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
@@ -46,14 +46,18 @@ module Google
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  super('https://genomics.googleapis.com/', '')
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  end
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- # Searches for reference sets which match the given criteria.
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- # For the definitions of references and other genomics resources, see
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- # [Fundamentals of Google
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- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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- # Implements
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- # [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/
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- # v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
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- # @param [Google::Apis::GenomicsV1::SearchReferenceSetsRequest] search_reference_sets_request_object
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+ # Updates an annotation set. The update must respect all mutability
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+ # restrictions and other invariants described on the annotation set resource.
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+ # Caller must have WRITE permission for the associated dataset.
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+ # @param [String] annotation_set_id
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+ # The ID of the annotation set to be updated.
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+ # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object
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+ # @param [String] update_mask
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+ # An optional mask specifying which fields to update. Mutable fields are
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+ # name,
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+ # source_uri, and
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+ # info. If unspecified, all
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+ # mutable fields will be updated.
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  # @param [String] fields
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  # Selector specifying which fields to include in a partial response.
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  # @param [String] quota_user
@@ -63,34 +67,35 @@ module Google
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  # Request-specific options
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  #
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  # @yield [result, err] Result & error if block supplied
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- # @yieldparam result [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] parsed result object
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+ # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
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  # @yieldparam err [StandardError] error object if request failed
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  #
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- # @return [Google::Apis::GenomicsV1::SearchReferenceSetsResponse]
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+ # @return [Google::Apis::GenomicsV1::AnnotationSet]
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  #
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  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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  # @raise [Google::Apis::AuthorizationError] Authorization is required
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- def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
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- command = make_simple_command(:post, 'v1/referencesets/search', options)
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- command.request_representation = Google::Apis::GenomicsV1::SearchReferenceSetsRequest::Representation
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- command.request_object = search_reference_sets_request_object
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- command.response_representation = Google::Apis::GenomicsV1::SearchReferenceSetsResponse::Representation
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- command.response_class = Google::Apis::GenomicsV1::SearchReferenceSetsResponse
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+ def update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
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+ command = make_simple_command(:put, 'v1/annotationsets/{annotationSetId}', options)
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+ command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
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+ command.request_object = annotation_set_object
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+ command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
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+ command.response_class = Google::Apis::GenomicsV1::AnnotationSet
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+ command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
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+ command.query['updateMask'] = update_mask unless update_mask.nil?
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  command.query['fields'] = fields unless fields.nil?
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  command.query['quotaUser'] = quota_user unless quota_user.nil?
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  execute_or_queue_command(command, &block)
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  end
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- # Gets a reference set.
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- # For the definitions of references and other genomics resources, see
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- # [Fundamentals of Google
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- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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- # Implements
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- # [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.
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- # 1/src/main/resources/avro/referencemethods.avdl#L83).
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- # @param [String] reference_set_id
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- # The ID of the reference set.
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+ # Creates a new annotation set. Caller must have WRITE permission for the
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+ # associated dataset.
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+ # The following fields are required:
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+ # * datasetId
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+ # * referenceSetId
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+ # All other fields may be optionally specified, unless documented as being
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+ # server-generated (for example, the `id` field).
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+ # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object
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  # @param [String] fields
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  # Selector specifying which fields to include in a partial response.
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  # @param [String] quota_user
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  # Request-specific options
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  #
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  # @yield [result, err] Result & error if block supplied
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- # @yieldparam result [Google::Apis::GenomicsV1::ReferenceSet] parsed result object
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+ # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
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  # @yieldparam err [StandardError] error object if request failed
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  #
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- # @return [Google::Apis::GenomicsV1::ReferenceSet]
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+ # @return [Google::Apis::GenomicsV1::AnnotationSet]
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  #
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  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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  # @raise [Google::Apis::AuthorizationError] Authorization is required
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- def get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil, &block)
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- command = make_simple_command(:get, 'v1/referencesets/{referenceSetId}', options)
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- command.response_representation = Google::Apis::GenomicsV1::ReferenceSet::Representation
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- command.response_class = Google::Apis::GenomicsV1::ReferenceSet
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- command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil?
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+ def create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
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+ command = make_simple_command(:post, 'v1/annotationsets', options)
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+ command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
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+ command.request_object = annotation_set_object
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+ command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
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+ command.response_class = Google::Apis::GenomicsV1::AnnotationSet
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  command.query['fields'] = fields unless fields.nil?
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  command.query['quotaUser'] = quota_user unless quota_user.nil?
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  execute_or_queue_command(command, &block)
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  end
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- # Creates a new call set.
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- # For the definitions of call sets and other genomics resources, see
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- # [Fundamentals of Google
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- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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- # @param [Google::Apis::GenomicsV1::CallSet] call_set_object
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+ # Deletes an annotation set. Caller must have WRITE permission
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+ # for the associated annotation set.
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+ # @param [String] annotation_set_id
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+ # The ID of the annotation set to be deleted.
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  # @param [String] fields
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  # Selector specifying which fields to include in a partial response.
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  # @param [String] quota_user
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  # Request-specific options
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  #
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  # @yield [result, err] Result & error if block supplied
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- # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
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+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
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  # @yieldparam err [StandardError] error object if request failed
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  #
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- # @return [Google::Apis::GenomicsV1::CallSet]
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+ # @return [Google::Apis::GenomicsV1::Empty]
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  #
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  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
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  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
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  # @raise [Google::Apis::AuthorizationError] Authorization is required
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- def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
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- command = make_simple_command(:post, 'v1/callsets', options)
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- command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
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- command.request_object = call_set_object
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- command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
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- command.response_class = Google::Apis::GenomicsV1::CallSet
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+ def delete_annotationset(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block)
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+ command = make_simple_command(:delete, 'v1/annotationsets/{annotationSetId}', options)
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+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
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+ command.response_class = Google::Apis::GenomicsV1::Empty
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+ command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
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  command.query['fields'] = fields unless fields.nil?
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  command.query['quotaUser'] = quota_user unless quota_user.nil?
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  execute_or_queue_command(command, &block)
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  end
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- # Deletes a call set.
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- # For the definitions of call sets and other genomics resources, see
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- # [Fundamentals of Google
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- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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- # @param [String] call_set_id
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- # The ID of the call set to be deleted.
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+ # Searches for annotation sets that match the given criteria. Annotation sets
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+ # are returned in an unspecified order. This order is consistent, such that
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+ # two queries for the same content (regardless of page size) yield annotation
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+ # sets in the same order across their respective streams of paginated
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+ # responses. Caller must have READ permission for the queried datasets.
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+ # @param [Google::Apis::GenomicsV1::SearchAnnotationSetsRequest] search_annotation_sets_request_object
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  # @param [String] fields
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  # Selector specifying which fields to include in a partial response.
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166
  # @param [String] quota_user
@@ -166,32 +170,29 @@ module Google
166
170
  # Request-specific options
167
171
  #
168
172
  # @yield [result, err] Result & error if block supplied
169
- # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
173
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse] parsed result object
170
174
  # @yieldparam err [StandardError] error object if request failed
171
175
  #
172
- # @return [Google::Apis::GenomicsV1::Empty]
176
+ # @return [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse]
173
177
  #
174
178
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
175
179
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
176
180
  # @raise [Google::Apis::AuthorizationError] Authorization is required
177
- def delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
178
- command = make_simple_command(:delete, 'v1/callsets/{callSetId}', options)
179
- command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
180
- command.response_class = Google::Apis::GenomicsV1::Empty
181
- command.params['callSetId'] = call_set_id unless call_set_id.nil?
181
+ def search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
182
+ command = make_simple_command(:post, 'v1/annotationsets/search', options)
183
+ command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsRequest::Representation
184
+ command.request_object = search_annotation_sets_request_object
185
+ command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse::Representation
186
+ command.response_class = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse
182
187
  command.query['fields'] = fields unless fields.nil?
183
188
  command.query['quotaUser'] = quota_user unless quota_user.nil?
184
189
  execute_or_queue_command(command, &block)
185
190
  end
186
191
 
187
- # Gets a list of call sets matching the criteria.
188
- # For the definitions of call sets and other genomics resources, see
189
- # [Fundamentals of Google
190
- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
191
- # Implements
192
- # [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.
193
- # 1/src/main/resources/avro/variantmethods.avdl#L178).
194
- # @param [Google::Apis::GenomicsV1::SearchCallSetsRequest] search_call_sets_request_object
192
+ # Gets an annotation set. Caller must have READ permission for
193
+ # the associated dataset.
194
+ # @param [String] annotation_set_id
195
+ # The ID of the annotation set to be retrieved.
195
196
  # @param [String] fields
196
197
  # Selector specifying which fields to include in a partial response.
197
198
  # @param [String] quota_user
@@ -201,38 +202,32 @@ module Google
201
202
  # Request-specific options
202
203
  #
203
204
  # @yield [result, err] Result & error if block supplied
204
- # @yieldparam result [Google::Apis::GenomicsV1::SearchCallSetsResponse] parsed result object
205
+ # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
205
206
  # @yieldparam err [StandardError] error object if request failed
206
207
  #
207
- # @return [Google::Apis::GenomicsV1::SearchCallSetsResponse]
208
+ # @return [Google::Apis::GenomicsV1::AnnotationSet]
208
209
  #
209
210
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
210
211
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
211
212
  # @raise [Google::Apis::AuthorizationError] Authorization is required
212
- def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
213
- command = make_simple_command(:post, 'v1/callsets/search', options)
214
- command.request_representation = Google::Apis::GenomicsV1::SearchCallSetsRequest::Representation
215
- command.request_object = search_call_sets_request_object
216
- command.response_representation = Google::Apis::GenomicsV1::SearchCallSetsResponse::Representation
217
- command.response_class = Google::Apis::GenomicsV1::SearchCallSetsResponse
213
+ def get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block)
214
+ command = make_simple_command(:get, 'v1/annotationsets/{annotationSetId}', options)
215
+ command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
216
+ command.response_class = Google::Apis::GenomicsV1::AnnotationSet
217
+ command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
218
218
  command.query['fields'] = fields unless fields.nil?
219
219
  command.query['quotaUser'] = quota_user unless quota_user.nil?
220
220
  execute_or_queue_command(command, &block)
221
221
  end
222
222
 
223
- # Updates a call set.
224
- # For the definitions of call sets and other genomics resources, see
223
+ # Gets a list of variants matching the criteria.
224
+ # For the definitions of variants and other genomics resources, see
225
225
  # [Fundamentals of Google
226
226
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
227
- # This method supports patch semantics.
228
- # @param [String] call_set_id
229
- # The ID of the call set to be updated.
230
- # @param [Google::Apis::GenomicsV1::CallSet] call_set_object
231
- # @param [String] update_mask
232
- # An optional mask specifying which fields to update. At this time, the only
233
- # mutable field is name. The only
234
- # acceptable value is "name". If unspecified, all mutable fields will be
235
- # updated.
227
+ # Implements
228
+ # [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.
229
+ # 1/src/main/resources/avro/variantmethods.avdl#L126).
230
+ # @param [Google::Apis::GenomicsV1::SearchVariantsRequest] search_variants_request_object
236
231
  # @param [String] fields
237
232
  # Selector specifying which fields to include in a partial response.
238
233
  # @param [String] quota_user
@@ -242,33 +237,39 @@ module Google
242
237
  # Request-specific options
243
238
  #
244
239
  # @yield [result, err] Result & error if block supplied
245
- # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
240
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantsResponse] parsed result object
246
241
  # @yieldparam err [StandardError] error object if request failed
247
242
  #
248
- # @return [Google::Apis::GenomicsV1::CallSet]
243
+ # @return [Google::Apis::GenomicsV1::SearchVariantsResponse]
249
244
  #
250
245
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
251
246
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
252
247
  # @raise [Google::Apis::AuthorizationError] Authorization is required
253
- def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
254
- command = make_simple_command(:patch, 'v1/callsets/{callSetId}', options)
255
- command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
256
- command.request_object = call_set_object
257
- command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
258
- command.response_class = Google::Apis::GenomicsV1::CallSet
259
- command.params['callSetId'] = call_set_id unless call_set_id.nil?
260
- command.query['updateMask'] = update_mask unless update_mask.nil?
248
+ def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
249
+ command = make_simple_command(:post, 'v1/variants/search', options)
250
+ command.request_representation = Google::Apis::GenomicsV1::SearchVariantsRequest::Representation
251
+ command.request_object = search_variants_request_object
252
+ command.response_representation = Google::Apis::GenomicsV1::SearchVariantsResponse::Representation
253
+ command.response_class = Google::Apis::GenomicsV1::SearchVariantsResponse
261
254
  command.query['fields'] = fields unless fields.nil?
262
255
  command.query['quotaUser'] = quota_user unless quota_user.nil?
263
256
  execute_or_queue_command(command, &block)
264
257
  end
265
258
 
266
- # Gets a call set by ID.
267
- # For the definitions of call sets and other genomics resources, see
259
+ # Updates a variant.
260
+ # For the definitions of variants and other genomics resources, see
268
261
  # [Fundamentals of Google
269
262
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
270
- # @param [String] call_set_id
271
- # The ID of the call set.
263
+ # This method supports patch semantics. Returns the modified variant without
264
+ # its calls.
265
+ # @param [String] variant_id
266
+ # The ID of the variant to be updated.
267
+ # @param [Google::Apis::GenomicsV1::Variant] variant_object
268
+ # @param [String] update_mask
269
+ # An optional mask specifying which fields to update. At this time, mutable
270
+ # fields are names and
271
+ # info. Acceptable values are "names" and
272
+ # "info". If unspecified, all mutable fields will be updated.
272
273
  # @param [String] fields
273
274
  # Selector specifying which fields to include in a partial response.
274
275
  # @param [String] quota_user
@@ -278,45 +279,33 @@ module Google
278
279
  # Request-specific options
279
280
  #
280
281
  # @yield [result, err] Result & error if block supplied
281
- # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
282
+ # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
282
283
  # @yieldparam err [StandardError] error object if request failed
283
284
  #
284
- # @return [Google::Apis::GenomicsV1::CallSet]
285
+ # @return [Google::Apis::GenomicsV1::Variant]
285
286
  #
286
287
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
287
288
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
288
289
  # @raise [Google::Apis::AuthorizationError] Authorization is required
289
- def get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
290
- command = make_simple_command(:get, 'v1/callsets/{callSetId}', options)
291
- command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
292
- command.response_class = Google::Apis::GenomicsV1::CallSet
293
- command.params['callSetId'] = call_set_id unless call_set_id.nil?
290
+ def patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
291
+ command = make_simple_command(:patch, 'v1/variants/{variantId}', options)
292
+ command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
293
+ command.request_object = variant_object
294
+ command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
295
+ command.response_class = Google::Apis::GenomicsV1::Variant
296
+ command.params['variantId'] = variant_id unless variant_id.nil?
297
+ command.query['updateMask'] = update_mask unless update_mask.nil?
294
298
  command.query['fields'] = fields unless fields.nil?
295
299
  command.query['quotaUser'] = quota_user unless quota_user.nil?
296
300
  execute_or_queue_command(command, &block)
297
301
  end
298
302
 
299
- # Gets a list of reads for one or more read group sets.
300
- # For the definitions of read group sets and other genomics resources, see
303
+ # Gets a variant by ID.
304
+ # For the definitions of variants and other genomics resources, see
301
305
  # [Fundamentals of Google
302
306
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
303
- # Reads search operates over a genomic coordinate space of reference sequence
304
- # & position defined over the reference sequences to which the requested
305
- # read group sets are aligned.
306
- # If a target positional range is specified, search returns all reads whose
307
- # alignment to the reference genome overlap the range. A query which
308
- # specifies only read group set IDs yields all reads in those read group
309
- # sets, including unmapped reads.
310
- # All reads returned (including reads on subsequent pages) are ordered by
311
- # genomic coordinate (by reference sequence, then position). Reads with
312
- # equivalent genomic coordinates are returned in an unspecified order. This
313
- # order is consistent, such that two queries for the same content (regardless
314
- # of page size) yield reads in the same order across their respective streams
315
- # of paginated responses.
316
- # Implements
317
- # [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/
318
- # src/main/resources/avro/readmethods.avdl#L85).
319
- # @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_request_object
307
+ # @param [String] variant_id
308
+ # The ID of the variant.
320
309
  # @param [String] fields
321
310
  # Selector specifying which fields to include in a partial response.
322
311
  # @param [String] quota_user
@@ -326,37 +315,40 @@ module Google
326
315
  # Request-specific options
327
316
  #
328
317
  # @yield [result, err] Result & error if block supplied
329
- # @yieldparam result [Google::Apis::GenomicsV1::SearchReadsResponse] parsed result object
318
+ # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
330
319
  # @yieldparam err [StandardError] error object if request failed
331
320
  #
332
- # @return [Google::Apis::GenomicsV1::SearchReadsResponse]
321
+ # @return [Google::Apis::GenomicsV1::Variant]
333
322
  #
334
323
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
335
324
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
336
325
  # @raise [Google::Apis::AuthorizationError] Authorization is required
337
- def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
338
- command = make_simple_command(:post, 'v1/reads/search', options)
339
- command.request_representation = Google::Apis::GenomicsV1::SearchReadsRequest::Representation
340
- command.request_object = search_reads_request_object
341
- command.response_representation = Google::Apis::GenomicsV1::SearchReadsResponse::Representation
342
- command.response_class = Google::Apis::GenomicsV1::SearchReadsResponse
326
+ def get_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
327
+ command = make_simple_command(:get, 'v1/variants/{variantId}', options)
328
+ command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
329
+ command.response_class = Google::Apis::GenomicsV1::Variant
330
+ command.params['variantId'] = variant_id unless variant_id.nil?
343
331
  command.query['fields'] = fields unless fields.nil?
344
332
  command.query['quotaUser'] = quota_user unless quota_user.nil?
345
333
  execute_or_queue_command(command, &block)
346
334
  end
347
335
 
348
- # Exports a read group set to a BAM file in Google Cloud Storage.
349
- # For the definitions of read group sets and other genomics resources, see
336
+ # Creates variant data by asynchronously importing the provided information.
337
+ # For the definitions of variant sets and other genomics resources, see
350
338
  # [Fundamentals of Google
351
339
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
352
- # Note that currently there may be some differences between exported BAM
353
- # files and the original BAM file at the time of import. See
354
- # ImportReadGroupSets
355
- # for caveats.
356
- # @param [String] read_group_set_id
357
- # Required. The ID of the read group set to export. The caller must have
358
- # READ access to this read group set.
359
- # @param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_request_object
340
+ # The variants for import will be merged with any existing variant that
341
+ # matches its reference sequence, start, end, reference bases, and
342
+ # alternative bases. If no such variant exists, a new one will be created.
343
+ # When variants are merged, the call information from the new variant
344
+ # is added to the existing variant, and Variant info fields are merged
345
+ # as specified in
346
+ # infoMergeConfig.
347
+ # As a special case, for single-sample VCF files, QUAL and FILTER fields will
348
+ # be moved to the call level; these are sometimes interpreted in a
349
+ # call-specific context.
350
+ # Imported VCF headers are appended to the metadata already in a variant set.
351
+ # @param [Google::Apis::GenomicsV1::ImportVariantsRequest] import_variants_request_object
360
352
  # @param [String] fields
361
353
  # Selector specifying which fields to include in a partial response.
362
354
  # @param [String] quota_user
@@ -374,26 +366,23 @@ module Google
374
366
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
375
367
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
376
368
  # @raise [Google::Apis::AuthorizationError] Authorization is required
377
- def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
378
- command = make_simple_command(:post, 'v1/readgroupsets/{readGroupSetId}:export', options)
379
- command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation
380
- command.request_object = export_read_group_set_request_object
369
+ def import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
370
+ command = make_simple_command(:post, 'v1/variants:import', options)
371
+ command.request_representation = Google::Apis::GenomicsV1::ImportVariantsRequest::Representation
372
+ command.request_object = import_variants_request_object
381
373
  command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
382
374
  command.response_class = Google::Apis::GenomicsV1::Operation
383
- command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
384
375
  command.query['fields'] = fields unless fields.nil?
385
376
  command.query['quotaUser'] = quota_user unless quota_user.nil?
386
377
  execute_or_queue_command(command, &block)
387
378
  end
388
379
 
389
- # Searches for read group sets matching the criteria.
390
- # For the definitions of read group sets and other genomics resources, see
380
+ # Deletes a variant.
381
+ # For the definitions of variants and other genomics resources, see
391
382
  # [Fundamentals of Google
392
383
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
393
- # Implements
394
- # [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/
395
- # v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
396
- # @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_request_object
384
+ # @param [String] variant_id
385
+ # The ID of the variant to be deleted.
397
386
  # @param [String] fields
398
387
  # Selector specifying which fields to include in a partial response.
399
388
  # @param [String] quota_user
@@ -403,40 +392,107 @@ module Google
403
392
  # Request-specific options
404
393
  #
405
394
  # @yield [result, err] Result & error if block supplied
406
- # @yieldparam result [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] parsed result object
395
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
407
396
  # @yieldparam err [StandardError] error object if request failed
408
397
  #
409
- # @return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse]
398
+ # @return [Google::Apis::GenomicsV1::Empty]
410
399
  #
411
400
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
412
401
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
413
402
  # @raise [Google::Apis::AuthorizationError] Authorization is required
414
- def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
415
- command = make_simple_command(:post, 'v1/readgroupsets/search', options)
416
- command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation
417
- command.request_object = search_read_group_sets_request_object
418
- command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation
419
- command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse
403
+ def delete_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
404
+ command = make_simple_command(:delete, 'v1/variants/{variantId}', options)
405
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
406
+ command.response_class = Google::Apis::GenomicsV1::Empty
407
+ command.params['variantId'] = variant_id unless variant_id.nil?
420
408
  command.query['fields'] = fields unless fields.nil?
421
409
  command.query['quotaUser'] = quota_user unless quota_user.nil?
422
410
  execute_or_queue_command(command, &block)
423
411
  end
424
412
 
425
- # Updates a read group set.
426
- # For the definitions of read group sets and other genomics resources, see
413
+ # Merges the given variants with existing variants.
414
+ # For the definitions of variants and other genomics resources, see
427
415
  # [Fundamentals of Google
428
416
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
429
- # This method supports patch semantics.
430
- # @param [String] read_group_set_id
431
- # The ID of the read group set to be updated. The caller must have WRITE
432
- # permissions to the dataset associated with this read group set.
433
- # @param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object
434
- # @param [String] update_mask
435
- # An optional mask specifying which fields to update. Supported fields:
436
- # * name.
437
- # * referenceSetId.
438
- # Leaving `updateMask` unset is equivalent to specifying all mutable
439
- # fields.
417
+ # Each variant will be
418
+ # merged with an existing variant that matches its reference sequence,
419
+ # start, end, reference bases, and alternative bases. If no such variant
420
+ # exists, a new one will be created.
421
+ # When variants are merged, the call information from the new variant
422
+ # is added to the existing variant. Variant info fields are merged as
423
+ # specified in the
424
+ # infoMergeConfig
425
+ # field of the MergeVariantsRequest.
426
+ # Please exercise caution when using this method! It is easy to introduce
427
+ # mistakes in existing variants and difficult to back out of them. For
428
+ # example,
429
+ # suppose you were trying to merge a new variant with an existing one and
430
+ # both
431
+ # variants contain calls that belong to callsets with the same callset ID.
432
+ # // Existing variant - irrelevant fields trimmed for clarity
433
+ # `
434
+ # "variantSetId": "10473108253681171589",
435
+ # "referenceName": "1",
436
+ # "start": "10582",
437
+ # "referenceBases": "G",
438
+ # "alternateBases": [
439
+ # "A"
440
+ # ],
441
+ # "calls": [
442
+ # `
443
+ # "callSetId": "10473108253681171589-0",
444
+ # "callSetName": "CALLSET0",
445
+ # "genotype": [
446
+ # 0,
447
+ # 1
448
+ # ],
449
+ # `
450
+ # ]
451
+ # `
452
+ # // New variant with conflicting call information
453
+ # `
454
+ # "variantSetId": "10473108253681171589",
455
+ # "referenceName": "1",
456
+ # "start": "10582",
457
+ # "referenceBases": "G",
458
+ # "alternateBases": [
459
+ # "A"
460
+ # ],
461
+ # "calls": [
462
+ # `
463
+ # "callSetId": "10473108253681171589-0",
464
+ # "callSetName": "CALLSET0",
465
+ # "genotype": [
466
+ # 1,
467
+ # 1
468
+ # ],
469
+ # `
470
+ # ]
471
+ # `
472
+ # The resulting merged variant would overwrite the existing calls with those
473
+ # from the new variant:
474
+ # `
475
+ # "variantSetId": "10473108253681171589",
476
+ # "referenceName": "1",
477
+ # "start": "10582",
478
+ # "referenceBases": "G",
479
+ # "alternateBases": [
480
+ # "A"
481
+ # ],
482
+ # "calls": [
483
+ # `
484
+ # "callSetId": "10473108253681171589-0",
485
+ # "callSetName": "CALLSET0",
486
+ # "genotype": [
487
+ # 1,
488
+ # 1
489
+ # ],
490
+ # `
491
+ # ]
492
+ # `
493
+ # This may be the desired outcome, but it is up to the user to determine if
494
+ # if that is indeed the case.
495
+ # @param [Google::Apis::GenomicsV1::MergeVariantsRequest] merge_variants_request_object
440
496
  # @param [String] fields
441
497
  # Selector specifying which fields to include in a partial response.
442
498
  # @param [String] quota_user
@@ -446,33 +502,30 @@ module Google
446
502
  # Request-specific options
447
503
  #
448
504
  # @yield [result, err] Result & error if block supplied
449
- # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
505
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
450
506
  # @yieldparam err [StandardError] error object if request failed
451
507
  #
452
- # @return [Google::Apis::GenomicsV1::ReadGroupSet]
508
+ # @return [Google::Apis::GenomicsV1::Empty]
453
509
  #
454
510
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
455
511
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
456
512
  # @raise [Google::Apis::AuthorizationError] Authorization is required
457
- def patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
458
- command = make_simple_command(:patch, 'v1/readgroupsets/{readGroupSetId}', options)
459
- command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
460
- command.request_object = read_group_set_object
461
- command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
462
- command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
463
- command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
464
- command.query['updateMask'] = update_mask unless update_mask.nil?
513
+ def merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
514
+ command = make_simple_command(:post, 'v1/variants:merge', options)
515
+ command.request_representation = Google::Apis::GenomicsV1::MergeVariantsRequest::Representation
516
+ command.request_object = merge_variants_request_object
517
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
518
+ command.response_class = Google::Apis::GenomicsV1::Empty
465
519
  command.query['fields'] = fields unless fields.nil?
466
520
  command.query['quotaUser'] = quota_user unless quota_user.nil?
467
521
  execute_or_queue_command(command, &block)
468
522
  end
469
523
 
470
- # Gets a read group set by ID.
471
- # For the definitions of read group sets and other genomics resources, see
524
+ # Creates a new variant.
525
+ # For the definitions of variants and other genomics resources, see
472
526
  # [Fundamentals of Google
473
527
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
474
- # @param [String] read_group_set_id
475
- # The ID of the read group set.
528
+ # @param [Google::Apis::GenomicsV1::Variant] variant_object
476
529
  # @param [String] fields
477
530
  # Selector specifying which fields to include in a partial response.
478
531
  # @param [String] quota_user
@@ -482,39 +535,33 @@ module Google
482
535
  # Request-specific options
483
536
  #
484
537
  # @yield [result, err] Result & error if block supplied
485
- # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
538
+ # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
486
539
  # @yieldparam err [StandardError] error object if request failed
487
540
  #
488
- # @return [Google::Apis::GenomicsV1::ReadGroupSet]
541
+ # @return [Google::Apis::GenomicsV1::Variant]
489
542
  #
490
543
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
491
544
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
492
545
  # @raise [Google::Apis::AuthorizationError] Authorization is required
493
- def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
494
- command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}', options)
495
- command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
496
- command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
497
- command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
546
+ def create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil, &block)
547
+ command = make_simple_command(:post, 'v1/variants', options)
548
+ command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
549
+ command.request_object = variant_object
550
+ command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
551
+ command.response_class = Google::Apis::GenomicsV1::Variant
498
552
  command.query['fields'] = fields unless fields.nil?
499
553
  command.query['quotaUser'] = quota_user unless quota_user.nil?
500
554
  execute_or_queue_command(command, &block)
501
555
  end
502
556
 
503
- # Creates read group sets by asynchronously importing the provided
504
- # information.
505
- # For the definitions of read group sets and other genomics resources, see
557
+ # Searches for references which match the given criteria.
558
+ # For the definitions of references and other genomics resources, see
506
559
  # [Fundamentals of Google
507
560
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
508
- # The caller must have WRITE permissions to the dataset.
509
- # ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
510
- # - Tags will be converted to strings - tag types are not preserved
511
- # - Comments (`@CO`) in the input file header will not be preserved
512
- # - Original header order of references (`@SQ`) will not be preserved
513
- # - Any reverse stranded unmapped reads will be reverse complemented, and
514
- # their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
515
- # - Unmapped reads will be stripped of positional information (reference name
516
- # and position)
517
- # @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_request_object
561
+ # Implements
562
+ # [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.
563
+ # 5.1/src/main/resources/avro/referencemethods.avdl#L146).
564
+ # @param [Google::Apis::GenomicsV1::SearchReferencesRequest] search_references_request_object
518
565
  # @param [String] fields
519
566
  # Selector specifying which fields to include in a partial response.
520
567
  # @param [String] quota_user
@@ -524,32 +571,34 @@ module Google
524
571
  # Request-specific options
525
572
  #
526
573
  # @yield [result, err] Result & error if block supplied
527
- # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
574
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchReferencesResponse] parsed result object
528
575
  # @yieldparam err [StandardError] error object if request failed
529
576
  #
530
- # @return [Google::Apis::GenomicsV1::Operation]
577
+ # @return [Google::Apis::GenomicsV1::SearchReferencesResponse]
531
578
  #
532
579
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
533
580
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
534
581
  # @raise [Google::Apis::AuthorizationError] Authorization is required
535
- def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
536
- command = make_simple_command(:post, 'v1/readgroupsets:import', options)
537
- command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation
538
- command.request_object = import_read_group_sets_request_object
539
- command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
540
- command.response_class = Google::Apis::GenomicsV1::Operation
582
+ def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
583
+ command = make_simple_command(:post, 'v1/references/search', options)
584
+ command.request_representation = Google::Apis::GenomicsV1::SearchReferencesRequest::Representation
585
+ command.request_object = search_references_request_object
586
+ command.response_representation = Google::Apis::GenomicsV1::SearchReferencesResponse::Representation
587
+ command.response_class = Google::Apis::GenomicsV1::SearchReferencesResponse
541
588
  command.query['fields'] = fields unless fields.nil?
542
589
  command.query['quotaUser'] = quota_user unless quota_user.nil?
543
590
  execute_or_queue_command(command, &block)
544
591
  end
545
592
 
546
- # Deletes a read group set.
547
- # For the definitions of read group sets and other genomics resources, see
593
+ # Gets a reference.
594
+ # For the definitions of references and other genomics resources, see
548
595
  # [Fundamentals of Google
549
596
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
550
- # @param [String] read_group_set_id
551
- # The ID of the read group set to be deleted. The caller must have WRITE
552
- # permissions to the dataset associated with this read group set.
597
+ # Implements
598
+ # [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/
599
+ # src/main/resources/avro/referencemethods.avdl#L158).
600
+ # @param [String] reference_id
601
+ # The ID of the reference.
553
602
  # @param [String] fields
554
603
  # Selector specifying which fields to include in a partial response.
555
604
  # @param [String] quota_user
@@ -559,62 +608,46 @@ module Google
559
608
  # Request-specific options
560
609
  #
561
610
  # @yield [result, err] Result & error if block supplied
562
- # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
611
+ # @yieldparam result [Google::Apis::GenomicsV1::Reference] parsed result object
563
612
  # @yieldparam err [StandardError] error object if request failed
564
613
  #
565
- # @return [Google::Apis::GenomicsV1::Empty]
614
+ # @return [Google::Apis::GenomicsV1::Reference]
566
615
  #
567
616
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
568
617
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
569
618
  # @raise [Google::Apis::AuthorizationError] Authorization is required
570
- def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
571
- command = make_simple_command(:delete, 'v1/readgroupsets/{readGroupSetId}', options)
572
- command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
573
- command.response_class = Google::Apis::GenomicsV1::Empty
574
- command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
619
+ def get_reference(reference_id, fields: nil, quota_user: nil, options: nil, &block)
620
+ command = make_simple_command(:get, 'v1/references/{referenceId}', options)
621
+ command.response_representation = Google::Apis::GenomicsV1::Reference::Representation
622
+ command.response_class = Google::Apis::GenomicsV1::Reference
623
+ command.params['referenceId'] = reference_id unless reference_id.nil?
575
624
  command.query['fields'] = fields unless fields.nil?
576
625
  command.query['quotaUser'] = quota_user unless quota_user.nil?
577
626
  execute_or_queue_command(command, &block)
578
627
  end
579
628
 
580
- # Lists fixed width coverage buckets for a read group set, each of which
581
- # correspond to a range of a reference sequence. Each bucket summarizes
582
- # coverage information across its corresponding genomic range.
583
- # For the definitions of read group sets and other genomics resources, see
584
- # [Fundamentals of Google
629
+ # Lists the bases in a reference, optionally restricted to a range.
630
+ # For the definitions of references and other genomics resources, see
631
+ # [Fundamentals of Google
585
632
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
586
- # Coverage is defined as the number of reads which are aligned to a given
587
- # base in the reference sequence. Coverage buckets are available at several
588
- # precomputed bucket widths, enabling retrieval of various coverage 'zoom
589
- # levels'. The caller must have READ permissions for the target read group
590
- # set.
591
- # @param [String] read_group_set_id
592
- # Required. The ID of the read group set over which coverage is requested.
633
+ # Implements
634
+ # [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.
635
+ # 5.1/src/main/resources/avro/referencemethods.avdl#L221).
636
+ # @param [String] reference_id
637
+ # The ID of the reference.
638
+ # @param [String] start_position
639
+ # The start position (0-based) of this query. Defaults to 0.
640
+ # @param [String] end_position
641
+ # The end position (0-based, exclusive) of this query. Defaults to the length
642
+ # of this reference.
593
643
  # @param [String] page_token
594
644
  # The continuation token, which is used to page through large result sets.
595
645
  # To get the next page of results, set this parameter to the value of
596
646
  # `nextPageToken` from the previous response.
597
647
  # @param [Fixnum] page_size
598
- # The maximum number of results to return in a single page. If unspecified,
599
- # defaults to 1024. The maximum value is 2048.
600
- # @param [String] start
601
- # The start position of the range on the reference, 0-based inclusive. If
602
- # specified, `referenceName` must also be specified. Defaults to 0.
603
- # @param [String] target_bucket_width
604
- # The desired width of each reported coverage bucket in base pairs. This
605
- # will be rounded down to the nearest precomputed bucket width; the value
606
- # of which is returned as `bucketWidth` in the response. Defaults
607
- # to infinity (each bucket spans an entire reference sequence) or the length
608
- # of the target range, if specified. The smallest precomputed
609
- # `bucketWidth` is currently 2048 base pairs; this is subject to
610
- # change.
611
- # @param [String] reference_name
612
- # The name of the reference to query, within the reference set associated
613
- # with this query. Optional.
614
- # @param [String] end_
615
- # The end position of the range on the reference, 0-based exclusive. If
616
- # specified, `referenceName` must also be specified. If unset or 0, defaults
617
- # to the length of the reference.
648
+ # The maximum number of bases to return in a single page. If unspecified,
649
+ # defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base
650
+ # pairs).
618
651
  # @param [String] fields
619
652
  # Selector specifying which fields to include in a partial response.
620
653
  # @param [String] quota_user
@@ -624,34 +657,33 @@ module Google
624
657
  # Request-specific options
625
658
  #
626
659
  # @yield [result, err] Result & error if block supplied
627
- # @yieldparam result [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] parsed result object
660
+ # @yieldparam result [Google::Apis::GenomicsV1::ListBasesResponse] parsed result object
628
661
  # @yieldparam err [StandardError] error object if request failed
629
662
  #
630
- # @return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse]
663
+ # @return [Google::Apis::GenomicsV1::ListBasesResponse]
631
664
  #
632
665
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
633
666
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
634
667
  # @raise [Google::Apis::AuthorizationError] Authorization is required
635
- def list_coverage_buckets(read_group_set_id, page_token: nil, page_size: nil, start: nil, target_bucket_width: nil, reference_name: nil, end_: nil, fields: nil, quota_user: nil, options: nil, &block)
636
- command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', options)
637
- command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation
638
- command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse
639
- command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
668
+ def list_reference_bases(reference_id, start_position: nil, end_position: nil, page_token: nil, page_size: nil, fields: nil, quota_user: nil, options: nil, &block)
669
+ command = make_simple_command(:get, 'v1/references/{referenceId}/bases', options)
670
+ command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation
671
+ command.response_class = Google::Apis::GenomicsV1::ListBasesResponse
672
+ command.params['referenceId'] = reference_id unless reference_id.nil?
673
+ command.query['start'] = start_position unless start_position.nil?
674
+ command.query['end'] = end_position unless end_position.nil?
640
675
  command.query['pageToken'] = page_token unless page_token.nil?
641
676
  command.query['pageSize'] = page_size unless page_size.nil?
642
- command.query['start'] = start unless start.nil?
643
- command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil?
644
- command.query['referenceName'] = reference_name unless reference_name.nil?
645
- command.query['end'] = end_ unless end_.nil?
646
677
  command.query['fields'] = fields unless fields.nil?
647
678
  command.query['quotaUser'] = quota_user unless quota_user.nil?
648
679
  execute_or_queue_command(command, &block)
649
680
  end
650
681
 
651
- # Deletes an annotation set. Caller must have WRITE permission
652
- # for the associated annotation set.
653
- # @param [String] annotation_set_id
654
- # The ID of the annotation set to be deleted.
682
+ # Creates a new dataset.
683
+ # For the definitions of datasets and other genomics resources, see
684
+ # [Fundamentals of Google
685
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
686
+ # @param [Google::Apis::GenomicsV1::Dataset] dataset_object
655
687
  # @param [String] fields
656
688
  # Selector specifying which fields to include in a partial response.
657
689
  # @param [String] quota_user
@@ -661,30 +693,36 @@ module Google
661
693
  # Request-specific options
662
694
  #
663
695
  # @yield [result, err] Result & error if block supplied
664
- # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
696
+ # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
665
697
  # @yieldparam err [StandardError] error object if request failed
666
698
  #
667
- # @return [Google::Apis::GenomicsV1::Empty]
699
+ # @return [Google::Apis::GenomicsV1::Dataset]
668
700
  #
669
701
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
670
702
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
671
703
  # @raise [Google::Apis::AuthorizationError] Authorization is required
672
- def delete_annotationset(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block)
673
- command = make_simple_command(:delete, 'v1/annotationsets/{annotationSetId}', options)
674
- command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
675
- command.response_class = Google::Apis::GenomicsV1::Empty
676
- command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
704
+ def create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil, &block)
705
+ command = make_simple_command(:post, 'v1/datasets', options)
706
+ command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation
707
+ command.request_object = dataset_object
708
+ command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
709
+ command.response_class = Google::Apis::GenomicsV1::Dataset
677
710
  command.query['fields'] = fields unless fields.nil?
678
711
  command.query['quotaUser'] = quota_user unless quota_user.nil?
679
712
  execute_or_queue_command(command, &block)
680
713
  end
681
714
 
682
- # Searches for annotation sets that match the given criteria. Annotation sets
683
- # are returned in an unspecified order. This order is consistent, such that
684
- # two queries for the same content (regardless of page size) yield annotation
685
- # sets in the same order across their respective streams of paginated
686
- # responses. Caller must have READ permission for the queried datasets.
687
- # @param [Google::Apis::GenomicsV1::SearchAnnotationSetsRequest] search_annotation_sets_request_object
715
+ # Sets the access control policy on the specified dataset. Replaces any
716
+ # existing policy.
717
+ # For the definitions of datasets and other genomics resources, see
718
+ # [Fundamentals of Google
719
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
720
+ # See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
721
+ # Policy</a> for more information.
722
+ # @param [String] resource
723
+ # REQUIRED: The resource for which policy is being specified. Format is
724
+ # `datasets/<dataset ID>`.
725
+ # @param [Google::Apis::GenomicsV1::SetIamPolicyRequest] set_iam_policy_request_object
688
726
  # @param [String] fields
689
727
  # Selector specifying which fields to include in a partial response.
690
728
  # @param [String] quota_user
@@ -694,29 +732,37 @@ module Google
694
732
  # Request-specific options
695
733
  #
696
734
  # @yield [result, err] Result & error if block supplied
697
- # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse] parsed result object
735
+ # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object
698
736
  # @yieldparam err [StandardError] error object if request failed
699
737
  #
700
- # @return [Google::Apis::GenomicsV1::SearchAnnotationSetsResponse]
738
+ # @return [Google::Apis::GenomicsV1::Policy]
701
739
  #
702
740
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
703
741
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
704
742
  # @raise [Google::Apis::AuthorizationError] Authorization is required
705
- def search_annotationset_annotation_sets(search_annotation_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
706
- command = make_simple_command(:post, 'v1/annotationsets/search', options)
707
- command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsRequest::Representation
708
- command.request_object = search_annotation_sets_request_object
709
- command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse::Representation
710
- command.response_class = Google::Apis::GenomicsV1::SearchAnnotationSetsResponse
743
+ def set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
744
+ command = make_simple_command(:post, 'v1/{+resource}:setIamPolicy', options)
745
+ command.request_representation = Google::Apis::GenomicsV1::SetIamPolicyRequest::Representation
746
+ command.request_object = set_iam_policy_request_object
747
+ command.response_representation = Google::Apis::GenomicsV1::Policy::Representation
748
+ command.response_class = Google::Apis::GenomicsV1::Policy
749
+ command.params['resource'] = resource unless resource.nil?
711
750
  command.query['fields'] = fields unless fields.nil?
712
751
  command.query['quotaUser'] = quota_user unless quota_user.nil?
713
752
  execute_or_queue_command(command, &block)
714
753
  end
715
754
 
716
- # Gets an annotation set. Caller must have READ permission for
717
- # the associated dataset.
718
- # @param [String] annotation_set_id
719
- # The ID of the annotation set to be retrieved.
755
+ # Gets the access control policy for the dataset. This is empty if the
756
+ # policy or resource does not exist.
757
+ # See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
758
+ # Policy</a> for more information.
759
+ # For the definitions of datasets and other genomics resources, see
760
+ # [Fundamentals of Google
761
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
762
+ # @param [String] resource
763
+ # REQUIRED: The resource for which policy is being specified. Format is
764
+ # `datasets/<dataset ID>`.
765
+ # @param [Google::Apis::GenomicsV1::GetIamPolicyRequest] get_iam_policy_request_object
720
766
  # @param [String] fields
721
767
  # Selector specifying which fields to include in a partial response.
722
768
  # @param [String] quota_user
@@ -726,36 +772,34 @@ module Google
726
772
  # Request-specific options
727
773
  #
728
774
  # @yield [result, err] Result & error if block supplied
729
- # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
775
+ # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object
730
776
  # @yieldparam err [StandardError] error object if request failed
731
777
  #
732
- # @return [Google::Apis::GenomicsV1::AnnotationSet]
778
+ # @return [Google::Apis::GenomicsV1::Policy]
733
779
  #
734
780
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
735
781
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
736
782
  # @raise [Google::Apis::AuthorizationError] Authorization is required
737
- def get_annotation_set(annotation_set_id, fields: nil, quota_user: nil, options: nil, &block)
738
- command = make_simple_command(:get, 'v1/annotationsets/{annotationSetId}', options)
739
- command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
740
- command.response_class = Google::Apis::GenomicsV1::AnnotationSet
741
- command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
783
+ def get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
784
+ command = make_simple_command(:post, 'v1/{+resource}:getIamPolicy', options)
785
+ command.request_representation = Google::Apis::GenomicsV1::GetIamPolicyRequest::Representation
786
+ command.request_object = get_iam_policy_request_object
787
+ command.response_representation = Google::Apis::GenomicsV1::Policy::Representation
788
+ command.response_class = Google::Apis::GenomicsV1::Policy
789
+ command.params['resource'] = resource unless resource.nil?
742
790
  command.query['fields'] = fields unless fields.nil?
743
791
  command.query['quotaUser'] = quota_user unless quota_user.nil?
744
792
  execute_or_queue_command(command, &block)
745
793
  end
746
794
 
747
- # Updates an annotation set. The update must respect all mutability
748
- # restrictions and other invariants described on the annotation set resource.
749
- # Caller must have WRITE permission for the associated dataset.
750
- # @param [String] annotation_set_id
751
- # The ID of the annotation set to be updated.
752
- # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object
753
- # @param [String] update_mask
754
- # An optional mask specifying which fields to update. Mutable fields are
755
- # name,
756
- # source_uri, and
757
- # info. If unspecified, all
758
- # mutable fields will be updated.
795
+ # Undeletes a dataset by restoring a dataset which was deleted via this API.
796
+ # For the definitions of datasets and other genomics resources, see
797
+ # [Fundamentals of Google
798
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
799
+ # This operation is only possible for a week after the deletion occurred.
800
+ # @param [String] dataset_id
801
+ # The ID of the dataset to be undeleted.
802
+ # @param [Google::Apis::GenomicsV1::UndeleteDatasetRequest] undelete_dataset_request_object
759
803
  # @param [String] fields
760
804
  # Selector specifying which fields to include in a partial response.
761
805
  # @param [String] quota_user
@@ -765,35 +809,39 @@ module Google
765
809
  # Request-specific options
766
810
  #
767
811
  # @yield [result, err] Result & error if block supplied
768
- # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
812
+ # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
769
813
  # @yieldparam err [StandardError] error object if request failed
770
814
  #
771
- # @return [Google::Apis::GenomicsV1::AnnotationSet]
815
+ # @return [Google::Apis::GenomicsV1::Dataset]
772
816
  #
773
817
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
774
818
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
775
819
  # @raise [Google::Apis::AuthorizationError] Authorization is required
776
- def update_annotationset(annotation_set_id, annotation_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
777
- command = make_simple_command(:put, 'v1/annotationsets/{annotationSetId}', options)
778
- command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
779
- command.request_object = annotation_set_object
780
- command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
781
- command.response_class = Google::Apis::GenomicsV1::AnnotationSet
782
- command.params['annotationSetId'] = annotation_set_id unless annotation_set_id.nil?
783
- command.query['updateMask'] = update_mask unless update_mask.nil?
820
+ def undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
821
+ command = make_simple_command(:post, 'v1/datasets/{datasetId}:undelete', options)
822
+ command.request_representation = Google::Apis::GenomicsV1::UndeleteDatasetRequest::Representation
823
+ command.request_object = undelete_dataset_request_object
824
+ command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
825
+ command.response_class = Google::Apis::GenomicsV1::Dataset
826
+ command.params['datasetId'] = dataset_id unless dataset_id.nil?
784
827
  command.query['fields'] = fields unless fields.nil?
785
828
  command.query['quotaUser'] = quota_user unless quota_user.nil?
786
829
  execute_or_queue_command(command, &block)
787
830
  end
788
831
 
789
- # Creates a new annotation set. Caller must have WRITE permission for the
790
- # associated dataset.
791
- # The following fields are required:
792
- # * datasetId
793
- # * referenceSetId
794
- # All other fields may be optionally specified, unless documented as being
795
- # server-generated (for example, the `id` field).
796
- # @param [Google::Apis::GenomicsV1::AnnotationSet] annotation_set_object
832
+ # Updates a dataset.
833
+ # For the definitions of datasets and other genomics resources, see
834
+ # [Fundamentals of Google
835
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
836
+ # This method supports patch semantics.
837
+ # @param [String] dataset_id
838
+ # The ID of the dataset to be updated.
839
+ # @param [Google::Apis::GenomicsV1::Dataset] dataset_object
840
+ # @param [String] update_mask
841
+ # An optional mask specifying which fields to update. At this time, the only
842
+ # mutable field is name. The only
843
+ # acceptable value is "name". If unspecified, all mutable fields will be
844
+ # updated.
797
845
  # @param [String] fields
798
846
  # Selector specifying which fields to include in a partial response.
799
847
  # @param [String] quota_user
@@ -803,31 +851,33 @@ module Google
803
851
  # Request-specific options
804
852
  #
805
853
  # @yield [result, err] Result & error if block supplied
806
- # @yieldparam result [Google::Apis::GenomicsV1::AnnotationSet] parsed result object
854
+ # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
807
855
  # @yieldparam err [StandardError] error object if request failed
808
856
  #
809
- # @return [Google::Apis::GenomicsV1::AnnotationSet]
857
+ # @return [Google::Apis::GenomicsV1::Dataset]
810
858
  #
811
859
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
812
860
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
813
861
  # @raise [Google::Apis::AuthorizationError] Authorization is required
814
- def create_annotation_set(annotation_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
815
- command = make_simple_command(:post, 'v1/annotationsets', options)
816
- command.request_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
817
- command.request_object = annotation_set_object
818
- command.response_representation = Google::Apis::GenomicsV1::AnnotationSet::Representation
819
- command.response_class = Google::Apis::GenomicsV1::AnnotationSet
862
+ def patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
863
+ command = make_simple_command(:patch, 'v1/datasets/{datasetId}', options)
864
+ command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation
865
+ command.request_object = dataset_object
866
+ command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
867
+ command.response_class = Google::Apis::GenomicsV1::Dataset
868
+ command.params['datasetId'] = dataset_id unless dataset_id.nil?
869
+ command.query['updateMask'] = update_mask unless update_mask.nil?
820
870
  command.query['fields'] = fields unless fields.nil?
821
871
  command.query['quotaUser'] = quota_user unless quota_user.nil?
822
872
  execute_or_queue_command(command, &block)
823
873
  end
824
874
 
825
- # Deletes a variant.
826
- # For the definitions of variants and other genomics resources, see
875
+ # Gets a dataset by ID.
876
+ # For the definitions of datasets and other genomics resources, see
827
877
  # [Fundamentals of Google
828
878
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
829
- # @param [String] variant_id
830
- # The ID of the variant to be deleted.
879
+ # @param [String] dataset_id
880
+ # The ID of the dataset.
831
881
  # @param [String] fields
832
882
  # Selector specifying which fields to include in a partial response.
833
883
  # @param [String] quota_user
@@ -837,40 +887,34 @@ module Google
837
887
  # Request-specific options
838
888
  #
839
889
  # @yield [result, err] Result & error if block supplied
840
- # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
890
+ # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
841
891
  # @yieldparam err [StandardError] error object if request failed
842
892
  #
843
- # @return [Google::Apis::GenomicsV1::Empty]
893
+ # @return [Google::Apis::GenomicsV1::Dataset]
844
894
  #
845
895
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
846
896
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
847
897
  # @raise [Google::Apis::AuthorizationError] Authorization is required
848
- def delete_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
849
- command = make_simple_command(:delete, 'v1/variants/{variantId}', options)
850
- command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
851
- command.response_class = Google::Apis::GenomicsV1::Empty
852
- command.params['variantId'] = variant_id unless variant_id.nil?
898
+ def get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block)
899
+ command = make_simple_command(:get, 'v1/datasets/{datasetId}', options)
900
+ command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
901
+ command.response_class = Google::Apis::GenomicsV1::Dataset
902
+ command.params['datasetId'] = dataset_id unless dataset_id.nil?
853
903
  command.query['fields'] = fields unless fields.nil?
854
904
  command.query['quotaUser'] = quota_user unless quota_user.nil?
855
905
  execute_or_queue_command(command, &block)
856
906
  end
857
907
 
858
- # Creates variant data by asynchronously importing the provided information.
859
- # For the definitions of variant sets and other genomics resources, see
908
+ # Returns permissions that a caller has on the specified resource.
909
+ # See <a href="/iam/docs/managing-policies#testing_permissions">Testing
910
+ # Permissions</a> for more information.
911
+ # For the definitions of datasets and other genomics resources, see
860
912
  # [Fundamentals of Google
861
913
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
862
- # The variants for import will be merged with any existing variant that
863
- # matches its reference sequence, start, end, reference bases, and
864
- # alternative bases. If no such variant exists, a new one will be created.
865
- # When variants are merged, the call information from the new variant
866
- # is added to the existing variant, and Variant info fields are merged
867
- # as specified in
868
- # infoMergeConfig.
869
- # As a special case, for single-sample VCF files, QUAL and FILTER fields will
870
- # be moved to the call level; these are sometimes interpreted in a
871
- # call-specific context.
872
- # Imported VCF headers are appended to the metadata already in a variant set.
873
- # @param [Google::Apis::GenomicsV1::ImportVariantsRequest] import_variants_request_object
914
+ # @param [String] resource
915
+ # REQUIRED: The resource for which policy is being specified. Format is
916
+ # `datasets/<dataset ID>`.
917
+ # @param [Google::Apis::GenomicsV1::TestIamPermissionsRequest] test_iam_permissions_request_object
874
918
  # @param [String] fields
875
919
  # Selector specifying which fields to include in a partial response.
876
920
  # @param [String] quota_user
@@ -880,108 +924,37 @@ module Google
880
924
  # Request-specific options
881
925
  #
882
926
  # @yield [result, err] Result & error if block supplied
883
- # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
927
+ # @yieldparam result [Google::Apis::GenomicsV1::TestIamPermissionsResponse] parsed result object
884
928
  # @yieldparam err [StandardError] error object if request failed
885
929
  #
886
- # @return [Google::Apis::GenomicsV1::Operation]
930
+ # @return [Google::Apis::GenomicsV1::TestIamPermissionsResponse]
887
931
  #
888
932
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
889
933
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
890
934
  # @raise [Google::Apis::AuthorizationError] Authorization is required
891
- def import_variants(import_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
892
- command = make_simple_command(:post, 'v1/variants:import', options)
893
- command.request_representation = Google::Apis::GenomicsV1::ImportVariantsRequest::Representation
894
- command.request_object = import_variants_request_object
895
- command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
896
- command.response_class = Google::Apis::GenomicsV1::Operation
935
+ def test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
936
+ command = make_simple_command(:post, 'v1/{+resource}:testIamPermissions', options)
937
+ command.request_representation = Google::Apis::GenomicsV1::TestIamPermissionsRequest::Representation
938
+ command.request_object = test_iam_permissions_request_object
939
+ command.response_representation = Google::Apis::GenomicsV1::TestIamPermissionsResponse::Representation
940
+ command.response_class = Google::Apis::GenomicsV1::TestIamPermissionsResponse
941
+ command.params['resource'] = resource unless resource.nil?
897
942
  command.query['fields'] = fields unless fields.nil?
898
943
  command.query['quotaUser'] = quota_user unless quota_user.nil?
899
944
  execute_or_queue_command(command, &block)
900
945
  end
901
946
 
902
- # Merges the given variants with existing variants.
903
- # For the definitions of variants and other genomics resources, see
947
+ # Deletes a dataset and all of its contents (all read group sets,
948
+ # reference sets, variant sets, call sets, annotation sets, etc.)
949
+ # This is reversible (up to one week after the deletion) via
950
+ # the
951
+ # datasets.undelete
952
+ # operation.
953
+ # For the definitions of datasets and other genomics resources, see
904
954
  # [Fundamentals of Google
905
955
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
906
- # Each variant will be
907
- # merged with an existing variant that matches its reference sequence,
908
- # start, end, reference bases, and alternative bases. If no such variant
909
- # exists, a new one will be created.
910
- # When variants are merged, the call information from the new variant
911
- # is added to the existing variant. Variant info fields are merged as
912
- # specified in the
913
- # infoMergeConfig
914
- # field of the MergeVariantsRequest.
915
- # Please exercise caution when using this method! It is easy to introduce
916
- # mistakes in existing variants and difficult to back out of them. For
917
- # example,
918
- # suppose you were trying to merge a new variant with an existing one and
919
- # both
920
- # variants contain calls that belong to callsets with the same callset ID.
921
- # // Existing variant - irrelevant fields trimmed for clarity
922
- # `
923
- # "variantSetId": "10473108253681171589",
924
- # "referenceName": "1",
925
- # "start": "10582",
926
- # "referenceBases": "G",
927
- # "alternateBases": [
928
- # "A"
929
- # ],
930
- # "calls": [
931
- # `
932
- # "callSetId": "10473108253681171589-0",
933
- # "callSetName": "CALLSET0",
934
- # "genotype": [
935
- # 0,
936
- # 1
937
- # ],
938
- # `
939
- # ]
940
- # `
941
- # // New variant with conflicting call information
942
- # `
943
- # "variantSetId": "10473108253681171589",
944
- # "referenceName": "1",
945
- # "start": "10582",
946
- # "referenceBases": "G",
947
- # "alternateBases": [
948
- # "A"
949
- # ],
950
- # "calls": [
951
- # `
952
- # "callSetId": "10473108253681171589-0",
953
- # "callSetName": "CALLSET0",
954
- # "genotype": [
955
- # 1,
956
- # 1
957
- # ],
958
- # `
959
- # ]
960
- # `
961
- # The resulting merged variant would overwrite the existing calls with those
962
- # from the new variant:
963
- # `
964
- # "variantSetId": "10473108253681171589",
965
- # "referenceName": "1",
966
- # "start": "10582",
967
- # "referenceBases": "G",
968
- # "alternateBases": [
969
- # "A"
970
- # ],
971
- # "calls": [
972
- # `
973
- # "callSetId": "10473108253681171589-0",
974
- # "callSetName": "CALLSET0",
975
- # "genotype": [
976
- # 1,
977
- # 1
978
- # ],
979
- # `
980
- # ]
981
- # `
982
- # This may be the desired outcome, but it is up to the user to determine if
983
- # if that is indeed the case.
984
- # @param [Google::Apis::GenomicsV1::MergeVariantsRequest] merge_variants_request_object
956
+ # @param [String] dataset_id
957
+ # The ID of the dataset to be deleted.
985
958
  # @param [String] fields
986
959
  # Selector specifying which fields to include in a partial response.
987
960
  # @param [String] quota_user
@@ -999,22 +972,29 @@ module Google
999
972
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1000
973
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1001
974
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1002
- def merge_variants(merge_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1003
- command = make_simple_command(:post, 'v1/variants:merge', options)
1004
- command.request_representation = Google::Apis::GenomicsV1::MergeVariantsRequest::Representation
1005
- command.request_object = merge_variants_request_object
975
+ def delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block)
976
+ command = make_simple_command(:delete, 'v1/datasets/{datasetId}', options)
1006
977
  command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
1007
978
  command.response_class = Google::Apis::GenomicsV1::Empty
979
+ command.params['datasetId'] = dataset_id unless dataset_id.nil?
1008
980
  command.query['fields'] = fields unless fields.nil?
1009
981
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1010
982
  execute_or_queue_command(command, &block)
1011
983
  end
1012
984
 
1013
- # Creates a new variant.
1014
- # For the definitions of variants and other genomics resources, see
985
+ # Lists datasets within a project.
986
+ # For the definitions of datasets and other genomics resources, see
1015
987
  # [Fundamentals of Google
1016
988
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1017
- # @param [Google::Apis::GenomicsV1::Variant] variant_object
989
+ # @param [String] page_token
990
+ # The continuation token, which is used to page through large result sets.
991
+ # To get the next page of results, set this parameter to the value of
992
+ # `nextPageToken` from the previous response.
993
+ # @param [Fixnum] page_size
994
+ # The maximum number of results to return in a single page. If unspecified,
995
+ # defaults to 50. The maximum value is 1024.
996
+ # @param [String] project_id
997
+ # Required. The Google Cloud project ID to list datasets for.
1018
998
  # @param [String] fields
1019
999
  # Selector specifying which fields to include in a partial response.
1020
1000
  # @param [String] quota_user
@@ -1024,33 +1004,33 @@ module Google
1024
1004
  # Request-specific options
1025
1005
  #
1026
1006
  # @yield [result, err] Result & error if block supplied
1027
- # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
1007
+ # @yieldparam result [Google::Apis::GenomicsV1::ListDatasetsResponse] parsed result object
1028
1008
  # @yieldparam err [StandardError] error object if request failed
1029
1009
  #
1030
- # @return [Google::Apis::GenomicsV1::Variant]
1010
+ # @return [Google::Apis::GenomicsV1::ListDatasetsResponse]
1031
1011
  #
1032
1012
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1033
1013
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1034
1014
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1035
- def create_variant(variant_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1036
- command = make_simple_command(:post, 'v1/variants', options)
1037
- command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
1038
- command.request_object = variant_object
1039
- command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
1040
- command.response_class = Google::Apis::GenomicsV1::Variant
1015
+ def list_datasets(page_token: nil, page_size: nil, project_id: nil, fields: nil, quota_user: nil, options: nil, &block)
1016
+ command = make_simple_command(:get, 'v1/datasets', options)
1017
+ command.response_representation = Google::Apis::GenomicsV1::ListDatasetsResponse::Representation
1018
+ command.response_class = Google::Apis::GenomicsV1::ListDatasetsResponse
1019
+ command.query['pageToken'] = page_token unless page_token.nil?
1020
+ command.query['pageSize'] = page_size unless page_size.nil?
1021
+ command.query['projectId'] = project_id unless project_id.nil?
1041
1022
  command.query['fields'] = fields unless fields.nil?
1042
1023
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1043
1024
  execute_or_queue_command(command, &block)
1044
1025
  end
1045
1026
 
1046
- # Gets a list of variants matching the criteria.
1047
- # For the definitions of variants and other genomics resources, see
1027
+ # Deletes a variant set including all variants, call sets, and calls within.
1028
+ # This is not reversible.
1029
+ # For the definitions of variant sets and other genomics resources, see
1048
1030
  # [Fundamentals of Google
1049
1031
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1050
- # Implements
1051
- # [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.
1052
- # 1/src/main/resources/avro/variantmethods.avdl#L126).
1053
- # @param [Google::Apis::GenomicsV1::SearchVariantsRequest] search_variants_request_object
1032
+ # @param [String] variant_set_id
1033
+ # The ID of the variant set to be deleted.
1054
1034
  # @param [String] fields
1055
1035
  # Selector specifying which fields to include in a partial response.
1056
1036
  # @param [String] quota_user
@@ -1060,39 +1040,32 @@ module Google
1060
1040
  # Request-specific options
1061
1041
  #
1062
1042
  # @yield [result, err] Result & error if block supplied
1063
- # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantsResponse] parsed result object
1043
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
1064
1044
  # @yieldparam err [StandardError] error object if request failed
1065
1045
  #
1066
- # @return [Google::Apis::GenomicsV1::SearchVariantsResponse]
1046
+ # @return [Google::Apis::GenomicsV1::Empty]
1067
1047
  #
1068
1048
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1069
1049
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1070
1050
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1071
- def search_variants(search_variants_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1072
- command = make_simple_command(:post, 'v1/variants/search', options)
1073
- command.request_representation = Google::Apis::GenomicsV1::SearchVariantsRequest::Representation
1074
- command.request_object = search_variants_request_object
1075
- command.response_representation = Google::Apis::GenomicsV1::SearchVariantsResponse::Representation
1076
- command.response_class = Google::Apis::GenomicsV1::SearchVariantsResponse
1051
+ def delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
1052
+ command = make_simple_command(:delete, 'v1/variantsets/{variantSetId}', options)
1053
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
1054
+ command.response_class = Google::Apis::GenomicsV1::Empty
1055
+ command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1077
1056
  command.query['fields'] = fields unless fields.nil?
1078
1057
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1079
1058
  execute_or_queue_command(command, &block)
1080
1059
  end
1081
1060
 
1082
- # Updates a variant.
1083
- # For the definitions of variants and other genomics resources, see
1061
+ # Creates a new variant set.
1062
+ # For the definitions of variant sets and other genomics resources, see
1084
1063
  # [Fundamentals of Google
1085
1064
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1086
- # This method supports patch semantics. Returns the modified variant without
1087
- # its calls.
1088
- # @param [String] variant_id
1089
- # The ID of the variant to be updated.
1090
- # @param [Google::Apis::GenomicsV1::Variant] variant_object
1091
- # @param [String] update_mask
1092
- # An optional mask specifying which fields to update. At this time, mutable
1093
- # fields are names and
1094
- # info. Acceptable values are "names" and
1095
- # "info". If unspecified, all mutable fields will be updated.
1065
+ # The provided variant set must have a valid `datasetId` set - all other
1066
+ # fields are optional. Note that the `id` field will be ignored, as this is
1067
+ # assigned by the server.
1068
+ # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
1096
1069
  # @param [String] fields
1097
1070
  # Selector specifying which fields to include in a partial response.
1098
1071
  # @param [String] quota_user
@@ -1102,33 +1075,33 @@ module Google
1102
1075
  # Request-specific options
1103
1076
  #
1104
1077
  # @yield [result, err] Result & error if block supplied
1105
- # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
1078
+ # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
1106
1079
  # @yieldparam err [StandardError] error object if request failed
1107
1080
  #
1108
- # @return [Google::Apis::GenomicsV1::Variant]
1081
+ # @return [Google::Apis::GenomicsV1::VariantSet]
1109
1082
  #
1110
1083
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1111
1084
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1112
1085
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1113
- def patch_variant(variant_id, variant_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
1114
- command = make_simple_command(:patch, 'v1/variants/{variantId}', options)
1115
- command.request_representation = Google::Apis::GenomicsV1::Variant::Representation
1116
- command.request_object = variant_object
1117
- command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
1118
- command.response_class = Google::Apis::GenomicsV1::Variant
1119
- command.params['variantId'] = variant_id unless variant_id.nil?
1120
- command.query['updateMask'] = update_mask unless update_mask.nil?
1086
+ def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1087
+ command = make_simple_command(:post, 'v1/variantsets', options)
1088
+ command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1089
+ command.request_object = variant_set_object
1090
+ command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1091
+ command.response_class = Google::Apis::GenomicsV1::VariantSet
1121
1092
  command.query['fields'] = fields unless fields.nil?
1122
1093
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1123
1094
  execute_or_queue_command(command, &block)
1124
1095
  end
1125
1096
 
1126
- # Gets a variant by ID.
1127
- # For the definitions of variants and other genomics resources, see
1097
+ # Exports variant set data to an external destination.
1098
+ # For the definitions of variant sets and other genomics resources, see
1128
1099
  # [Fundamentals of Google
1129
1100
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1130
- # @param [String] variant_id
1131
- # The ID of the variant.
1101
+ # @param [String] variant_set_id
1102
+ # Required. The ID of the variant set that contains variant data which
1103
+ # should be exported. The caller must have READ access to this variant set.
1104
+ # @param [Google::Apis::GenomicsV1::ExportVariantSetRequest] export_variant_set_request_object
1132
1105
  # @param [String] fields
1133
1106
  # Selector specifying which fields to include in a partial response.
1134
1107
  # @param [String] quota_user
@@ -1138,32 +1111,34 @@ module Google
1138
1111
  # Request-specific options
1139
1112
  #
1140
1113
  # @yield [result, err] Result & error if block supplied
1141
- # @yieldparam result [Google::Apis::GenomicsV1::Variant] parsed result object
1114
+ # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
1142
1115
  # @yieldparam err [StandardError] error object if request failed
1143
1116
  #
1144
- # @return [Google::Apis::GenomicsV1::Variant]
1117
+ # @return [Google::Apis::GenomicsV1::Operation]
1145
1118
  #
1146
1119
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1147
1120
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1148
1121
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1149
- def get_variant(variant_id, fields: nil, quota_user: nil, options: nil, &block)
1150
- command = make_simple_command(:get, 'v1/variants/{variantId}', options)
1151
- command.response_representation = Google::Apis::GenomicsV1::Variant::Representation
1152
- command.response_class = Google::Apis::GenomicsV1::Variant
1153
- command.params['variantId'] = variant_id unless variant_id.nil?
1122
+ def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1123
+ command = make_simple_command(:post, 'v1/variantsets/{variantSetId}:export', options)
1124
+ command.request_representation = Google::Apis::GenomicsV1::ExportVariantSetRequest::Representation
1125
+ command.request_object = export_variant_set_request_object
1126
+ command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
1127
+ command.response_class = Google::Apis::GenomicsV1::Operation
1128
+ command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1154
1129
  command.query['fields'] = fields unless fields.nil?
1155
1130
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1156
1131
  execute_or_queue_command(command, &block)
1157
1132
  end
1158
1133
 
1159
- # Searches for references which match the given criteria.
1160
- # For the definitions of references and other genomics resources, see
1134
+ # Returns a list of all variant sets matching search criteria.
1135
+ # For the definitions of variant sets and other genomics resources, see
1161
1136
  # [Fundamentals of Google
1162
1137
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1163
1138
  # Implements
1164
- # [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.
1165
- # 5.1/src/main/resources/avro/referencemethods.avdl#L146).
1166
- # @param [Google::Apis::GenomicsV1::SearchReferencesRequest] search_references_request_object
1139
+ # [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.
1140
+ # 5.1/src/main/resources/avro/variantmethods.avdl#L49).
1141
+ # @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_request_object
1167
1142
  # @param [String] fields
1168
1143
  # Selector specifying which fields to include in a partial response.
1169
1144
  # @param [String] quota_user
@@ -1173,34 +1148,39 @@ module Google
1173
1148
  # Request-specific options
1174
1149
  #
1175
1150
  # @yield [result, err] Result & error if block supplied
1176
- # @yieldparam result [Google::Apis::GenomicsV1::SearchReferencesResponse] parsed result object
1151
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantSetsResponse] parsed result object
1177
1152
  # @yieldparam err [StandardError] error object if request failed
1178
1153
  #
1179
- # @return [Google::Apis::GenomicsV1::SearchReferencesResponse]
1154
+ # @return [Google::Apis::GenomicsV1::SearchVariantSetsResponse]
1180
1155
  #
1181
1156
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1182
1157
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1183
1158
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1184
- def search_references(search_references_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1185
- command = make_simple_command(:post, 'v1/references/search', options)
1186
- command.request_representation = Google::Apis::GenomicsV1::SearchReferencesRequest::Representation
1187
- command.request_object = search_references_request_object
1188
- command.response_representation = Google::Apis::GenomicsV1::SearchReferencesResponse::Representation
1189
- command.response_class = Google::Apis::GenomicsV1::SearchReferencesResponse
1159
+ def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1160
+ command = make_simple_command(:post, 'v1/variantsets/search', options)
1161
+ command.request_representation = Google::Apis::GenomicsV1::SearchVariantSetsRequest::Representation
1162
+ command.request_object = search_variant_sets_request_object
1163
+ command.response_representation = Google::Apis::GenomicsV1::SearchVariantSetsResponse::Representation
1164
+ command.response_class = Google::Apis::GenomicsV1::SearchVariantSetsResponse
1190
1165
  command.query['fields'] = fields unless fields.nil?
1191
1166
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1192
1167
  execute_or_queue_command(command, &block)
1193
1168
  end
1194
1169
 
1195
- # Gets a reference.
1196
- # For the definitions of references and other genomics resources, see
1170
+ # Updates a variant set using patch semantics.
1171
+ # For the definitions of variant sets and other genomics resources, see
1197
1172
  # [Fundamentals of Google
1198
1173
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1199
- # Implements
1200
- # [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/
1201
- # src/main/resources/avro/referencemethods.avdl#L158).
1202
- # @param [String] reference_id
1203
- # The ID of the reference.
1174
+ # @param [String] variant_set_id
1175
+ # The ID of the variant to be updated (must already exist).
1176
+ # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
1177
+ # @param [String] update_mask
1178
+ # An optional mask specifying which fields to update. Supported fields:
1179
+ # * metadata.
1180
+ # * name.
1181
+ # * description.
1182
+ # Leaving `updateMask` unset is equivalent to specifying all mutable
1183
+ # fields.
1204
1184
  # @param [String] fields
1205
1185
  # Selector specifying which fields to include in a partial response.
1206
1186
  # @param [String] quota_user
@@ -1210,46 +1190,33 @@ module Google
1210
1190
  # Request-specific options
1211
1191
  #
1212
1192
  # @yield [result, err] Result & error if block supplied
1213
- # @yieldparam result [Google::Apis::GenomicsV1::Reference] parsed result object
1193
+ # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
1214
1194
  # @yieldparam err [StandardError] error object if request failed
1215
1195
  #
1216
- # @return [Google::Apis::GenomicsV1::Reference]
1196
+ # @return [Google::Apis::GenomicsV1::VariantSet]
1217
1197
  #
1218
1198
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1219
1199
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1220
1200
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1221
- def get_reference(reference_id, fields: nil, quota_user: nil, options: nil, &block)
1222
- command = make_simple_command(:get, 'v1/references/{referenceId}', options)
1223
- command.response_representation = Google::Apis::GenomicsV1::Reference::Representation
1224
- command.response_class = Google::Apis::GenomicsV1::Reference
1225
- command.params['referenceId'] = reference_id unless reference_id.nil?
1201
+ def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
1202
+ command = make_simple_command(:patch, 'v1/variantsets/{variantSetId}', options)
1203
+ command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1204
+ command.request_object = variant_set_object
1205
+ command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1206
+ command.response_class = Google::Apis::GenomicsV1::VariantSet
1207
+ command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1208
+ command.query['updateMask'] = update_mask unless update_mask.nil?
1226
1209
  command.query['fields'] = fields unless fields.nil?
1227
1210
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1228
1211
  execute_or_queue_command(command, &block)
1229
1212
  end
1230
1213
 
1231
- # Lists the bases in a reference, optionally restricted to a range.
1232
- # For the definitions of references and other genomics resources, see
1214
+ # Gets a variant set by ID.
1215
+ # For the definitions of variant sets and other genomics resources, see
1233
1216
  # [Fundamentals of Google
1234
1217
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1235
- # Implements
1236
- # [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.
1237
- # 5.1/src/main/resources/avro/referencemethods.avdl#L221).
1238
- # @param [String] reference_id
1239
- # The ID of the reference.
1240
- # @param [String] page_token
1241
- # The continuation token, which is used to page through large result sets.
1242
- # To get the next page of results, set this parameter to the value of
1243
- # `nextPageToken` from the previous response.
1244
- # @param [Fixnum] page_size
1245
- # The maximum number of bases to return in a single page. If unspecified,
1246
- # defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base
1247
- # pairs).
1248
- # @param [String] start_position
1249
- # The start position (0-based) of this query. Defaults to 0.
1250
- # @param [String] end_position
1251
- # The end position (0-based, exclusive) of this query. Defaults to the length
1252
- # of this reference.
1218
+ # @param [String] variant_set_id
1219
+ # Required. The ID of the variant set.
1253
1220
  # @param [String] fields
1254
1221
  # Selector specifying which fields to include in a partial response.
1255
1222
  # @param [String] quota_user
@@ -1259,38 +1226,41 @@ module Google
1259
1226
  # Request-specific options
1260
1227
  #
1261
1228
  # @yield [result, err] Result & error if block supplied
1262
- # @yieldparam result [Google::Apis::GenomicsV1::ListBasesResponse] parsed result object
1229
+ # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
1263
1230
  # @yieldparam err [StandardError] error object if request failed
1264
1231
  #
1265
- # @return [Google::Apis::GenomicsV1::ListBasesResponse]
1232
+ # @return [Google::Apis::GenomicsV1::VariantSet]
1266
1233
  #
1267
1234
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1268
1235
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1269
1236
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1270
- def list_reference_bases(reference_id, page_token: nil, page_size: nil, start_position: nil, end_position: nil, fields: nil, quota_user: nil, options: nil, &block)
1271
- command = make_simple_command(:get, 'v1/references/{referenceId}/bases', options)
1272
- command.response_representation = Google::Apis::GenomicsV1::ListBasesResponse::Representation
1273
- command.response_class = Google::Apis::GenomicsV1::ListBasesResponse
1274
- command.params['referenceId'] = reference_id unless reference_id.nil?
1275
- command.query['pageToken'] = page_token unless page_token.nil?
1276
- command.query['pageSize'] = page_size unless page_size.nil?
1277
- command.query['start'] = start_position unless start_position.nil?
1278
- command.query['end'] = end_position unless end_position.nil?
1237
+ def get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
1238
+ command = make_simple_command(:get, 'v1/variantsets/{variantSetId}', options)
1239
+ command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1240
+ command.response_class = Google::Apis::GenomicsV1::VariantSet
1241
+ command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1279
1242
  command.query['fields'] = fields unless fields.nil?
1280
1243
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1281
1244
  execute_or_queue_command(command, &block)
1282
1245
  end
1283
1246
 
1284
- # Returns permissions that a caller has on the specified resource.
1285
- # See <a href="/iam/docs/managing-policies#testing_permissions">Testing
1286
- # Permissions</a> for more information.
1287
- # For the definitions of datasets and other genomics resources, see
1288
- # [Fundamentals of Google
1289
- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1290
- # @param [String] resource
1291
- # REQUIRED: The resource for which policy is being specified. Format is
1292
- # `datasets/<dataset ID>`.
1293
- # @param [Google::Apis::GenomicsV1::TestIamPermissionsRequest] test_iam_permissions_request_object
1247
+ # Creates a new annotation. Caller must have WRITE permission
1248
+ # for the associated annotation set.
1249
+ # The following fields are required:
1250
+ # * annotationSetId
1251
+ # * referenceName or
1252
+ # referenceId
1253
+ # ### Transcripts
1254
+ # For annotations of type TRANSCRIPT, the following fields of
1255
+ # transcript must be provided:
1256
+ # * exons.start
1257
+ # * exons.end
1258
+ # All other fields may be optionally specified, unless documented as being
1259
+ # server-generated (for example, the `id` field). The annotated
1260
+ # range must be no longer than 100Mbp (mega base pairs). See the
1261
+ # Annotation resource
1262
+ # for additional restrictions on each field.
1263
+ # @param [Google::Apis::GenomicsV1::Annotation] annotation_object
1294
1264
  # @param [String] fields
1295
1265
  # Selector specifying which fields to include in a partial response.
1296
1266
  # @param [String] quota_user
@@ -1300,37 +1270,38 @@ module Google
1300
1270
  # Request-specific options
1301
1271
  #
1302
1272
  # @yield [result, err] Result & error if block supplied
1303
- # @yieldparam result [Google::Apis::GenomicsV1::TestIamPermissionsResponse] parsed result object
1273
+ # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
1304
1274
  # @yieldparam err [StandardError] error object if request failed
1305
1275
  #
1306
- # @return [Google::Apis::GenomicsV1::TestIamPermissionsResponse]
1276
+ # @return [Google::Apis::GenomicsV1::Annotation]
1307
1277
  #
1308
1278
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1309
1279
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1310
1280
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1311
- def test_dataset_iam_permissions(resource, test_iam_permissions_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1312
- command = make_simple_command(:post, 'v1/{+resource}:testIamPermissions', options)
1313
- command.request_representation = Google::Apis::GenomicsV1::TestIamPermissionsRequest::Representation
1314
- command.request_object = test_iam_permissions_request_object
1315
- command.response_representation = Google::Apis::GenomicsV1::TestIamPermissionsResponse::Representation
1316
- command.response_class = Google::Apis::GenomicsV1::TestIamPermissionsResponse
1317
- command.params['resource'] = resource unless resource.nil?
1281
+ def create_annotation(annotation_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1282
+ command = make_simple_command(:post, 'v1/annotations', options)
1283
+ command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation
1284
+ command.request_object = annotation_object
1285
+ command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation
1286
+ command.response_class = Google::Apis::GenomicsV1::Annotation
1318
1287
  command.query['fields'] = fields unless fields.nil?
1319
1288
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1320
1289
  execute_or_queue_command(command, &block)
1321
1290
  end
1322
1291
 
1323
- # Deletes a dataset and all of its contents (all read group sets,
1324
- # reference sets, variant sets, call sets, annotation sets, etc.)
1325
- # This is reversible (up to one week after the deletion) via
1326
- # the
1327
- # datasets.undelete
1328
- # operation.
1329
- # For the definitions of datasets and other genomics resources, see
1330
- # [Fundamentals of Google
1331
- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1332
- # @param [String] dataset_id
1333
- # The ID of the dataset to be deleted.
1292
+ # Creates one or more new annotations atomically. All annotations must
1293
+ # belong to the same annotation set. Caller must have WRITE
1294
+ # permission for this annotation set. For optimal performance, batch
1295
+ # positionally adjacent annotations together.
1296
+ # If the request has a systemic issue, such as an attempt to write to
1297
+ # an inaccessible annotation set, the entire RPC will fail accordingly. For
1298
+ # lesser data issues, when possible an error will be isolated to the
1299
+ # corresponding batch entry in the response; the remaining well formed
1300
+ # annotations will be created normally.
1301
+ # For details on the requirements for each individual annotation resource,
1302
+ # see
1303
+ # CreateAnnotation.
1304
+ # @param [Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest] batch_create_annotations_request_object
1334
1305
  # @param [String] fields
1335
1306
  # Selector specifying which fields to include in a partial response.
1336
1307
  # @param [String] quota_user
@@ -1340,37 +1311,33 @@ module Google
1340
1311
  # Request-specific options
1341
1312
  #
1342
1313
  # @yield [result, err] Result & error if block supplied
1343
- # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
1314
+ # @yieldparam result [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse] parsed result object
1344
1315
  # @yieldparam err [StandardError] error object if request failed
1345
1316
  #
1346
- # @return [Google::Apis::GenomicsV1::Empty]
1317
+ # @return [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse]
1347
1318
  #
1348
1319
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1349
1320
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1350
1321
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1351
- def delete_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block)
1352
- command = make_simple_command(:delete, 'v1/datasets/{datasetId}', options)
1353
- command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
1354
- command.response_class = Google::Apis::GenomicsV1::Empty
1355
- command.params['datasetId'] = dataset_id unless dataset_id.nil?
1322
+ def batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1323
+ command = make_simple_command(:post, 'v1/annotations:batchCreate', options)
1324
+ command.request_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest::Representation
1325
+ command.request_object = batch_create_annotations_request_object
1326
+ command.response_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse::Representation
1327
+ command.response_class = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse
1356
1328
  command.query['fields'] = fields unless fields.nil?
1357
1329
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1358
1330
  execute_or_queue_command(command, &block)
1359
1331
  end
1360
1332
 
1361
- # Lists datasets within a project.
1362
- # For the definitions of datasets and other genomics resources, see
1363
- # [Fundamentals of Google
1364
- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1365
- # @param [String] page_token
1366
- # The continuation token, which is used to page through large result sets.
1367
- # To get the next page of results, set this parameter to the value of
1368
- # `nextPageToken` from the previous response.
1369
- # @param [Fixnum] page_size
1370
- # The maximum number of results to return in a single page. If unspecified,
1371
- # defaults to 50. The maximum value is 1024.
1372
- # @param [String] project_id
1373
- # Required. The Google Cloud project ID to list datasets for.
1333
+ # Searches for annotations that match the given criteria. Results are
1334
+ # ordered by genomic coordinate (by reference sequence, then position).
1335
+ # Annotations with equivalent genomic coordinates are returned in an
1336
+ # unspecified order. This order is consistent, such that two queries for the
1337
+ # same content (regardless of page size) yield annotations in the same order
1338
+ # across their respective streams of paginated responses. Caller must have
1339
+ # READ permission for the queried annotation sets.
1340
+ # @param [Google::Apis::GenomicsV1::SearchAnnotationsRequest] search_annotations_request_object
1374
1341
  # @param [String] fields
1375
1342
  # Selector specifying which fields to include in a partial response.
1376
1343
  # @param [String] quota_user
@@ -1380,37 +1347,29 @@ module Google
1380
1347
  # Request-specific options
1381
1348
  #
1382
1349
  # @yield [result, err] Result & error if block supplied
1383
- # @yieldparam result [Google::Apis::GenomicsV1::ListDatasetsResponse] parsed result object
1350
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationsResponse] parsed result object
1384
1351
  # @yieldparam err [StandardError] error object if request failed
1385
1352
  #
1386
- # @return [Google::Apis::GenomicsV1::ListDatasetsResponse]
1353
+ # @return [Google::Apis::GenomicsV1::SearchAnnotationsResponse]
1387
1354
  #
1388
1355
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1389
1356
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1390
1357
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1391
- def list_datasets(page_token: nil, page_size: nil, project_id: nil, fields: nil, quota_user: nil, options: nil, &block)
1392
- command = make_simple_command(:get, 'v1/datasets', options)
1393
- command.response_representation = Google::Apis::GenomicsV1::ListDatasetsResponse::Representation
1394
- command.response_class = Google::Apis::GenomicsV1::ListDatasetsResponse
1395
- command.query['pageToken'] = page_token unless page_token.nil?
1396
- command.query['pageSize'] = page_size unless page_size.nil?
1397
- command.query['projectId'] = project_id unless project_id.nil?
1358
+ def search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1359
+ command = make_simple_command(:post, 'v1/annotations/search', options)
1360
+ command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationsRequest::Representation
1361
+ command.request_object = search_annotations_request_object
1362
+ command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationsResponse::Representation
1363
+ command.response_class = Google::Apis::GenomicsV1::SearchAnnotationsResponse
1398
1364
  command.query['fields'] = fields unless fields.nil?
1399
1365
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1400
1366
  execute_or_queue_command(command, &block)
1401
1367
  end
1402
1368
 
1403
- # Sets the access control policy on the specified dataset. Replaces any
1404
- # existing policy.
1405
- # For the definitions of datasets and other genomics resources, see
1406
- # [Fundamentals of Google
1407
- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1408
- # See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
1409
- # Policy</a> for more information.
1410
- # @param [String] resource
1411
- # REQUIRED: The resource for which policy is being specified. Format is
1412
- # `datasets/<dataset ID>`.
1413
- # @param [Google::Apis::GenomicsV1::SetIamPolicyRequest] set_iam_policy_request_object
1369
+ # Gets an annotation. Caller must have READ permission
1370
+ # for the associated annotation set.
1371
+ # @param [String] annotation_id
1372
+ # The ID of the annotation to be retrieved.
1414
1373
  # @param [String] fields
1415
1374
  # Selector specifying which fields to include in a partial response.
1416
1375
  # @param [String] quota_user
@@ -1420,70 +1379,70 @@ module Google
1420
1379
  # Request-specific options
1421
1380
  #
1422
1381
  # @yield [result, err] Result & error if block supplied
1423
- # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object
1382
+ # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
1424
1383
  # @yieldparam err [StandardError] error object if request failed
1425
1384
  #
1426
- # @return [Google::Apis::GenomicsV1::Policy]
1385
+ # @return [Google::Apis::GenomicsV1::Annotation]
1427
1386
  #
1428
1387
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1429
1388
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1430
1389
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1431
- def set_dataset_iam_policy(resource, set_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1432
- command = make_simple_command(:post, 'v1/{+resource}:setIamPolicy', options)
1433
- command.request_representation = Google::Apis::GenomicsV1::SetIamPolicyRequest::Representation
1434
- command.request_object = set_iam_policy_request_object
1435
- command.response_representation = Google::Apis::GenomicsV1::Policy::Representation
1436
- command.response_class = Google::Apis::GenomicsV1::Policy
1437
- command.params['resource'] = resource unless resource.nil?
1390
+ def get_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block)
1391
+ command = make_simple_command(:get, 'v1/annotations/{annotationId}', options)
1392
+ command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation
1393
+ command.response_class = Google::Apis::GenomicsV1::Annotation
1394
+ command.params['annotationId'] = annotation_id unless annotation_id.nil?
1438
1395
  command.query['fields'] = fields unless fields.nil?
1439
1396
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1440
1397
  execute_or_queue_command(command, &block)
1441
1398
  end
1442
1399
 
1443
- # Creates a new dataset.
1444
- # For the definitions of datasets and other genomics resources, see
1445
- # [Fundamentals of Google
1446
- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1447
- # @param [Google::Apis::GenomicsV1::Dataset] dataset_object
1448
- # @param [String] fields
1449
- # Selector specifying which fields to include in a partial response.
1450
- # @param [String] quota_user
1400
+ # Updates an annotation. Caller must have
1401
+ # WRITE permission for the associated dataset.
1402
+ # @param [String] annotation_id
1403
+ # The ID of the annotation to be updated.
1404
+ # @param [Google::Apis::GenomicsV1::Annotation] annotation_object
1405
+ # @param [String] update_mask
1406
+ # An optional mask specifying which fields to update. Mutable fields are
1407
+ # name,
1408
+ # variant,
1409
+ # transcript, and
1410
+ # info. If unspecified, all mutable
1411
+ # fields will be updated.
1412
+ # @param [String] fields
1413
+ # Selector specifying which fields to include in a partial response.
1414
+ # @param [String] quota_user
1451
1415
  # Available to use for quota purposes for server-side applications. Can be any
1452
1416
  # arbitrary string assigned to a user, but should not exceed 40 characters.
1453
1417
  # @param [Google::Apis::RequestOptions] options
1454
1418
  # Request-specific options
1455
1419
  #
1456
1420
  # @yield [result, err] Result & error if block supplied
1457
- # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
1421
+ # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
1458
1422
  # @yieldparam err [StandardError] error object if request failed
1459
1423
  #
1460
- # @return [Google::Apis::GenomicsV1::Dataset]
1424
+ # @return [Google::Apis::GenomicsV1::Annotation]
1461
1425
  #
1462
1426
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1463
1427
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1464
1428
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1465
- def create_dataset(dataset_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1466
- command = make_simple_command(:post, 'v1/datasets', options)
1467
- command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation
1468
- command.request_object = dataset_object
1469
- command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
1470
- command.response_class = Google::Apis::GenomicsV1::Dataset
1429
+ def update_annotation(annotation_id, annotation_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
1430
+ command = make_simple_command(:put, 'v1/annotations/{annotationId}', options)
1431
+ command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation
1432
+ command.request_object = annotation_object
1433
+ command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation
1434
+ command.response_class = Google::Apis::GenomicsV1::Annotation
1435
+ command.params['annotationId'] = annotation_id unless annotation_id.nil?
1436
+ command.query['updateMask'] = update_mask unless update_mask.nil?
1471
1437
  command.query['fields'] = fields unless fields.nil?
1472
1438
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1473
1439
  execute_or_queue_command(command, &block)
1474
1440
  end
1475
1441
 
1476
- # Gets the access control policy for the dataset. This is empty if the
1477
- # policy or resource does not exist.
1478
- # See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
1479
- # Policy</a> for more information.
1480
- # For the definitions of datasets and other genomics resources, see
1481
- # [Fundamentals of Google
1482
- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1483
- # @param [String] resource
1484
- # REQUIRED: The resource for which policy is being specified. Format is
1485
- # `datasets/<dataset ID>`.
1486
- # @param [Google::Apis::GenomicsV1::GetIamPolicyRequest] get_iam_policy_request_object
1442
+ # Deletes an annotation. Caller must have WRITE permission for
1443
+ # the associated annotation set.
1444
+ # @param [String] annotation_id
1445
+ # The ID of the annotation to be deleted.
1487
1446
  # @param [String] fields
1488
1447
  # Selector specifying which fields to include in a partial response.
1489
1448
  # @param [String] quota_user
@@ -1493,32 +1452,31 @@ module Google
1493
1452
  # Request-specific options
1494
1453
  #
1495
1454
  # @yield [result, err] Result & error if block supplied
1496
- # @yieldparam result [Google::Apis::GenomicsV1::Policy] parsed result object
1455
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
1497
1456
  # @yieldparam err [StandardError] error object if request failed
1498
1457
  #
1499
- # @return [Google::Apis::GenomicsV1::Policy]
1458
+ # @return [Google::Apis::GenomicsV1::Empty]
1500
1459
  #
1501
1460
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1502
1461
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1503
1462
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1504
- def get_dataset_iam_policy(resource, get_iam_policy_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1505
- command = make_simple_command(:post, 'v1/{+resource}:getIamPolicy', options)
1506
- command.request_representation = Google::Apis::GenomicsV1::GetIamPolicyRequest::Representation
1507
- command.request_object = get_iam_policy_request_object
1508
- command.response_representation = Google::Apis::GenomicsV1::Policy::Representation
1509
- command.response_class = Google::Apis::GenomicsV1::Policy
1510
- command.params['resource'] = resource unless resource.nil?
1463
+ def delete_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block)
1464
+ command = make_simple_command(:delete, 'v1/annotations/{annotationId}', options)
1465
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
1466
+ command.response_class = Google::Apis::GenomicsV1::Empty
1467
+ command.params['annotationId'] = annotation_id unless annotation_id.nil?
1511
1468
  command.query['fields'] = fields unless fields.nil?
1512
1469
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1513
1470
  execute_or_queue_command(command, &block)
1514
1471
  end
1515
1472
 
1516
- # Gets a dataset by ID.
1517
- # For the definitions of datasets and other genomics resources, see
1518
- # [Fundamentals of Google
1519
- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1520
- # @param [String] dataset_id
1521
- # The ID of the dataset.
1473
+ # Starts asynchronous cancellation on a long-running operation. The server makes
1474
+ # a best effort to cancel the operation, but success is not guaranteed. Clients
1475
+ # may use Operations.GetOperation or Operations.ListOperations to check whether
1476
+ # the cancellation succeeded or the operation completed despite cancellation.
1477
+ # @param [String] name
1478
+ # The name of the operation resource to be cancelled.
1479
+ # @param [Google::Apis::GenomicsV1::CancelOperationRequest] cancel_operation_request_object
1522
1480
  # @param [String] fields
1523
1481
  # Selector specifying which fields to include in a partial response.
1524
1482
  # @param [String] quota_user
@@ -1528,37 +1486,51 @@ module Google
1528
1486
  # Request-specific options
1529
1487
  #
1530
1488
  # @yield [result, err] Result & error if block supplied
1531
- # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
1489
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
1532
1490
  # @yieldparam err [StandardError] error object if request failed
1533
1491
  #
1534
- # @return [Google::Apis::GenomicsV1::Dataset]
1492
+ # @return [Google::Apis::GenomicsV1::Empty]
1535
1493
  #
1536
1494
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1537
1495
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1538
1496
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1539
- def get_dataset(dataset_id, fields: nil, quota_user: nil, options: nil, &block)
1540
- command = make_simple_command(:get, 'v1/datasets/{datasetId}', options)
1541
- command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
1542
- command.response_class = Google::Apis::GenomicsV1::Dataset
1543
- command.params['datasetId'] = dataset_id unless dataset_id.nil?
1497
+ def cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1498
+ command = make_simple_command(:post, 'v1/{+name}:cancel', options)
1499
+ command.request_representation = Google::Apis::GenomicsV1::CancelOperationRequest::Representation
1500
+ command.request_object = cancel_operation_request_object
1501
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
1502
+ command.response_class = Google::Apis::GenomicsV1::Empty
1503
+ command.params['name'] = name unless name.nil?
1544
1504
  command.query['fields'] = fields unless fields.nil?
1545
1505
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1546
1506
  execute_or_queue_command(command, &block)
1547
1507
  end
1548
1508
 
1549
- # Updates a dataset.
1550
- # For the definitions of datasets and other genomics resources, see
1551
- # [Fundamentals of Google
1552
- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1553
- # This method supports patch semantics.
1554
- # @param [String] dataset_id
1555
- # The ID of the dataset to be updated.
1556
- # @param [Google::Apis::GenomicsV1::Dataset] dataset_object
1557
- # @param [String] update_mask
1558
- # An optional mask specifying which fields to update. At this time, the only
1559
- # mutable field is name. The only
1560
- # acceptable value is "name". If unspecified, all mutable fields will be
1561
- # updated.
1509
+ # Lists operations that match the specified filter in the request.
1510
+ # @param [String] name
1511
+ # The name of the operation collection.
1512
+ # @param [String] page_token
1513
+ # The standard list page token.
1514
+ # @param [Fixnum] page_size
1515
+ # The maximum number of results to return. If unspecified, defaults to
1516
+ # 256. The maximum value is 2048.
1517
+ # @param [String] filter
1518
+ # A string for filtering Operations.
1519
+ # The following filter fields are supported&#58;
1520
+ # * projectId&#58; Required. Corresponds to
1521
+ # OperationMetadata.projectId.
1522
+ # * createTime&#58; The time this job was created, in seconds from the
1523
+ # [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`
1524
+ # operators.
1525
+ # * status&#58; Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only
1526
+ # one status may be specified.
1527
+ # * labels.key where key is a label key.
1528
+ # Examples&#58;
1529
+ # * `projectId = my-project AND createTime >= 1432140000`
1530
+ # * `projectId = my-project AND createTime >= 1432140000 AND createTime <=
1531
+ # 1432150000 AND status = RUNNING`
1532
+ # * `projectId = my-project AND labels.color = *`
1533
+ # * `projectId = my-project AND labels.color = red`
1562
1534
  # @param [String] fields
1563
1535
  # Selector specifying which fields to include in a partial response.
1564
1536
  # @param [String] quota_user
@@ -1568,35 +1540,32 @@ module Google
1568
1540
  # Request-specific options
1569
1541
  #
1570
1542
  # @yield [result, err] Result & error if block supplied
1571
- # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
1543
+ # @yieldparam result [Google::Apis::GenomicsV1::ListOperationsResponse] parsed result object
1572
1544
  # @yieldparam err [StandardError] error object if request failed
1573
1545
  #
1574
- # @return [Google::Apis::GenomicsV1::Dataset]
1546
+ # @return [Google::Apis::GenomicsV1::ListOperationsResponse]
1575
1547
  #
1576
1548
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1577
1549
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1578
1550
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1579
- def patch_dataset(dataset_id, dataset_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
1580
- command = make_simple_command(:patch, 'v1/datasets/{datasetId}', options)
1581
- command.request_representation = Google::Apis::GenomicsV1::Dataset::Representation
1582
- command.request_object = dataset_object
1583
- command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
1584
- command.response_class = Google::Apis::GenomicsV1::Dataset
1585
- command.params['datasetId'] = dataset_id unless dataset_id.nil?
1586
- command.query['updateMask'] = update_mask unless update_mask.nil?
1551
+ def list_operations(name, page_token: nil, page_size: nil, filter: nil, fields: nil, quota_user: nil, options: nil, &block)
1552
+ command = make_simple_command(:get, 'v1/{+name}', options)
1553
+ command.response_representation = Google::Apis::GenomicsV1::ListOperationsResponse::Representation
1554
+ command.response_class = Google::Apis::GenomicsV1::ListOperationsResponse
1555
+ command.params['name'] = name unless name.nil?
1556
+ command.query['pageToken'] = page_token unless page_token.nil?
1557
+ command.query['pageSize'] = page_size unless page_size.nil?
1558
+ command.query['filter'] = filter unless filter.nil?
1587
1559
  command.query['fields'] = fields unless fields.nil?
1588
1560
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1589
1561
  execute_or_queue_command(command, &block)
1590
1562
  end
1591
1563
 
1592
- # Undeletes a dataset by restoring a dataset which was deleted via this API.
1593
- # For the definitions of datasets and other genomics resources, see
1594
- # [Fundamentals of Google
1595
- # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1596
- # This operation is only possible for a week after the deletion occurred.
1597
- # @param [String] dataset_id
1598
- # The ID of the dataset to be undeleted.
1599
- # @param [Google::Apis::GenomicsV1::UndeleteDatasetRequest] undelete_dataset_request_object
1564
+ # Gets the latest state of a long-running operation. Clients can use this
1565
+ # method to poll the operation result at intervals as recommended by the API
1566
+ # service.
1567
+ # @param [String] name
1568
+ # The name of the operation resource.
1600
1569
  # @param [String] fields
1601
1570
  # Selector specifying which fields to include in a partial response.
1602
1571
  # @param [String] quota_user
@@ -1606,33 +1575,32 @@ module Google
1606
1575
  # Request-specific options
1607
1576
  #
1608
1577
  # @yield [result, err] Result & error if block supplied
1609
- # @yieldparam result [Google::Apis::GenomicsV1::Dataset] parsed result object
1578
+ # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
1610
1579
  # @yieldparam err [StandardError] error object if request failed
1611
1580
  #
1612
- # @return [Google::Apis::GenomicsV1::Dataset]
1581
+ # @return [Google::Apis::GenomicsV1::Operation]
1613
1582
  #
1614
1583
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1615
1584
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1616
1585
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1617
- def undelete_dataset(dataset_id, undelete_dataset_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1618
- command = make_simple_command(:post, 'v1/datasets/{datasetId}:undelete', options)
1619
- command.request_representation = Google::Apis::GenomicsV1::UndeleteDatasetRequest::Representation
1620
- command.request_object = undelete_dataset_request_object
1621
- command.response_representation = Google::Apis::GenomicsV1::Dataset::Representation
1622
- command.response_class = Google::Apis::GenomicsV1::Dataset
1623
- command.params['datasetId'] = dataset_id unless dataset_id.nil?
1586
+ def get_operation(name, fields: nil, quota_user: nil, options: nil, &block)
1587
+ command = make_simple_command(:get, 'v1/{+name}', options)
1588
+ command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
1589
+ command.response_class = Google::Apis::GenomicsV1::Operation
1590
+ command.params['name'] = name unless name.nil?
1624
1591
  command.query['fields'] = fields unless fields.nil?
1625
1592
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1626
1593
  execute_or_queue_command(command, &block)
1627
1594
  end
1628
1595
 
1629
- # Deletes a variant set including all variants, call sets, and calls within.
1630
- # This is not reversible.
1631
- # For the definitions of variant sets and other genomics resources, see
1596
+ # Searches for reference sets which match the given criteria.
1597
+ # For the definitions of references and other genomics resources, see
1632
1598
  # [Fundamentals of Google
1633
1599
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1634
- # @param [String] variant_set_id
1635
- # The ID of the variant set to be deleted.
1600
+ # Implements
1601
+ # [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/
1602
+ # v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
1603
+ # @param [Google::Apis::GenomicsV1::SearchReferenceSetsRequest] search_reference_sets_request_object
1636
1604
  # @param [String] fields
1637
1605
  # Selector specifying which fields to include in a partial response.
1638
1606
  # @param [String] quota_user
@@ -1642,32 +1610,34 @@ module Google
1642
1610
  # Request-specific options
1643
1611
  #
1644
1612
  # @yield [result, err] Result & error if block supplied
1645
- # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
1613
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchReferenceSetsResponse] parsed result object
1646
1614
  # @yieldparam err [StandardError] error object if request failed
1647
1615
  #
1648
- # @return [Google::Apis::GenomicsV1::Empty]
1616
+ # @return [Google::Apis::GenomicsV1::SearchReferenceSetsResponse]
1649
1617
  #
1650
1618
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1651
1619
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1652
1620
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1653
- def delete_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
1654
- command = make_simple_command(:delete, 'v1/variantsets/{variantSetId}', options)
1655
- command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
1656
- command.response_class = Google::Apis::GenomicsV1::Empty
1657
- command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1621
+ def search_reference_sets(search_reference_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1622
+ command = make_simple_command(:post, 'v1/referencesets/search', options)
1623
+ command.request_representation = Google::Apis::GenomicsV1::SearchReferenceSetsRequest::Representation
1624
+ command.request_object = search_reference_sets_request_object
1625
+ command.response_representation = Google::Apis::GenomicsV1::SearchReferenceSetsResponse::Representation
1626
+ command.response_class = Google::Apis::GenomicsV1::SearchReferenceSetsResponse
1658
1627
  command.query['fields'] = fields unless fields.nil?
1659
1628
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1660
1629
  execute_or_queue_command(command, &block)
1661
1630
  end
1662
1631
 
1663
- # Creates a new variant set.
1664
- # For the definitions of variant sets and other genomics resources, see
1632
+ # Gets a reference set.
1633
+ # For the definitions of references and other genomics resources, see
1665
1634
  # [Fundamentals of Google
1666
1635
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1667
- # The provided variant set must have a valid `datasetId` set - all other
1668
- # fields are optional. Note that the `id` field will be ignored, as this is
1669
- # assigned by the server.
1670
- # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
1636
+ # Implements
1637
+ # [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.
1638
+ # 1/src/main/resources/avro/referencemethods.avdl#L83).
1639
+ # @param [String] reference_set_id
1640
+ # The ID of the reference set.
1671
1641
  # @param [String] fields
1672
1642
  # Selector specifying which fields to include in a partial response.
1673
1643
  # @param [String] quota_user
@@ -1677,33 +1647,36 @@ module Google
1677
1647
  # Request-specific options
1678
1648
  #
1679
1649
  # @yield [result, err] Result & error if block supplied
1680
- # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
1650
+ # @yieldparam result [Google::Apis::GenomicsV1::ReferenceSet] parsed result object
1681
1651
  # @yieldparam err [StandardError] error object if request failed
1682
1652
  #
1683
- # @return [Google::Apis::GenomicsV1::VariantSet]
1653
+ # @return [Google::Apis::GenomicsV1::ReferenceSet]
1684
1654
  #
1685
1655
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1686
1656
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1687
1657
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1688
- def create_variantset(variant_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1689
- command = make_simple_command(:post, 'v1/variantsets', options)
1690
- command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1691
- command.request_object = variant_set_object
1692
- command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1693
- command.response_class = Google::Apis::GenomicsV1::VariantSet
1658
+ def get_reference_set(reference_set_id, fields: nil, quota_user: nil, options: nil, &block)
1659
+ command = make_simple_command(:get, 'v1/referencesets/{referenceSetId}', options)
1660
+ command.response_representation = Google::Apis::GenomicsV1::ReferenceSet::Representation
1661
+ command.response_class = Google::Apis::GenomicsV1::ReferenceSet
1662
+ command.params['referenceSetId'] = reference_set_id unless reference_set_id.nil?
1694
1663
  command.query['fields'] = fields unless fields.nil?
1695
1664
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1696
1665
  execute_or_queue_command(command, &block)
1697
1666
  end
1698
1667
 
1699
- # Exports variant set data to an external destination.
1700
- # For the definitions of variant sets and other genomics resources, see
1668
+ # Exports a read group set to a BAM file in Google Cloud Storage.
1669
+ # For the definitions of read group sets and other genomics resources, see
1701
1670
  # [Fundamentals of Google
1702
1671
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1703
- # @param [String] variant_set_id
1704
- # Required. The ID of the variant set that contains variant data which
1705
- # should be exported. The caller must have READ access to this variant set.
1706
- # @param [Google::Apis::GenomicsV1::ExportVariantSetRequest] export_variant_set_request_object
1672
+ # Note that currently there may be some differences between exported BAM
1673
+ # files and the original BAM file at the time of import. See
1674
+ # ImportReadGroupSets
1675
+ # for caveats.
1676
+ # @param [String] read_group_set_id
1677
+ # Required. The ID of the read group set to export. The caller must have
1678
+ # READ access to this read group set.
1679
+ # @param [Google::Apis::GenomicsV1::ExportReadGroupSetRequest] export_read_group_set_request_object
1707
1680
  # @param [String] fields
1708
1681
  # Selector specifying which fields to include in a partial response.
1709
1682
  # @param [String] quota_user
@@ -1721,26 +1694,26 @@ module Google
1721
1694
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1722
1695
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1723
1696
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1724
- def export_variant_set(variant_set_id, export_variant_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1725
- command = make_simple_command(:post, 'v1/variantsets/{variantSetId}:export', options)
1726
- command.request_representation = Google::Apis::GenomicsV1::ExportVariantSetRequest::Representation
1727
- command.request_object = export_variant_set_request_object
1728
- command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
1729
- command.response_class = Google::Apis::GenomicsV1::Operation
1730
- command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1697
+ def export_read_group_sets(read_group_set_id, export_read_group_set_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1698
+ command = make_simple_command(:post, 'v1/readgroupsets/{readGroupSetId}:export', options)
1699
+ command.request_representation = Google::Apis::GenomicsV1::ExportReadGroupSetRequest::Representation
1700
+ command.request_object = export_read_group_set_request_object
1701
+ command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
1702
+ command.response_class = Google::Apis::GenomicsV1::Operation
1703
+ command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
1731
1704
  command.query['fields'] = fields unless fields.nil?
1732
1705
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1733
1706
  execute_or_queue_command(command, &block)
1734
1707
  end
1735
1708
 
1736
- # Returns a list of all variant sets matching search criteria.
1737
- # For the definitions of variant sets and other genomics resources, see
1709
+ # Searches for read group sets matching the criteria.
1710
+ # For the definitions of read group sets and other genomics resources, see
1738
1711
  # [Fundamentals of Google
1739
1712
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1740
1713
  # Implements
1741
- # [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.
1742
- # 5.1/src/main/resources/avro/variantmethods.avdl#L49).
1743
- # @param [Google::Apis::GenomicsV1::SearchVariantSetsRequest] search_variant_sets_request_object
1714
+ # [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/
1715
+ # v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
1716
+ # @param [Google::Apis::GenomicsV1::SearchReadGroupSetsRequest] search_read_group_sets_request_object
1744
1717
  # @param [String] fields
1745
1718
  # Selector specifying which fields to include in a partial response.
1746
1719
  # @param [String] quota_user
@@ -1750,37 +1723,38 @@ module Google
1750
1723
  # Request-specific options
1751
1724
  #
1752
1725
  # @yield [result, err] Result & error if block supplied
1753
- # @yieldparam result [Google::Apis::GenomicsV1::SearchVariantSetsResponse] parsed result object
1726
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse] parsed result object
1754
1727
  # @yieldparam err [StandardError] error object if request failed
1755
1728
  #
1756
- # @return [Google::Apis::GenomicsV1::SearchVariantSetsResponse]
1729
+ # @return [Google::Apis::GenomicsV1::SearchReadGroupSetsResponse]
1757
1730
  #
1758
1731
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1759
1732
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1760
1733
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1761
- def search_variant_sets(search_variant_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1762
- command = make_simple_command(:post, 'v1/variantsets/search', options)
1763
- command.request_representation = Google::Apis::GenomicsV1::SearchVariantSetsRequest::Representation
1764
- command.request_object = search_variant_sets_request_object
1765
- command.response_representation = Google::Apis::GenomicsV1::SearchVariantSetsResponse::Representation
1766
- command.response_class = Google::Apis::GenomicsV1::SearchVariantSetsResponse
1734
+ def search_read_group_sets(search_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1735
+ command = make_simple_command(:post, 'v1/readgroupsets/search', options)
1736
+ command.request_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsRequest::Representation
1737
+ command.request_object = search_read_group_sets_request_object
1738
+ command.response_representation = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse::Representation
1739
+ command.response_class = Google::Apis::GenomicsV1::SearchReadGroupSetsResponse
1767
1740
  command.query['fields'] = fields unless fields.nil?
1768
1741
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1769
1742
  execute_or_queue_command(command, &block)
1770
1743
  end
1771
1744
 
1772
- # Updates a variant set using patch semantics.
1773
- # For the definitions of variant sets and other genomics resources, see
1745
+ # Updates a read group set.
1746
+ # For the definitions of read group sets and other genomics resources, see
1774
1747
  # [Fundamentals of Google
1775
1748
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1776
- # @param [String] variant_set_id
1777
- # The ID of the variant to be updated (must already exist).
1778
- # @param [Google::Apis::GenomicsV1::VariantSet] variant_set_object
1749
+ # This method supports patch semantics.
1750
+ # @param [String] read_group_set_id
1751
+ # The ID of the read group set to be updated. The caller must have WRITE
1752
+ # permissions to the dataset associated with this read group set.
1753
+ # @param [Google::Apis::GenomicsV1::ReadGroupSet] read_group_set_object
1779
1754
  # @param [String] update_mask
1780
1755
  # An optional mask specifying which fields to update. Supported fields:
1781
- # * metadata.
1782
1756
  # * name.
1783
- # * description.
1757
+ # * referenceSetId.
1784
1758
  # Leaving `updateMask` unset is equivalent to specifying all mutable
1785
1759
  # fields.
1786
1760
  # @param [String] fields
@@ -1792,33 +1766,33 @@ module Google
1792
1766
  # Request-specific options
1793
1767
  #
1794
1768
  # @yield [result, err] Result & error if block supplied
1795
- # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
1769
+ # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
1796
1770
  # @yieldparam err [StandardError] error object if request failed
1797
1771
  #
1798
- # @return [Google::Apis::GenomicsV1::VariantSet]
1772
+ # @return [Google::Apis::GenomicsV1::ReadGroupSet]
1799
1773
  #
1800
1774
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1801
1775
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1802
1776
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1803
- def patch_variantset(variant_set_id, variant_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
1804
- command = make_simple_command(:patch, 'v1/variantsets/{variantSetId}', options)
1805
- command.request_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1806
- command.request_object = variant_set_object
1807
- command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1808
- command.response_class = Google::Apis::GenomicsV1::VariantSet
1809
- command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1777
+ def patch_read_group_set(read_group_set_id, read_group_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
1778
+ command = make_simple_command(:patch, 'v1/readgroupsets/{readGroupSetId}', options)
1779
+ command.request_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
1780
+ command.request_object = read_group_set_object
1781
+ command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
1782
+ command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
1783
+ command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
1810
1784
  command.query['updateMask'] = update_mask unless update_mask.nil?
1811
1785
  command.query['fields'] = fields unless fields.nil?
1812
1786
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1813
1787
  execute_or_queue_command(command, &block)
1814
1788
  end
1815
1789
 
1816
- # Gets a variant set by ID.
1817
- # For the definitions of variant sets and other genomics resources, see
1790
+ # Gets a read group set by ID.
1791
+ # For the definitions of read group sets and other genomics resources, see
1818
1792
  # [Fundamentals of Google
1819
1793
  # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1820
- # @param [String] variant_set_id
1821
- # Required. The ID of the variant set.
1794
+ # @param [String] read_group_set_id
1795
+ # The ID of the read group set.
1822
1796
  # @param [String] fields
1823
1797
  # Selector specifying which fields to include in a partial response.
1824
1798
  # @param [String] quota_user
@@ -1828,41 +1802,39 @@ module Google
1828
1802
  # Request-specific options
1829
1803
  #
1830
1804
  # @yield [result, err] Result & error if block supplied
1831
- # @yieldparam result [Google::Apis::GenomicsV1::VariantSet] parsed result object
1805
+ # @yieldparam result [Google::Apis::GenomicsV1::ReadGroupSet] parsed result object
1832
1806
  # @yieldparam err [StandardError] error object if request failed
1833
1807
  #
1834
- # @return [Google::Apis::GenomicsV1::VariantSet]
1808
+ # @return [Google::Apis::GenomicsV1::ReadGroupSet]
1835
1809
  #
1836
1810
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1837
1811
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1838
1812
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1839
- def get_variantset(variant_set_id, fields: nil, quota_user: nil, options: nil, &block)
1840
- command = make_simple_command(:get, 'v1/variantsets/{variantSetId}', options)
1841
- command.response_representation = Google::Apis::GenomicsV1::VariantSet::Representation
1842
- command.response_class = Google::Apis::GenomicsV1::VariantSet
1843
- command.params['variantSetId'] = variant_set_id unless variant_set_id.nil?
1813
+ def get_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
1814
+ command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}', options)
1815
+ command.response_representation = Google::Apis::GenomicsV1::ReadGroupSet::Representation
1816
+ command.response_class = Google::Apis::GenomicsV1::ReadGroupSet
1817
+ command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
1844
1818
  command.query['fields'] = fields unless fields.nil?
1845
1819
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1846
1820
  execute_or_queue_command(command, &block)
1847
1821
  end
1848
1822
 
1849
- # Creates a new annotation. Caller must have WRITE permission
1850
- # for the associated annotation set.
1851
- # The following fields are required:
1852
- # * annotationSetId
1853
- # * referenceName or
1854
- # referenceId
1855
- # ### Transcripts
1856
- # For annotations of type TRANSCRIPT, the following fields of
1857
- # transcript must be provided:
1858
- # * exons.start
1859
- # * exons.end
1860
- # All other fields may be optionally specified, unless documented as being
1861
- # server-generated (for example, the `id` field). The annotated
1862
- # range must be no longer than 100Mbp (mega base pairs). See the
1863
- # Annotation resource
1864
- # for additional restrictions on each field.
1865
- # @param [Google::Apis::GenomicsV1::Annotation] annotation_object
1823
+ # Creates read group sets by asynchronously importing the provided
1824
+ # information.
1825
+ # For the definitions of read group sets and other genomics resources, see
1826
+ # [Fundamentals of Google
1827
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1828
+ # The caller must have WRITE permissions to the dataset.
1829
+ # ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
1830
+ # - Tags will be converted to strings - tag types are not preserved
1831
+ # - Comments (`@CO`) in the input file header will not be preserved
1832
+ # - Original header order of references (`@SQ`) will not be preserved
1833
+ # - Any reverse stranded unmapped reads will be reverse complemented, and
1834
+ # their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
1835
+ # - Unmapped reads will be stripped of positional information (reference name
1836
+ # and position)
1837
+ # @param [Google::Apis::GenomicsV1::ImportReadGroupSetsRequest] import_read_group_sets_request_object
1866
1838
  # @param [String] fields
1867
1839
  # Selector specifying which fields to include in a partial response.
1868
1840
  # @param [String] quota_user
@@ -1872,38 +1844,32 @@ module Google
1872
1844
  # Request-specific options
1873
1845
  #
1874
1846
  # @yield [result, err] Result & error if block supplied
1875
- # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
1847
+ # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
1876
1848
  # @yieldparam err [StandardError] error object if request failed
1877
1849
  #
1878
- # @return [Google::Apis::GenomicsV1::Annotation]
1850
+ # @return [Google::Apis::GenomicsV1::Operation]
1879
1851
  #
1880
1852
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1881
1853
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1882
1854
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1883
- def create_annotation(annotation_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1884
- command = make_simple_command(:post, 'v1/annotations', options)
1885
- command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation
1886
- command.request_object = annotation_object
1887
- command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation
1888
- command.response_class = Google::Apis::GenomicsV1::Annotation
1855
+ def import_read_group_sets(import_read_group_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1856
+ command = make_simple_command(:post, 'v1/readgroupsets:import', options)
1857
+ command.request_representation = Google::Apis::GenomicsV1::ImportReadGroupSetsRequest::Representation
1858
+ command.request_object = import_read_group_sets_request_object
1859
+ command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
1860
+ command.response_class = Google::Apis::GenomicsV1::Operation
1889
1861
  command.query['fields'] = fields unless fields.nil?
1890
1862
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1891
1863
  execute_or_queue_command(command, &block)
1892
1864
  end
1893
1865
 
1894
- # Creates one or more new annotations atomically. All annotations must
1895
- # belong to the same annotation set. Caller must have WRITE
1896
- # permission for this annotation set. For optimal performance, batch
1897
- # positionally adjacent annotations together.
1898
- # If the request has a systemic issue, such as an attempt to write to
1899
- # an inaccessible annotation set, the entire RPC will fail accordingly. For
1900
- # lesser data issues, when possible an error will be isolated to the
1901
- # corresponding batch entry in the response; the remaining well formed
1902
- # annotations will be created normally.
1903
- # For details on the requirements for each individual annotation resource,
1904
- # see
1905
- # CreateAnnotation.
1906
- # @param [Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest] batch_create_annotations_request_object
1866
+ # Deletes a read group set.
1867
+ # For the definitions of read group sets and other genomics resources, see
1868
+ # [Fundamentals of Google
1869
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1870
+ # @param [String] read_group_set_id
1871
+ # The ID of the read group set to be deleted. The caller must have WRITE
1872
+ # permissions to the dataset associated with this read group set.
1907
1873
  # @param [String] fields
1908
1874
  # Selector specifying which fields to include in a partial response.
1909
1875
  # @param [String] quota_user
@@ -1913,33 +1879,62 @@ module Google
1913
1879
  # Request-specific options
1914
1880
  #
1915
1881
  # @yield [result, err] Result & error if block supplied
1916
- # @yieldparam result [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse] parsed result object
1882
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
1917
1883
  # @yieldparam err [StandardError] error object if request failed
1918
1884
  #
1919
- # @return [Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse]
1885
+ # @return [Google::Apis::GenomicsV1::Empty]
1920
1886
  #
1921
1887
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1922
1888
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1923
1889
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1924
- def batch_create_annotations(batch_create_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1925
- command = make_simple_command(:post, 'v1/annotations:batchCreate', options)
1926
- command.request_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsRequest::Representation
1927
- command.request_object = batch_create_annotations_request_object
1928
- command.response_representation = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse::Representation
1929
- command.response_class = Google::Apis::GenomicsV1::BatchCreateAnnotationsResponse
1890
+ def delete_read_group_set(read_group_set_id, fields: nil, quota_user: nil, options: nil, &block)
1891
+ command = make_simple_command(:delete, 'v1/readgroupsets/{readGroupSetId}', options)
1892
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
1893
+ command.response_class = Google::Apis::GenomicsV1::Empty
1894
+ command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
1930
1895
  command.query['fields'] = fields unless fields.nil?
1931
1896
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1932
1897
  execute_or_queue_command(command, &block)
1933
1898
  end
1934
1899
 
1935
- # Searches for annotations that match the given criteria. Results are
1936
- # ordered by genomic coordinate (by reference sequence, then position).
1937
- # Annotations with equivalent genomic coordinates are returned in an
1938
- # unspecified order. This order is consistent, such that two queries for the
1939
- # same content (regardless of page size) yield annotations in the same order
1940
- # across their respective streams of paginated responses. Caller must have
1941
- # READ permission for the queried annotation sets.
1942
- # @param [Google::Apis::GenomicsV1::SearchAnnotationsRequest] search_annotations_request_object
1900
+ # Lists fixed width coverage buckets for a read group set, each of which
1901
+ # correspond to a range of a reference sequence. Each bucket summarizes
1902
+ # coverage information across its corresponding genomic range.
1903
+ # For the definitions of read group sets and other genomics resources, see
1904
+ # [Fundamentals of Google
1905
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1906
+ # Coverage is defined as the number of reads which are aligned to a given
1907
+ # base in the reference sequence. Coverage buckets are available at several
1908
+ # precomputed bucket widths, enabling retrieval of various coverage 'zoom
1909
+ # levels'. The caller must have READ permissions for the target read group
1910
+ # set.
1911
+ # @param [String] read_group_set_id
1912
+ # Required. The ID of the read group set over which coverage is requested.
1913
+ # @param [String] reference_name
1914
+ # The name of the reference to query, within the reference set associated
1915
+ # with this query. Optional.
1916
+ # @param [String] end_
1917
+ # The end position of the range on the reference, 0-based exclusive. If
1918
+ # specified, `referenceName` must also be specified. If unset or 0, defaults
1919
+ # to the length of the reference.
1920
+ # @param [String] page_token
1921
+ # The continuation token, which is used to page through large result sets.
1922
+ # To get the next page of results, set this parameter to the value of
1923
+ # `nextPageToken` from the previous response.
1924
+ # @param [Fixnum] page_size
1925
+ # The maximum number of results to return in a single page. If unspecified,
1926
+ # defaults to 1024. The maximum value is 2048.
1927
+ # @param [String] start
1928
+ # The start position of the range on the reference, 0-based inclusive. If
1929
+ # specified, `referenceName` must also be specified. Defaults to 0.
1930
+ # @param [String] target_bucket_width
1931
+ # The desired width of each reported coverage bucket in base pairs. This
1932
+ # will be rounded down to the nearest precomputed bucket width; the value
1933
+ # of which is returned as `bucketWidth` in the response. Defaults
1934
+ # to infinity (each bucket spans an entire reference sequence) or the length
1935
+ # of the target range, if specified. The smallest precomputed
1936
+ # `bucketWidth` is currently 2048 base pairs; this is subject to
1937
+ # change.
1943
1938
  # @param [String] fields
1944
1939
  # Selector specifying which fields to include in a partial response.
1945
1940
  # @param [String] quota_user
@@ -1949,29 +1944,51 @@ module Google
1949
1944
  # Request-specific options
1950
1945
  #
1951
1946
  # @yield [result, err] Result & error if block supplied
1952
- # @yieldparam result [Google::Apis::GenomicsV1::SearchAnnotationsResponse] parsed result object
1947
+ # @yieldparam result [Google::Apis::GenomicsV1::ListCoverageBucketsResponse] parsed result object
1953
1948
  # @yieldparam err [StandardError] error object if request failed
1954
1949
  #
1955
- # @return [Google::Apis::GenomicsV1::SearchAnnotationsResponse]
1950
+ # @return [Google::Apis::GenomicsV1::ListCoverageBucketsResponse]
1956
1951
  #
1957
1952
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1958
1953
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1959
1954
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1960
- def search_annotations(search_annotations_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
1961
- command = make_simple_command(:post, 'v1/annotations/search', options)
1962
- command.request_representation = Google::Apis::GenomicsV1::SearchAnnotationsRequest::Representation
1963
- command.request_object = search_annotations_request_object
1964
- command.response_representation = Google::Apis::GenomicsV1::SearchAnnotationsResponse::Representation
1965
- command.response_class = Google::Apis::GenomicsV1::SearchAnnotationsResponse
1955
+ def list_coverage_buckets(read_group_set_id, reference_name: nil, end_: nil, page_token: nil, page_size: nil, start: nil, target_bucket_width: nil, fields: nil, quota_user: nil, options: nil, &block)
1956
+ command = make_simple_command(:get, 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', options)
1957
+ command.response_representation = Google::Apis::GenomicsV1::ListCoverageBucketsResponse::Representation
1958
+ command.response_class = Google::Apis::GenomicsV1::ListCoverageBucketsResponse
1959
+ command.params['readGroupSetId'] = read_group_set_id unless read_group_set_id.nil?
1960
+ command.query['referenceName'] = reference_name unless reference_name.nil?
1961
+ command.query['end'] = end_ unless end_.nil?
1962
+ command.query['pageToken'] = page_token unless page_token.nil?
1963
+ command.query['pageSize'] = page_size unless page_size.nil?
1964
+ command.query['start'] = start unless start.nil?
1965
+ command.query['targetBucketWidth'] = target_bucket_width unless target_bucket_width.nil?
1966
1966
  command.query['fields'] = fields unless fields.nil?
1967
1967
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1968
1968
  execute_or_queue_command(command, &block)
1969
1969
  end
1970
1970
 
1971
- # Gets an annotation. Caller must have READ permission
1972
- # for the associated annotation set.
1973
- # @param [String] annotation_id
1974
- # The ID of the annotation to be retrieved.
1971
+ # Gets a list of reads for one or more read group sets.
1972
+ # For the definitions of read group sets and other genomics resources, see
1973
+ # [Fundamentals of Google
1974
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1975
+ # Reads search operates over a genomic coordinate space of reference sequence
1976
+ # & position defined over the reference sequences to which the requested
1977
+ # read group sets are aligned.
1978
+ # If a target positional range is specified, search returns all reads whose
1979
+ # alignment to the reference genome overlap the range. A query which
1980
+ # specifies only read group set IDs yields all reads in those read group
1981
+ # sets, including unmapped reads.
1982
+ # All reads returned (including reads on subsequent pages) are ordered by
1983
+ # genomic coordinate (by reference sequence, then position). Reads with
1984
+ # equivalent genomic coordinates are returned in an unspecified order. This
1985
+ # order is consistent, such that two queries for the same content (regardless
1986
+ # of page size) yield reads in the same order across their respective streams
1987
+ # of paginated responses.
1988
+ # Implements
1989
+ # [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/
1990
+ # src/main/resources/avro/readmethods.avdl#L85).
1991
+ # @param [Google::Apis::GenomicsV1::SearchReadsRequest] search_reads_request_object
1975
1992
  # @param [String] fields
1976
1993
  # Selector specifying which fields to include in a partial response.
1977
1994
  # @param [String] quota_user
@@ -1981,36 +1998,31 @@ module Google
1981
1998
  # Request-specific options
1982
1999
  #
1983
2000
  # @yield [result, err] Result & error if block supplied
1984
- # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
2001
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchReadsResponse] parsed result object
1985
2002
  # @yieldparam err [StandardError] error object if request failed
1986
2003
  #
1987
- # @return [Google::Apis::GenomicsV1::Annotation]
2004
+ # @return [Google::Apis::GenomicsV1::SearchReadsResponse]
1988
2005
  #
1989
2006
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
1990
2007
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
1991
2008
  # @raise [Google::Apis::AuthorizationError] Authorization is required
1992
- def get_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block)
1993
- command = make_simple_command(:get, 'v1/annotations/{annotationId}', options)
1994
- command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation
1995
- command.response_class = Google::Apis::GenomicsV1::Annotation
1996
- command.params['annotationId'] = annotation_id unless annotation_id.nil?
2009
+ def search_reads(search_reads_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
2010
+ command = make_simple_command(:post, 'v1/reads/search', options)
2011
+ command.request_representation = Google::Apis::GenomicsV1::SearchReadsRequest::Representation
2012
+ command.request_object = search_reads_request_object
2013
+ command.response_representation = Google::Apis::GenomicsV1::SearchReadsResponse::Representation
2014
+ command.response_class = Google::Apis::GenomicsV1::SearchReadsResponse
1997
2015
  command.query['fields'] = fields unless fields.nil?
1998
2016
  command.query['quotaUser'] = quota_user unless quota_user.nil?
1999
2017
  execute_or_queue_command(command, &block)
2000
2018
  end
2001
2019
 
2002
- # Updates an annotation. Caller must have
2003
- # WRITE permission for the associated dataset.
2004
- # @param [String] annotation_id
2005
- # The ID of the annotation to be updated.
2006
- # @param [Google::Apis::GenomicsV1::Annotation] annotation_object
2007
- # @param [String] update_mask
2008
- # An optional mask specifying which fields to update. Mutable fields are
2009
- # name,
2010
- # variant,
2011
- # transcript, and
2012
- # info. If unspecified, all mutable
2013
- # fields will be updated.
2020
+ # Deletes a call set.
2021
+ # For the definitions of call sets and other genomics resources, see
2022
+ # [Fundamentals of Google
2023
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
2024
+ # @param [String] call_set_id
2025
+ # The ID of the call set to be deleted.
2014
2026
  # @param [String] fields
2015
2027
  # Selector specifying which fields to include in a partial response.
2016
2028
  # @param [String] quota_user
@@ -2020,31 +2032,32 @@ module Google
2020
2032
  # Request-specific options
2021
2033
  #
2022
2034
  # @yield [result, err] Result & error if block supplied
2023
- # @yieldparam result [Google::Apis::GenomicsV1::Annotation] parsed result object
2035
+ # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
2024
2036
  # @yieldparam err [StandardError] error object if request failed
2025
2037
  #
2026
- # @return [Google::Apis::GenomicsV1::Annotation]
2038
+ # @return [Google::Apis::GenomicsV1::Empty]
2027
2039
  #
2028
2040
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
2029
2041
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
2030
2042
  # @raise [Google::Apis::AuthorizationError] Authorization is required
2031
- def update_annotation(annotation_id, annotation_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
2032
- command = make_simple_command(:put, 'v1/annotations/{annotationId}', options)
2033
- command.request_representation = Google::Apis::GenomicsV1::Annotation::Representation
2034
- command.request_object = annotation_object
2035
- command.response_representation = Google::Apis::GenomicsV1::Annotation::Representation
2036
- command.response_class = Google::Apis::GenomicsV1::Annotation
2037
- command.params['annotationId'] = annotation_id unless annotation_id.nil?
2038
- command.query['updateMask'] = update_mask unless update_mask.nil?
2043
+ def delete_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
2044
+ command = make_simple_command(:delete, 'v1/callsets/{callSetId}', options)
2045
+ command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
2046
+ command.response_class = Google::Apis::GenomicsV1::Empty
2047
+ command.params['callSetId'] = call_set_id unless call_set_id.nil?
2039
2048
  command.query['fields'] = fields unless fields.nil?
2040
2049
  command.query['quotaUser'] = quota_user unless quota_user.nil?
2041
2050
  execute_or_queue_command(command, &block)
2042
2051
  end
2043
2052
 
2044
- # Deletes an annotation. Caller must have WRITE permission for
2045
- # the associated annotation set.
2046
- # @param [String] annotation_id
2047
- # The ID of the annotation to be deleted.
2053
+ # Gets a list of call sets matching the criteria.
2054
+ # For the definitions of call sets and other genomics resources, see
2055
+ # [Fundamentals of Google
2056
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
2057
+ # Implements
2058
+ # [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.
2059
+ # 1/src/main/resources/avro/variantmethods.avdl#L178).
2060
+ # @param [Google::Apis::GenomicsV1::SearchCallSetsRequest] search_call_sets_request_object
2048
2061
  # @param [String] fields
2049
2062
  # Selector specifying which fields to include in a partial response.
2050
2063
  # @param [String] quota_user
@@ -2054,49 +2067,38 @@ module Google
2054
2067
  # Request-specific options
2055
2068
  #
2056
2069
  # @yield [result, err] Result & error if block supplied
2057
- # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
2070
+ # @yieldparam result [Google::Apis::GenomicsV1::SearchCallSetsResponse] parsed result object
2058
2071
  # @yieldparam err [StandardError] error object if request failed
2059
2072
  #
2060
- # @return [Google::Apis::GenomicsV1::Empty]
2073
+ # @return [Google::Apis::GenomicsV1::SearchCallSetsResponse]
2061
2074
  #
2062
2075
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
2063
2076
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
2064
2077
  # @raise [Google::Apis::AuthorizationError] Authorization is required
2065
- def delete_annotation(annotation_id, fields: nil, quota_user: nil, options: nil, &block)
2066
- command = make_simple_command(:delete, 'v1/annotations/{annotationId}', options)
2067
- command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
2068
- command.response_class = Google::Apis::GenomicsV1::Empty
2069
- command.params['annotationId'] = annotation_id unless annotation_id.nil?
2078
+ def search_call_sets(search_call_sets_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
2079
+ command = make_simple_command(:post, 'v1/callsets/search', options)
2080
+ command.request_representation = Google::Apis::GenomicsV1::SearchCallSetsRequest::Representation
2081
+ command.request_object = search_call_sets_request_object
2082
+ command.response_representation = Google::Apis::GenomicsV1::SearchCallSetsResponse::Representation
2083
+ command.response_class = Google::Apis::GenomicsV1::SearchCallSetsResponse
2070
2084
  command.query['fields'] = fields unless fields.nil?
2071
2085
  command.query['quotaUser'] = quota_user unless quota_user.nil?
2072
2086
  execute_or_queue_command(command, &block)
2073
2087
  end
2074
2088
 
2075
- # Lists operations that match the specified filter in the request.
2076
- # @param [String] name
2077
- # The name of the operation collection.
2078
- # @param [String] filter
2079
- # A string for filtering Operations.
2080
- # The following filter fields are supported&#58;
2081
- # * projectId&#58; Required. Corresponds to
2082
- # OperationMetadata.projectId.
2083
- # * createTime&#58; The time this job was created, in seconds from the
2084
- # [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`
2085
- # operators.
2086
- # * status&#58; Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only
2087
- # one status may be specified.
2088
- # * labels.key where key is a label key.
2089
- # Examples&#58;
2090
- # * `projectId = my-project AND createTime >= 1432140000`
2091
- # * `projectId = my-project AND createTime >= 1432140000 AND createTime <=
2092
- # 1432150000 AND status = RUNNING`
2093
- # * `projectId = my-project AND labels.color = *`
2094
- # * `projectId = my-project AND labels.color = red`
2095
- # @param [String] page_token
2096
- # The standard list page token.
2097
- # @param [Fixnum] page_size
2098
- # The maximum number of results to return. If unspecified, defaults to
2099
- # 256. The maximum value is 2048.
2089
+ # Updates a call set.
2090
+ # For the definitions of call sets and other genomics resources, see
2091
+ # [Fundamentals of Google
2092
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
2093
+ # This method supports patch semantics.
2094
+ # @param [String] call_set_id
2095
+ # The ID of the call set to be updated.
2096
+ # @param [Google::Apis::GenomicsV1::CallSet] call_set_object
2097
+ # @param [String] update_mask
2098
+ # An optional mask specifying which fields to update. At this time, the only
2099
+ # mutable field is name. The only
2100
+ # acceptable value is "name". If unspecified, all mutable fields will be
2101
+ # updated.
2100
2102
  # @param [String] fields
2101
2103
  # Selector specifying which fields to include in a partial response.
2102
2104
  # @param [String] quota_user
@@ -2106,32 +2108,33 @@ module Google
2106
2108
  # Request-specific options
2107
2109
  #
2108
2110
  # @yield [result, err] Result & error if block supplied
2109
- # @yieldparam result [Google::Apis::GenomicsV1::ListOperationsResponse] parsed result object
2111
+ # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
2110
2112
  # @yieldparam err [StandardError] error object if request failed
2111
2113
  #
2112
- # @return [Google::Apis::GenomicsV1::ListOperationsResponse]
2114
+ # @return [Google::Apis::GenomicsV1::CallSet]
2113
2115
  #
2114
2116
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
2115
2117
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
2116
2118
  # @raise [Google::Apis::AuthorizationError] Authorization is required
2117
- def list_operations(name, filter: nil, page_token: nil, page_size: nil, fields: nil, quota_user: nil, options: nil, &block)
2118
- command = make_simple_command(:get, 'v1/{+name}', options)
2119
- command.response_representation = Google::Apis::GenomicsV1::ListOperationsResponse::Representation
2120
- command.response_class = Google::Apis::GenomicsV1::ListOperationsResponse
2121
- command.params['name'] = name unless name.nil?
2122
- command.query['filter'] = filter unless filter.nil?
2123
- command.query['pageToken'] = page_token unless page_token.nil?
2124
- command.query['pageSize'] = page_size unless page_size.nil?
2119
+ def patch_call_set(call_set_id, call_set_object = nil, update_mask: nil, fields: nil, quota_user: nil, options: nil, &block)
2120
+ command = make_simple_command(:patch, 'v1/callsets/{callSetId}', options)
2121
+ command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
2122
+ command.request_object = call_set_object
2123
+ command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
2124
+ command.response_class = Google::Apis::GenomicsV1::CallSet
2125
+ command.params['callSetId'] = call_set_id unless call_set_id.nil?
2126
+ command.query['updateMask'] = update_mask unless update_mask.nil?
2125
2127
  command.query['fields'] = fields unless fields.nil?
2126
2128
  command.query['quotaUser'] = quota_user unless quota_user.nil?
2127
2129
  execute_or_queue_command(command, &block)
2128
2130
  end
2129
2131
 
2130
- # Gets the latest state of a long-running operation. Clients can use this
2131
- # method to poll the operation result at intervals as recommended by the API
2132
- # service.
2133
- # @param [String] name
2134
- # The name of the operation resource.
2132
+ # Gets a call set by ID.
2133
+ # For the definitions of call sets and other genomics resources, see
2134
+ # [Fundamentals of Google
2135
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
2136
+ # @param [String] call_set_id
2137
+ # The ID of the call set.
2135
2138
  # @param [String] fields
2136
2139
  # Selector specifying which fields to include in a partial response.
2137
2140
  # @param [String] quota_user
@@ -2141,31 +2144,29 @@ module Google
2141
2144
  # Request-specific options
2142
2145
  #
2143
2146
  # @yield [result, err] Result & error if block supplied
2144
- # @yieldparam result [Google::Apis::GenomicsV1::Operation] parsed result object
2147
+ # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
2145
2148
  # @yieldparam err [StandardError] error object if request failed
2146
2149
  #
2147
- # @return [Google::Apis::GenomicsV1::Operation]
2150
+ # @return [Google::Apis::GenomicsV1::CallSet]
2148
2151
  #
2149
2152
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
2150
2153
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
2151
2154
  # @raise [Google::Apis::AuthorizationError] Authorization is required
2152
- def get_operation(name, fields: nil, quota_user: nil, options: nil, &block)
2153
- command = make_simple_command(:get, 'v1/{+name}', options)
2154
- command.response_representation = Google::Apis::GenomicsV1::Operation::Representation
2155
- command.response_class = Google::Apis::GenomicsV1::Operation
2156
- command.params['name'] = name unless name.nil?
2155
+ def get_call_set(call_set_id, fields: nil, quota_user: nil, options: nil, &block)
2156
+ command = make_simple_command(:get, 'v1/callsets/{callSetId}', options)
2157
+ command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
2158
+ command.response_class = Google::Apis::GenomicsV1::CallSet
2159
+ command.params['callSetId'] = call_set_id unless call_set_id.nil?
2157
2160
  command.query['fields'] = fields unless fields.nil?
2158
2161
  command.query['quotaUser'] = quota_user unless quota_user.nil?
2159
2162
  execute_or_queue_command(command, &block)
2160
2163
  end
2161
2164
 
2162
- # Starts asynchronous cancellation on a long-running operation. The server makes
2163
- # a best effort to cancel the operation, but success is not guaranteed. Clients
2164
- # may use Operations.GetOperation or Operations.ListOperations to check whether
2165
- # the cancellation succeeded or the operation completed despite cancellation.
2166
- # @param [String] name
2167
- # The name of the operation resource to be cancelled.
2168
- # @param [Google::Apis::GenomicsV1::CancelOperationRequest] cancel_operation_request_object
2165
+ # Creates a new call set.
2166
+ # For the definitions of call sets and other genomics resources, see
2167
+ # [Fundamentals of Google
2168
+ # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
2169
+ # @param [Google::Apis::GenomicsV1::CallSet] call_set_object
2169
2170
  # @param [String] fields
2170
2171
  # Selector specifying which fields to include in a partial response.
2171
2172
  # @param [String] quota_user
@@ -2175,21 +2176,20 @@ module Google
2175
2176
  # Request-specific options
2176
2177
  #
2177
2178
  # @yield [result, err] Result & error if block supplied
2178
- # @yieldparam result [Google::Apis::GenomicsV1::Empty] parsed result object
2179
+ # @yieldparam result [Google::Apis::GenomicsV1::CallSet] parsed result object
2179
2180
  # @yieldparam err [StandardError] error object if request failed
2180
2181
  #
2181
- # @return [Google::Apis::GenomicsV1::Empty]
2182
+ # @return [Google::Apis::GenomicsV1::CallSet]
2182
2183
  #
2183
2184
  # @raise [Google::Apis::ServerError] An error occurred on the server and the request can be retried
2184
2185
  # @raise [Google::Apis::ClientError] The request is invalid and should not be retried without modification
2185
2186
  # @raise [Google::Apis::AuthorizationError] Authorization is required
2186
- def cancel_operation(name, cancel_operation_request_object = nil, fields: nil, quota_user: nil, options: nil, &block)
2187
- command = make_simple_command(:post, 'v1/{+name}:cancel', options)
2188
- command.request_representation = Google::Apis::GenomicsV1::CancelOperationRequest::Representation
2189
- command.request_object = cancel_operation_request_object
2190
- command.response_representation = Google::Apis::GenomicsV1::Empty::Representation
2191
- command.response_class = Google::Apis::GenomicsV1::Empty
2192
- command.params['name'] = name unless name.nil?
2187
+ def create_call_set(call_set_object = nil, fields: nil, quota_user: nil, options: nil, &block)
2188
+ command = make_simple_command(:post, 'v1/callsets', options)
2189
+ command.request_representation = Google::Apis::GenomicsV1::CallSet::Representation
2190
+ command.request_object = call_set_object
2191
+ command.response_representation = Google::Apis::GenomicsV1::CallSet::Representation
2192
+ command.response_class = Google::Apis::GenomicsV1::CallSet
2193
2193
  command.query['fields'] = fields unless fields.nil?
2194
2194
  command.query['quotaUser'] = quota_user unless quota_user.nil?
2195
2195
  execute_or_queue_command(command, &block)