google::Apis::Core::Hashable
3429
+
3430
+ # If present, return references for which a prefix of any of
3431
+ # sourceAccessions match
3432
+ # any of these strings. Accession numbers typically have a main number and a
3433
+ # version, for example `GCF_000001405.26`.
3434
+ # Corresponds to the JSON property `accessions`
3435
+ # @return [Array<String>]
3436
+ attr_accessor :accessions
3437
+
3438
+ # The continuation token, which is used to page through large result sets.
3439
+ # To get the next page of results, set this parameter to the value of
3440
+ # `nextPageToken` from the previous response.
3441
+ # Corresponds to the JSON property `pageToken`
3442
+ # @return [String]
3443
+ attr_accessor :page_token
3444
+
3445
+ # If present, return only references which belong to this reference set.
3446
+ # Corresponds to the JSON property `referenceSetId`
3447
+ # @return [String]
3448
+ attr_accessor :reference_set_id
3449
+
3450
+ # The maximum number of results to return in a single page. If unspecified,
3451
+ # defaults to 1024. The maximum value is 4096.
3452
+ # Corresponds to the JSON property `pageSize`
3453
+ # @return [Fixnum]
3454
+ attr_accessor :page_size
3455
+
3456
+ # If present, return references for which the
3457
+ # md5checksum matches exactly.
3458
+ # Corresponds to the JSON property `md5checksums`
3459
+ # @return [Array<String>]
3460
+ attr_accessor :md5checksums
3461
+
3462
+ def initialize(**args)
3463
+ update!(**args)
3464
+ end
3465
+
3466
+ # Update properties of this object
3467
+ def update!(**args)
3468
+ @accessions = args[:accessions] if args.key?(:accessions)
3469
+ @page_token = args[:page_token] if args.key?(:page_token)
3470
+ @reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
3471
+ @page_size = args[:page_size] if args.key?(:page_size)
3472
+ @md5checksums = args[:md5checksums] if args.key?(:md5checksums)
3473
+ end
3474
+ end
3475
3475
  end
3476
3476
  end
3477
3477
  end