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Unified Diff: discovery/googleapis/genomics__v1.json

Issue 2779563003: Api-roll 47: 2017-03-27 (Closed)
Patch Set: Created 3 years, 9 months ago
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Index: discovery/googleapis/genomics__v1.json
diff --git a/discovery/googleapis/genomics__v1.json b/discovery/googleapis/genomics__v1.json
index 83b77a41c848c9494df94f0d508577c3a293c29c..be62bbc2bcbbf433431f7b0a7d7be0b5cc8a0b74 100644
--- a/discovery/googleapis/genomics__v1.json
+++ b/discovery/googleapis/genomics__v1.json
@@ -2,6 +2,12 @@
"auth": {
"oauth2": {
"scopes": {
+ "https://www.googleapis.com/auth/bigquery": {
+ "description": "View and manage your data in Google BigQuery"
+ },
+ "https://www.googleapis.com/auth/devstorage.read_write": {
+ "description": "Manage your data in Google Cloud Storage"
+ },
"https://www.googleapis.com/auth/cloud-platform": {
"description": "View and manage your data across Google Cloud Platform services"
},
@@ -10,12 +16,6 @@
},
"https://www.googleapis.com/auth/genomics": {
"description": "View and manage Genomics data"
- },
- "https://www.googleapis.com/auth/bigquery": {
- "description": "View and manage your data in Google BigQuery"
- },
- "https://www.googleapis.com/auth/devstorage.read_write": {
- "description": "Manage your data in Google Cloud Storage"
}
}
}
@@ -36,27 +36,6 @@
"ownerDomain": "google.com",
"ownerName": "Google",
"parameters": {
- "quotaUser": {
- "description": "Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.",
- "location": "query",
- "type": "string"
- },
- "pp": {
- "default": "true",
- "description": "Pretty-print response.",
- "location": "query",
- "type": "boolean"
- },
- "bearer_token": {
- "description": "OAuth bearer token.",
- "location": "query",
- "type": "string"
- },
- "oauth_token": {
- "description": "OAuth 2.0 token for the current user.",
- "location": "query",
- "type": "string"
- },
"upload_protocol": {
"description": "Upload protocol for media (e.g. \"raw\", \"multipart\").",
"location": "query",
@@ -68,13 +47,13 @@
"location": "query",
"type": "boolean"
},
- "fields": {
- "description": "Selector specifying which fields to include in a partial response.",
+ "uploadType": {
+ "description": "Legacy upload protocol for media (e.g. \"media\", \"multipart\").",
"location": "query",
"type": "string"
},
- "uploadType": {
- "description": "Legacy upload protocol for media (e.g. \"media\", \"multipart\").",
+ "fields": {
+ "description": "Selector specifying which fields to include in a partial response.",
"location": "query",
"type": "string"
},
@@ -112,13 +91,34 @@
"location": "query",
"type": "string"
},
+ "key": {
+ "description": "API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.",
+ "location": "query",
+ "type": "string"
+ },
"access_token": {
"description": "OAuth access token.",
"location": "query",
"type": "string"
},
- "key": {
- "description": "API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.",
+ "quotaUser": {
+ "description": "Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.",
+ "location": "query",
+ "type": "string"
+ },
+ "pp": {
+ "default": "true",
+ "description": "Pretty-print response.",
+ "location": "query",
+ "type": "boolean"
+ },
+ "bearer_token": {
+ "description": "OAuth bearer token.",
+ "location": "query",
+ "type": "string"
+ },
+ "oauth_token": {
+ "description": "OAuth 2.0 token for the current user.",
"location": "query",
"type": "string"
}
@@ -127,6 +127,34 @@
"resources": {
"operations": {
"methods": {
+ "cancel": {
+ "description": "Starts asynchronous cancellation on a long-running operation. The server makes a best effort to cancel the operation, but success is not guaranteed. Clients may use Operations.GetOperation or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite cancellation.",
+ "httpMethod": "POST",
+ "id": "genomics.operations.cancel",
+ "parameterOrder": [
+ "name"
+ ],
+ "parameters": {
+ "name": {
+ "description": "The name of the operation resource to be cancelled.",
+ "location": "path",
+ "pattern": "^operations/.+$",
+ "required": true,
+ "type": "string"
+ }
+ },
+ "path": "v1/{+name}:cancel",
+ "request": {
+ "$ref": "CancelOperationRequest"
+ },
+ "response": {
+ "$ref": "Empty"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics"
+ ]
+ },
"list": {
"description": "Lists operations that match the specified filter in the request.",
"httpMethod": "GET",
@@ -135,6 +163,11 @@
"name"
],
"parameters": {
+ "filter": {
+ "description": "A string for filtering Operations.\nThe following filter fields are supported&#58;\n\n* projectId&#58; Required. Corresponds to\n OperationMetadata.projectId.\n* createTime&#58; The time this job was created, in seconds from the\n [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`\n operators.\n* status&#58; Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only\n one status may be specified.\n* labels.key where key is a label key.\n\nExamples&#58;\n\n* `projectId = my-project AND createTime >= 1432140000`\n* `projectId = my-project AND createTime >= 1432140000 AND createTime <= 1432150000 AND status = RUNNING`\n* `projectId = my-project AND labels.color = *`\n* `projectId = my-project AND labels.color = red`",
+ "location": "query",
+ "type": "string"
+ },
"name": {
"description": "The name of the operation collection.",
"location": "path",
@@ -152,11 +185,6 @@
"format": "int32",
"location": "query",
"type": "integer"
- },
- "filter": {
- "description": "A string for filtering Operations.\nThe following filter fields are supported&#58;\n\n* projectId&#58; Required. Corresponds to\n OperationMetadata.projectId.\n* createTime&#58; The time this job was created, in seconds from the\n [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`\n operators.\n* status&#58; Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only\n one status may be specified.\n* labels.key where key is a label key.\n\nExamples&#58;\n\n* `projectId = my-project AND createTime >= 1432140000`\n* `projectId = my-project AND createTime >= 1432140000 AND createTime <= 1432150000 AND status = RUNNING`\n* `projectId = my-project AND labels.color = *`\n* `projectId = my-project AND labels.color = red`",
- "location": "query",
- "type": "string"
}
},
"path": "v1/{+name}",
@@ -192,34 +220,6 @@
"https://www.googleapis.com/auth/cloud-platform",
"https://www.googleapis.com/auth/genomics"
]
- },
- "cancel": {
- "description": "Starts asynchronous cancellation on a long-running operation. The server makes a best effort to cancel the operation, but success is not guaranteed. Clients may use Operations.GetOperation or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite cancellation.",
- "httpMethod": "POST",
- "id": "genomics.operations.cancel",
- "parameterOrder": [
- "name"
- ],
- "parameters": {
- "name": {
- "description": "The name of the operation resource to be cancelled.",
- "location": "path",
- "pattern": "^operations/.+$",
- "required": true,
- "type": "string"
- }
- },
- "path": "v1/{+name}:cancel",
- "request": {
- "$ref": "CancelOperationRequest"
- },
- "response": {
- "$ref": "Empty"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics"
- ]
}
}
},
@@ -271,43 +271,24 @@
}
}
},
- "readgroupsets": {
+ "callsets": {
"methods": {
- "import": {
- "description": "Creates read group sets by asynchronously importing the provided\ninformation.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThe caller must have WRITE permissions to the dataset.\n\n## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import\n\n- Tags will be converted to strings - tag types are not preserved\n- Comments (`@CO`) in the input file header will not be preserved\n- Original header order of references (`@SQ`) will not be preserved\n- Any reverse stranded unmapped reads will be reverse complemented, and\ntheir qualities (also the \"BQ\" and \"OQ\" tags, if any) will be reversed\n- Unmapped reads will be stripped of positional information (reference name\nand position)",
- "httpMethod": "POST",
- "id": "genomics.readgroupsets.import",
- "parameterOrder": [],
- "parameters": {},
- "path": "v1/readgroupsets:import",
- "request": {
- "$ref": "ImportReadGroupSetsRequest"
- },
- "response": {
- "$ref": "Operation"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/devstorage.read_write",
- "https://www.googleapis.com/auth/genomics"
- ]
- },
"delete": {
- "description": "Deletes a read group set.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
+ "description": "Deletes a call set.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
"httpMethod": "DELETE",
- "id": "genomics.readgroupsets.delete",
+ "id": "genomics.callsets.delete",
"parameterOrder": [
- "readGroupSetId"
+ "callSetId"
],
"parameters": {
- "readGroupSetId": {
- "description": "The ID of the read group set to be deleted. The caller must have WRITE\npermissions to the dataset associated with this read group set.",
+ "callSetId": {
+ "description": "The ID of the call set to be deleted.",
"location": "path",
"required": true,
"type": "string"
}
},
- "path": "v1/readgroupsets/{readGroupSetId}",
+ "path": "v1/callsets/{callSetId}",
"response": {
"$ref": "Empty"
},
@@ -316,46 +297,18 @@
"https://www.googleapis.com/auth/genomics"
]
},
- "export": {
- "description": "Exports a read group set to a BAM file in Google Cloud Storage.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nNote that currently there may be some differences between exported BAM\nfiles and the original BAM file at the time of import. See\nImportReadGroupSets\nfor caveats.",
- "httpMethod": "POST",
- "id": "genomics.readgroupsets.export",
- "parameterOrder": [
- "readGroupSetId"
- ],
- "parameters": {
- "readGroupSetId": {
- "description": "Required. The ID of the read group set to export. The caller must have\nREAD access to this read group set.",
- "location": "path",
- "required": true,
- "type": "string"
- }
- },
- "path": "v1/readgroupsets/{readGroupSetId}:export",
- "request": {
- "$ref": "ExportReadGroupSetRequest"
- },
- "response": {
- "$ref": "Operation"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/devstorage.read_write",
- "https://www.googleapis.com/auth/genomics"
- ]
- },
"search": {
- "description": "Searches for read group sets matching the criteria.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).",
+ "description": "Gets a list of call sets matching the criteria.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).",
"httpMethod": "POST",
- "id": "genomics.readgroupsets.search",
+ "id": "genomics.callsets.search",
"parameterOrder": [],
"parameters": {},
- "path": "v1/readgroupsets/search",
+ "path": "v1/callsets/search",
"request": {
- "$ref": "SearchReadGroupSetsRequest"
+ "$ref": "SearchCallSetsRequest"
},
"response": {
- "$ref": "SearchReadGroupSetsResponse"
+ "$ref": "SearchCallSetsResponse"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
@@ -364,32 +317,32 @@
]
},
"patch": {
- "description": "Updates a read group set.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis method supports patch semantics.",
+ "description": "Updates a call set.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis method supports patch semantics.",
"httpMethod": "PATCH",
- "id": "genomics.readgroupsets.patch",
+ "id": "genomics.callsets.patch",
"parameterOrder": [
- "readGroupSetId"
+ "callSetId"
],
"parameters": {
- "readGroupSetId": {
- "description": "The ID of the read group set to be updated. The caller must have WRITE\npermissions to the dataset associated with this read group set.",
+ "callSetId": {
+ "description": "The ID of the call set to be updated.",
"location": "path",
"required": true,
"type": "string"
},
"updateMask": {
- "description": "An optional mask specifying which fields to update. Supported fields:\n\n* name.\n* referenceSetId.\n\nLeaving `updateMask` unset is equivalent to specifying all mutable\nfields.",
+ "description": "An optional mask specifying which fields to update. At this time, the only\nmutable field is name. The only\nacceptable value is \"name\". If unspecified, all mutable fields will be\nupdated.",
"format": "google-fieldmask",
"location": "query",
"type": "string"
}
},
- "path": "v1/readgroupsets/{readGroupSetId}",
+ "path": "v1/callsets/{callSetId}",
"request": {
- "$ref": "ReadGroupSet"
+ "$ref": "CallSet"
},
"response": {
- "$ref": "ReadGroupSet"
+ "$ref": "CallSet"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
@@ -397,95 +350,48 @@
]
},
"get": {
- "description": "Gets a read group set by ID.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
+ "description": "Gets a call set by ID.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
"httpMethod": "GET",
- "id": "genomics.readgroupsets.get",
+ "id": "genomics.callsets.get",
"parameterOrder": [
- "readGroupSetId"
+ "callSetId"
],
"parameters": {
- "readGroupSetId": {
- "description": "The ID of the read group set.",
+ "callSetId": {
+ "description": "The ID of the call set.",
"location": "path",
"required": true,
"type": "string"
}
},
- "path": "v1/readgroupsets/{readGroupSetId}",
+ "path": "v1/callsets/{callSetId}",
"response": {
- "$ref": "ReadGroupSet"
+ "$ref": "CallSet"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
"https://www.googleapis.com/auth/genomics",
"https://www.googleapis.com/auth/genomics.readonly"
]
+ },
+ "create": {
+ "description": "Creates a new call set.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
+ "httpMethod": "POST",
+ "id": "genomics.callsets.create",
+ "parameterOrder": [],
+ "parameters": {},
+ "path": "v1/callsets",
+ "request": {
+ "$ref": "CallSet"
+ },
+ "response": {
+ "$ref": "CallSet"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics"
+ ]
}
- },
- "resources": {
- "coveragebuckets": {
- "methods": {
- "list": {
- "description": "Lists fixed width coverage buckets for a read group set, each of which\ncorrespond to a range of a reference sequence. Each bucket summarizes\ncoverage information across its corresponding genomic range.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nCoverage is defined as the number of reads which are aligned to a given\nbase in the reference sequence. Coverage buckets are available at several\nprecomputed bucket widths, enabling retrieval of various coverage 'zoom\nlevels'. The caller must have READ permissions for the target read group\nset.",
- "httpMethod": "GET",
- "id": "genomics.readgroupsets.coveragebuckets.list",
- "parameterOrder": [
- "readGroupSetId"
- ],
- "parameters": {
- "start": {
- "description": "The start position of the range on the reference, 0-based inclusive. If\nspecified, `referenceName` must also be specified. Defaults to 0.",
- "format": "int64",
- "location": "query",
- "type": "string"
- },
- "targetBucketWidth": {
- "description": "The desired width of each reported coverage bucket in base pairs. This\nwill be rounded down to the nearest precomputed bucket width; the value\nof which is returned as `bucketWidth` in the response. Defaults\nto infinity (each bucket spans an entire reference sequence) or the length\nof the target range, if specified. The smallest precomputed\n`bucketWidth` is currently 2048 base pairs; this is subject to\nchange.",
- "format": "int64",
- "location": "query",
- "type": "string"
- },
- "readGroupSetId": {
- "description": "Required. The ID of the read group set over which coverage is requested.",
- "location": "path",
- "required": true,
- "type": "string"
- },
- "referenceName": {
- "description": "The name of the reference to query, within the reference set associated\nwith this query. Optional.",
- "location": "query",
- "type": "string"
- },
- "end": {
- "description": "The end position of the range on the reference, 0-based exclusive. If\nspecified, `referenceName` must also be specified. If unset or 0, defaults\nto the length of the reference.",
- "format": "int64",
- "location": "query",
- "type": "string"
- },
- "pageToken": {
- "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
- "location": "query",
- "type": "string"
- },
- "pageSize": {
- "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024. The maximum value is 2048.",
- "format": "int32",
- "location": "query",
- "type": "integer"
- }
- },
- "path": "v1/readgroupsets/{readGroupSetId}/coveragebuckets",
- "response": {
- "$ref": "ListCoverageBucketsResponse"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics",
- "https://www.googleapis.com/auth/genomics.readonly"
- ]
- }
- }
- }
}
},
"reads": {
@@ -511,205 +417,240 @@
}
}
},
- "callsets": {
+ "readgroupsets": {
"methods": {
- "patch": {
- "description": "Updates a call set.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis method supports patch semantics.",
- "httpMethod": "PATCH",
- "id": "genomics.callsets.patch",
- "parameterOrder": [
- "callSetId"
- ],
- "parameters": {
- "callSetId": {
- "description": "The ID of the call set to be updated.",
- "location": "path",
- "required": true,
- "type": "string"
- },
- "updateMask": {
- "description": "An optional mask specifying which fields to update. At this time, the only\nmutable field is name. The only\nacceptable value is \"name\". If unspecified, all mutable fields will be\nupdated.",
- "format": "google-fieldmask",
- "location": "query",
- "type": "string"
- }
- },
- "path": "v1/callsets/{callSetId}",
+ "import": {
+ "description": "Creates read group sets by asynchronously importing the provided\ninformation.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThe caller must have WRITE permissions to the dataset.\n\n## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import\n\n- Tags will be converted to strings - tag types are not preserved\n- Comments (`@CO`) in the input file header will not be preserved\n- Original header order of references (`@SQ`) will not be preserved\n- Any reverse stranded unmapped reads will be reverse complemented, and\ntheir qualities (also the \"BQ\" and \"OQ\" tags, if any) will be reversed\n- Unmapped reads will be stripped of positional information (reference name\nand position)",
+ "httpMethod": "POST",
+ "id": "genomics.readgroupsets.import",
+ "parameterOrder": [],
+ "parameters": {},
+ "path": "v1/readgroupsets:import",
"request": {
- "$ref": "CallSet"
+ "$ref": "ImportReadGroupSetsRequest"
},
"response": {
- "$ref": "CallSet"
+ "$ref": "Operation"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/devstorage.read_write",
"https://www.googleapis.com/auth/genomics"
]
},
- "get": {
- "description": "Gets a call set by ID.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
- "httpMethod": "GET",
- "id": "genomics.callsets.get",
+ "delete": {
+ "description": "Deletes a read group set.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
+ "httpMethod": "DELETE",
+ "id": "genomics.readgroupsets.delete",
"parameterOrder": [
- "callSetId"
+ "readGroupSetId"
],
"parameters": {
- "callSetId": {
- "description": "The ID of the call set.",
+ "readGroupSetId": {
+ "description": "The ID of the read group set to be deleted. The caller must have WRITE\npermissions to the dataset associated with this read group set.",
"location": "path",
"required": true,
"type": "string"
}
},
- "path": "v1/callsets/{callSetId}",
- "response": {
- "$ref": "CallSet"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics",
- "https://www.googleapis.com/auth/genomics.readonly"
- ]
- },
- "create": {
- "description": "Creates a new call set.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
- "httpMethod": "POST",
- "id": "genomics.callsets.create",
- "parameterOrder": [],
- "parameters": {},
- "path": "v1/callsets",
- "request": {
- "$ref": "CallSet"
- },
+ "path": "v1/readgroupsets/{readGroupSetId}",
"response": {
- "$ref": "CallSet"
+ "$ref": "Empty"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
"https://www.googleapis.com/auth/genomics"
]
},
- "delete": {
- "description": "Deletes a call set.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
- "httpMethod": "DELETE",
- "id": "genomics.callsets.delete",
+ "export": {
+ "description": "Exports a read group set to a BAM file in Google Cloud Storage.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nNote that currently there may be some differences between exported BAM\nfiles and the original BAM file at the time of import. See\nImportReadGroupSets\nfor caveats.",
+ "httpMethod": "POST",
+ "id": "genomics.readgroupsets.export",
"parameterOrder": [
- "callSetId"
+ "readGroupSetId"
],
"parameters": {
- "callSetId": {
- "description": "The ID of the call set to be deleted.",
+ "readGroupSetId": {
+ "description": "Required. The ID of the read group set to export. The caller must have\nREAD access to this read group set.",
"location": "path",
"required": true,
"type": "string"
}
},
- "path": "v1/callsets/{callSetId}",
+ "path": "v1/readgroupsets/{readGroupSetId}:export",
+ "request": {
+ "$ref": "ExportReadGroupSetRequest"
+ },
"response": {
- "$ref": "Empty"
+ "$ref": "Operation"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/devstorage.read_write",
"https://www.googleapis.com/auth/genomics"
]
},
"search": {
- "description": "Gets a list of call sets matching the criteria.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).",
+ "description": "Searches for read group sets matching the criteria.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).",
"httpMethod": "POST",
- "id": "genomics.callsets.search",
+ "id": "genomics.readgroupsets.search",
"parameterOrder": [],
"parameters": {},
- "path": "v1/callsets/search",
+ "path": "v1/readgroupsets/search",
"request": {
- "$ref": "SearchCallSetsRequest"
+ "$ref": "SearchReadGroupSetsRequest"
},
"response": {
- "$ref": "SearchCallSetsResponse"
+ "$ref": "SearchReadGroupSetsResponse"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
"https://www.googleapis.com/auth/genomics",
"https://www.googleapis.com/auth/genomics.readonly"
]
- }
- }
- },
- "variants": {
- "methods": {
- "patch": {
- "description": "Updates a variant.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis method supports patch semantics. Returns the modified variant without\nits calls.",
- "httpMethod": "PATCH",
- "id": "genomics.variants.patch",
+ },
+ "get": {
+ "description": "Gets a read group set by ID.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
+ "httpMethod": "GET",
+ "id": "genomics.readgroupsets.get",
"parameterOrder": [
- "variantId"
+ "readGroupSetId"
],
"parameters": {
- "variantId": {
- "description": "The ID of the variant to be updated.",
+ "readGroupSetId": {
+ "description": "The ID of the read group set.",
"location": "path",
"required": true,
"type": "string"
- },
- "updateMask": {
- "description": "An optional mask specifying which fields to update. At this time, mutable\nfields are names and\ninfo. Acceptable values are \"names\" and\n\"info\". If unspecified, all mutable fields will be updated.",
- "format": "google-fieldmask",
- "location": "query",
- "type": "string"
}
},
- "path": "v1/variants/{variantId}",
- "request": {
- "$ref": "Variant"
- },
+ "path": "v1/readgroupsets/{readGroupSetId}",
"response": {
- "$ref": "Variant"
+ "$ref": "ReadGroupSet"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics"
+ "https://www.googleapis.com/auth/genomics",
+ "https://www.googleapis.com/auth/genomics.readonly"
]
},
- "get": {
- "description": "Gets a variant by ID.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
- "httpMethod": "GET",
- "id": "genomics.variants.get",
+ "patch": {
+ "description": "Updates a read group set.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis method supports patch semantics.",
+ "httpMethod": "PATCH",
+ "id": "genomics.readgroupsets.patch",
"parameterOrder": [
- "variantId"
+ "readGroupSetId"
],
"parameters": {
- "variantId": {
- "description": "The ID of the variant.",
+ "readGroupSetId": {
+ "description": "The ID of the read group set to be updated. The caller must have WRITE\npermissions to the dataset associated with this read group set.",
"location": "path",
"required": true,
"type": "string"
+ },
+ "updateMask": {
+ "description": "An optional mask specifying which fields to update. Supported fields:\n\n* name.\n* referenceSetId.\n\nLeaving `updateMask` unset is equivalent to specifying all mutable\nfields.",
+ "format": "google-fieldmask",
+ "location": "query",
+ "type": "string"
}
},
- "path": "v1/variants/{variantId}",
+ "path": "v1/readgroupsets/{readGroupSetId}",
+ "request": {
+ "$ref": "ReadGroupSet"
+ },
"response": {
- "$ref": "Variant"
+ "$ref": "ReadGroupSet"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics",
- "https://www.googleapis.com/auth/genomics.readonly"
+ "https://www.googleapis.com/auth/genomics"
]
- },
- "import": {
- "description": "Creates variant data by asynchronously importing the provided information.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThe variants for import will be merged with any existing variant that\nmatches its reference sequence, start, end, reference bases, and\nalternative bases. If no such variant exists, a new one will be created.\n\nWhen variants are merged, the call information from the new variant\nis added to the existing variant, and Variant info fields are merged\nas specified in\ninfoMergeConfig.\nAs a special case, for single-sample VCF files, QUAL and FILTER fields will\nbe moved to the call level; these are sometimes interpreted in a\ncall-specific context.\nImported VCF headers are appended to the metadata already in a variant set.",
+ }
+ },
+ "resources": {
+ "coveragebuckets": {
+ "methods": {
+ "list": {
+ "description": "Lists fixed width coverage buckets for a read group set, each of which\ncorrespond to a range of a reference sequence. Each bucket summarizes\ncoverage information across its corresponding genomic range.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nCoverage is defined as the number of reads which are aligned to a given\nbase in the reference sequence. Coverage buckets are available at several\nprecomputed bucket widths, enabling retrieval of various coverage 'zoom\nlevels'. The caller must have READ permissions for the target read group\nset.",
+ "httpMethod": "GET",
+ "id": "genomics.readgroupsets.coveragebuckets.list",
+ "parameterOrder": [
+ "readGroupSetId"
+ ],
+ "parameters": {
+ "referenceName": {
+ "description": "The name of the reference to query, within the reference set associated\nwith this query. Optional.",
+ "location": "query",
+ "type": "string"
+ },
+ "end": {
+ "description": "The end position of the range on the reference, 0-based exclusive. If\nspecified, `referenceName` must also be specified. If unset or 0, defaults\nto the length of the reference.",
+ "format": "int64",
+ "location": "query",
+ "type": "string"
+ },
+ "pageToken": {
+ "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
+ "location": "query",
+ "type": "string"
+ },
+ "pageSize": {
+ "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024. The maximum value is 2048.",
+ "format": "int32",
+ "location": "query",
+ "type": "integer"
+ },
+ "start": {
+ "description": "The start position of the range on the reference, 0-based inclusive. If\nspecified, `referenceName` must also be specified. Defaults to 0.",
+ "format": "int64",
+ "location": "query",
+ "type": "string"
+ },
+ "targetBucketWidth": {
+ "description": "The desired width of each reported coverage bucket in base pairs. This\nwill be rounded down to the nearest precomputed bucket width; the value\nof which is returned as `bucketWidth` in the response. Defaults\nto infinity (each bucket spans an entire reference sequence) or the length\nof the target range, if specified. The smallest precomputed\n`bucketWidth` is currently 2048 base pairs; this is subject to\nchange.",
+ "format": "int64",
+ "location": "query",
+ "type": "string"
+ },
+ "readGroupSetId": {
+ "description": "Required. The ID of the read group set over which coverage is requested.",
+ "location": "path",
+ "required": true,
+ "type": "string"
+ }
+ },
+ "path": "v1/readgroupsets/{readGroupSetId}/coveragebuckets",
+ "response": {
+ "$ref": "ListCoverageBucketsResponse"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics",
+ "https://www.googleapis.com/auth/genomics.readonly"
+ ]
+ }
+ }
+ }
+ }
+ },
+ "variants": {
+ "methods": {
+ "merge": {
+ "description": "Merges the given variants with existing variants.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nEach variant will be\nmerged with an existing variant that matches its reference sequence,\nstart, end, reference bases, and alternative bases. If no such variant\nexists, a new one will be created.\n\nWhen variants are merged, the call information from the new variant\nis added to the existing variant. Variant info fields are merged as\nspecified in the\ninfoMergeConfig\nfield of the MergeVariantsRequest.\n\nPlease exercise caution when using this method! It is easy to introduce\nmistakes in existing variants and difficult to back out of them. For\nexample,\nsuppose you were trying to merge a new variant with an existing one and\nboth\nvariants contain calls that belong to callsets with the same callset ID.\n\n // Existing variant - irrelevant fields trimmed for clarity\n {\n \"variantSetId\": \"10473108253681171589\",\n \"referenceName\": \"1\",\n \"start\": \"10582\",\n \"referenceBases\": \"G\",\n \"alternateBases\": [\n \"A\"\n ],\n \"calls\": [\n {\n \"callSetId\": \"10473108253681171589-0\",\n \"callSetName\": \"CALLSET0\",\n \"genotype\": [\n 0,\n 1\n ],\n }\n ]\n }\n\n // New variant with conflicting call information\n {\n \"variantSetId\": \"10473108253681171589\",\n \"referenceName\": \"1\",\n \"start\": \"10582\",\n \"referenceBases\": \"G\",\n \"alternateBases\": [\n \"A\"\n ],\n \"calls\": [\n {\n \"callSetId\": \"10473108253681171589-0\",\n \"callSetName\": \"CALLSET0\",\n \"genotype\": [\n 1,\n 1\n ],\n }\n ]\n }\n\nThe resulting merged variant would overwrite the existing calls with those\nfrom the new variant:\n\n {\n \"variantSetId\": \"10473108253681171589\",\n \"referenceName\": \"1\",\n \"start\": \"10582\",\n \"referenceBases\": \"G\",\n \"alternateBases\": [\n \"A\"\n ],\n \"calls\": [\n {\n \"callSetId\": \"10473108253681171589-0\",\n \"callSetName\": \"CALLSET0\",\n \"genotype\": [\n 1,\n 1\n ],\n }\n ]\n }\n\nThis may be the desired outcome, but it is up to the user to determine if\nif that is indeed the case.",
"httpMethod": "POST",
- "id": "genomics.variants.import",
+ "id": "genomics.variants.merge",
"parameterOrder": [],
"parameters": {},
- "path": "v1/variants:import",
+ "path": "v1/variants:merge",
"request": {
- "$ref": "ImportVariantsRequest"
+ "$ref": "MergeVariantsRequest"
},
"response": {
- "$ref": "Operation"
+ "$ref": "Empty"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/devstorage.read_write",
"https://www.googleapis.com/auth/genomics"
]
},
@@ -737,21 +678,22 @@
"https://www.googleapis.com/auth/genomics"
]
},
- "merge": {
- "description": "Merges the given variants with existing variants.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nEach variant will be\nmerged with an existing variant that matches its reference sequence,\nstart, end, reference bases, and alternative bases. If no such variant\nexists, a new one will be created.\n\nWhen variants are merged, the call information from the new variant\nis added to the existing variant. Variant info fields are merged as\nspecified in the\ninfoMergeConfig\nfield of the MergeVariantsRequest.\n\nPlease exercise caution when using this method! It is easy to introduce\nmistakes in existing variants and difficult to back out of them. For\nexample,\nsuppose you were trying to merge a new variant with an existing one and\nboth\nvariants contain calls that belong to callsets with the same callset ID.\n\n // Existing variant - irrelevant fields trimmed for clarity\n {\n \"variantSetId\": \"10473108253681171589\",\n \"referenceName\": \"1\",\n \"start\": \"10582\",\n \"referenceBases\": \"G\",\n \"alternateBases\": [\n \"A\"\n ],\n \"calls\": [\n {\n \"callSetId\": \"10473108253681171589-0\",\n \"callSetName\": \"CALLSET0\",\n \"genotype\": [\n 0,\n 1\n ],\n }\n ]\n }\n\n // New variant with conflicting call information\n {\n \"variantSetId\": \"10473108253681171589\",\n \"referenceName\": \"1\",\n \"start\": \"10582\",\n \"referenceBases\": \"G\",\n \"alternateBases\": [\n \"A\"\n ],\n \"calls\": [\n {\n \"callSetId\": \"10473108253681171589-0\",\n \"callSetName\": \"CALLSET0\",\n \"genotype\": [\n 1,\n 1\n ],\n }\n ]\n }\n\nThe resulting merged variant would overwrite the existing calls with those\nfrom the new variant:\n\n {\n \"variantSetId\": \"10473108253681171589\",\n \"referenceName\": \"1\",\n \"start\": \"10582\",\n \"referenceBases\": \"G\",\n \"alternateBases\": [\n \"A\"\n ],\n \"calls\": [\n {\n \"callSetId\": \"10473108253681171589-0\",\n \"callSetName\": \"CALLSET0\",\n \"genotype\": [\n 1,\n 1\n ],\n }\n ]\n }\n\nThis may be the desired outcome, but it is up to the user to determine if\nif that is indeed the case.",
+ "import": {
+ "description": "Creates variant data by asynchronously importing the provided information.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThe variants for import will be merged with any existing variant that\nmatches its reference sequence, start, end, reference bases, and\nalternative bases. If no such variant exists, a new one will be created.\n\nWhen variants are merged, the call information from the new variant\nis added to the existing variant, and Variant info fields are merged\nas specified in\ninfoMergeConfig.\nAs a special case, for single-sample VCF files, QUAL and FILTER fields will\nbe moved to the call level; these are sometimes interpreted in a\ncall-specific context.\nImported VCF headers are appended to the metadata already in a variant set.",
"httpMethod": "POST",
- "id": "genomics.variants.merge",
+ "id": "genomics.variants.import",
"parameterOrder": [],
"parameters": {},
- "path": "v1/variants:merge",
+ "path": "v1/variants:import",
"request": {
- "$ref": "MergeVariantsRequest"
+ "$ref": "ImportVariantsRequest"
},
"response": {
- "$ref": "Empty"
+ "$ref": "Operation"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/devstorage.read_write",
"https://www.googleapis.com/auth/genomics"
]
},
@@ -791,6 +733,64 @@
"https://www.googleapis.com/auth/genomics",
"https://www.googleapis.com/auth/genomics.readonly"
]
+ },
+ "get": {
+ "description": "Gets a variant by ID.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
+ "httpMethod": "GET",
+ "id": "genomics.variants.get",
+ "parameterOrder": [
+ "variantId"
+ ],
+ "parameters": {
+ "variantId": {
+ "description": "The ID of the variant.",
+ "location": "path",
+ "required": true,
+ "type": "string"
+ }
+ },
+ "path": "v1/variants/{variantId}",
+ "response": {
+ "$ref": "Variant"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics",
+ "https://www.googleapis.com/auth/genomics.readonly"
+ ]
+ },
+ "patch": {
+ "description": "Updates a variant.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis method supports patch semantics. Returns the modified variant without\nits calls.",
+ "httpMethod": "PATCH",
+ "id": "genomics.variants.patch",
+ "parameterOrder": [
+ "variantId"
+ ],
+ "parameters": {
+ "variantId": {
+ "description": "The ID of the variant to be updated.",
+ "location": "path",
+ "required": true,
+ "type": "string"
+ },
+ "updateMask": {
+ "description": "An optional mask specifying which fields to update. At this time, mutable\nfields are names and\ninfo. Acceptable values are \"names\" and\n\"info\". If unspecified, all mutable fields will be updated.",
+ "format": "google-fieldmask",
+ "location": "query",
+ "type": "string"
+ }
+ },
+ "path": "v1/variants/{variantId}",
+ "request": {
+ "$ref": "Variant"
+ },
+ "response": {
+ "$ref": "Variant"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics"
+ ]
}
}
},
@@ -872,17 +872,17 @@
"annotationSetId"
],
"parameters": {
- "annotationSetId": {
- "description": "The ID of the annotation set to be updated.",
- "location": "path",
- "required": true,
- "type": "string"
- },
"updateMask": {
"description": "An optional mask specifying which fields to update. Mutable fields are\nname,\nsource_uri, and\ninfo. If unspecified, all\nmutable fields will be updated.",
"format": "google-fieldmask",
"location": "query",
"type": "string"
+ },
+ "annotationSetId": {
+ "description": "The ID of the annotation set to be updated.",
+ "location": "path",
+ "required": true,
+ "type": "string"
}
},
"path": "v1/annotationsets/{annotationSetId}",
@@ -919,25 +919,6 @@
},
"references": {
"methods": {
- "search": {
- "description": "Searches for references which match the given criteria.\n\nFor the definitions of references and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).",
- "httpMethod": "POST",
- "id": "genomics.references.search",
- "parameterOrder": [],
- "parameters": {},
- "path": "v1/references/search",
- "request": {
- "$ref": "SearchReferencesRequest"
- },
- "response": {
- "$ref": "SearchReferencesResponse"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics",
- "https://www.googleapis.com/auth/genomics.readonly"
- ]
- },
"get": {
"description": "Gets a reference.\n\nFor the definitions of references and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).",
"httpMethod": "GET",
@@ -962,6 +943,25 @@
"https://www.googleapis.com/auth/genomics",
"https://www.googleapis.com/auth/genomics.readonly"
]
+ },
+ "search": {
+ "description": "Searches for references which match the given criteria.\n\nFor the definitions of references and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).",
+ "httpMethod": "POST",
+ "id": "genomics.references.search",
+ "parameterOrder": [],
+ "parameters": {},
+ "path": "v1/references/search",
+ "request": {
+ "$ref": "SearchReferencesRequest"
+ },
+ "response": {
+ "$ref": "SearchReferencesResponse"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics",
+ "https://www.googleapis.com/auth/genomics.readonly"
+ ]
}
},
"resources": {
@@ -975,17 +975,6 @@
"referenceId"
],
"parameters": {
- "pageToken": {
- "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
- "location": "query",
- "type": "string"
- },
- "pageSize": {
- "description": "The maximum number of bases to return in a single page. If unspecified,\ndefaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base\npairs).",
- "format": "int32",
- "location": "query",
- "type": "integer"
- },
"start": {
"description": "The start position (0-based) of this query. Defaults to 0.",
"format": "int64",
@@ -1003,76 +992,53 @@
"format": "int64",
"location": "query",
"type": "string"
+ },
+ "pageToken": {
+ "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
+ "location": "query",
+ "type": "string"
+ },
+ "pageSize": {
+ "description": "The maximum number of bases to return in a single page. If unspecified,\ndefaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base\npairs).",
+ "format": "int32",
+ "location": "query",
+ "type": "integer"
}
},
"path": "v1/references/{referenceId}/bases",
"response": {
"$ref": "ListBasesResponse"
},
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics",
- "https://www.googleapis.com/auth/genomics.readonly"
- ]
- }
- }
- }
- }
- },
- "datasets": {
- "methods": {
- "getIamPolicy": {
- "description": "Gets the access control policy for the dataset. This is empty if the\npolicy or resource does not exist.\n\nSee <a href=\"/iam/docs/managing-policies#getting_a_policy\">Getting a\nPolicy</a> for more information.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
- "httpMethod": "POST",
- "id": "genomics.datasets.getIamPolicy",
- "parameterOrder": [
- "resource"
- ],
- "parameters": {
- "resource": {
- "description": "REQUIRED: The resource for which policy is being specified. Format is\n`datasets/<dataset ID>`.",
- "location": "path",
- "pattern": "^datasets/[^/]+$",
- "required": true,
- "type": "string"
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics",
+ "https://www.googleapis.com/auth/genomics.readonly"
+ ]
}
- },
- "path": "v1/{+resource}:getIamPolicy",
- "request": {
- "$ref": "GetIamPolicyRequest"
- },
- "response": {
- "$ref": "Policy"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics"
- ]
- },
- "patch": {
- "description": "Updates a dataset.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis method supports patch semantics.",
- "httpMethod": "PATCH",
- "id": "genomics.datasets.patch",
+ }
+ }
+ }
+ },
+ "datasets": {
+ "methods": {
+ "undelete": {
+ "description": "Undeletes a dataset by restoring a dataset which was deleted via this API.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis operation is only possible for a week after the deletion occurred.",
+ "httpMethod": "POST",
+ "id": "genomics.datasets.undelete",
"parameterOrder": [
"datasetId"
],
"parameters": {
"datasetId": {
- "description": "The ID of the dataset to be updated.",
+ "description": "The ID of the dataset to be undeleted.",
"location": "path",
"required": true,
"type": "string"
- },
- "updateMask": {
- "description": "An optional mask specifying which fields to update. At this time, the only\nmutable field is name. The only\nacceptable value is \"name\". If unspecified, all mutable fields will be\nupdated.",
- "format": "google-fieldmask",
- "location": "query",
- "type": "string"
}
},
- "path": "v1/datasets/{datasetId}",
+ "path": "v1/datasets/{datasetId}:undelete",
"request": {
- "$ref": "Dataset"
+ "$ref": "UndeleteDatasetRequest"
},
"response": {
"$ref": "Dataset"
@@ -1107,24 +1073,30 @@
"https://www.googleapis.com/auth/genomics.readonly"
]
},
- "undelete": {
- "description": "Undeletes a dataset by restoring a dataset which was deleted via this API.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis operation is only possible for a week after the deletion occurred.",
- "httpMethod": "POST",
- "id": "genomics.datasets.undelete",
+ "patch": {
+ "description": "Updates a dataset.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis method supports patch semantics.",
+ "httpMethod": "PATCH",
+ "id": "genomics.datasets.patch",
"parameterOrder": [
"datasetId"
],
"parameters": {
"datasetId": {
- "description": "The ID of the dataset to be undeleted.",
+ "description": "The ID of the dataset to be updated.",
"location": "path",
"required": true,
"type": "string"
+ },
+ "updateMask": {
+ "description": "An optional mask specifying which fields to update. At this time, the only\nmutable field is name. The only\nacceptable value is \"name\". If unspecified, all mutable fields will be\nupdated.",
+ "format": "google-fieldmask",
+ "location": "query",
+ "type": "string"
}
},
- "path": "v1/datasets/{datasetId}:undelete",
+ "path": "v1/datasets/{datasetId}",
"request": {
- "$ref": "UndeleteDatasetRequest"
+ "$ref": "Dataset"
},
"response": {
"$ref": "Dataset"
@@ -1192,6 +1164,11 @@
"id": "genomics.datasets.list",
"parameterOrder": [],
"parameters": {
+ "projectId": {
+ "description": "Required. The Google Cloud project ID to list datasets for.",
+ "location": "query",
+ "type": "string"
+ },
"pageToken": {
"description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
"location": "query",
@@ -1202,16 +1179,193 @@
"format": "int32",
"location": "query",
"type": "integer"
- },
- "projectId": {
- "description": "Required. The Google Cloud project ID to list datasets for.",
- "location": "query",
- "type": "string"
}
},
"path": "v1/datasets",
"response": {
- "$ref": "ListDatasetsResponse"
+ "$ref": "ListDatasetsResponse"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics",
+ "https://www.googleapis.com/auth/genomics.readonly"
+ ]
+ },
+ "create": {
+ "description": "Creates a new dataset.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
+ "httpMethod": "POST",
+ "id": "genomics.datasets.create",
+ "parameterOrder": [],
+ "parameters": {},
+ "path": "v1/datasets",
+ "request": {
+ "$ref": "Dataset"
+ },
+ "response": {
+ "$ref": "Dataset"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics"
+ ]
+ },
+ "setIamPolicy": {
+ "description": "Sets the access control policy on the specified dataset. Replaces any\nexisting policy.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nSee <a href=\"/iam/docs/managing-policies#setting_a_policy\">Setting a\nPolicy</a> for more information.",
+ "httpMethod": "POST",
+ "id": "genomics.datasets.setIamPolicy",
+ "parameterOrder": [
+ "resource"
+ ],
+ "parameters": {
+ "resource": {
+ "description": "REQUIRED: The resource for which policy is being specified. Format is\n`datasets/<dataset ID>`.",
+ "location": "path",
+ "pattern": "^datasets/[^/]+$",
+ "required": true,
+ "type": "string"
+ }
+ },
+ "path": "v1/{+resource}:setIamPolicy",
+ "request": {
+ "$ref": "SetIamPolicyRequest"
+ },
+ "response": {
+ "$ref": "Policy"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics"
+ ]
+ },
+ "getIamPolicy": {
+ "description": "Gets the access control policy for the dataset. This is empty if the\npolicy or resource does not exist.\n\nSee <a href=\"/iam/docs/managing-policies#getting_a_policy\">Getting a\nPolicy</a> for more information.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
+ "httpMethod": "POST",
+ "id": "genomics.datasets.getIamPolicy",
+ "parameterOrder": [
+ "resource"
+ ],
+ "parameters": {
+ "resource": {
+ "description": "REQUIRED: The resource for which policy is being specified. Format is\n`datasets/<dataset ID>`.",
+ "location": "path",
+ "pattern": "^datasets/[^/]+$",
+ "required": true,
+ "type": "string"
+ }
+ },
+ "path": "v1/{+resource}:getIamPolicy",
+ "request": {
+ "$ref": "GetIamPolicyRequest"
+ },
+ "response": {
+ "$ref": "Policy"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics"
+ ]
+ }
+ }
+ },
+ "annotations": {
+ "methods": {
+ "delete": {
+ "description": "Deletes an annotation. Caller must have WRITE permission for\nthe associated annotation set.",
+ "httpMethod": "DELETE",
+ "id": "genomics.annotations.delete",
+ "parameterOrder": [
+ "annotationId"
+ ],
+ "parameters": {
+ "annotationId": {
+ "description": "The ID of the annotation to be deleted.",
+ "location": "path",
+ "required": true,
+ "type": "string"
+ }
+ },
+ "path": "v1/annotations/{annotationId}",
+ "response": {
+ "$ref": "Empty"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics"
+ ]
+ },
+ "create": {
+ "description": "Creates a new annotation. Caller must have WRITE permission\nfor the associated annotation set.\n\nThe following fields are required:\n\n* annotationSetId\n* referenceName or\n referenceId\n\n### Transcripts\n\nFor annotations of type TRANSCRIPT, the following fields of\ntranscript must be provided:\n\n* exons.start\n* exons.end\n\nAll other fields may be optionally specified, unless documented as being\nserver-generated (for example, the `id` field). The annotated\nrange must be no longer than 100Mbp (mega base pairs). See the\nAnnotation resource\nfor additional restrictions on each field.",
+ "httpMethod": "POST",
+ "id": "genomics.annotations.create",
+ "parameterOrder": [],
+ "parameters": {},
+ "path": "v1/annotations",
+ "request": {
+ "$ref": "Annotation"
+ },
+ "response": {
+ "$ref": "Annotation"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics"
+ ]
+ },
+ "batchCreate": {
+ "description": "Creates one or more new annotations atomically. All annotations must\nbelong to the same annotation set. Caller must have WRITE\npermission for this annotation set. For optimal performance, batch\npositionally adjacent annotations together.\n\nIf the request has a systemic issue, such as an attempt to write to\nan inaccessible annotation set, the entire RPC will fail accordingly. For\nlesser data issues, when possible an error will be isolated to the\ncorresponding batch entry in the response; the remaining well formed\nannotations will be created normally.\n\nFor details on the requirements for each individual annotation resource,\nsee\nCreateAnnotation.",
+ "httpMethod": "POST",
+ "id": "genomics.annotations.batchCreate",
+ "parameterOrder": [],
+ "parameters": {},
+ "path": "v1/annotations:batchCreate",
+ "request": {
+ "$ref": "BatchCreateAnnotationsRequest"
+ },
+ "response": {
+ "$ref": "BatchCreateAnnotationsResponse"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics"
+ ]
+ },
+ "search": {
+ "description": "Searches for annotations that match the given criteria. Results are\nordered by genomic coordinate (by reference sequence, then position).\nAnnotations with equivalent genomic coordinates are returned in an\nunspecified order. This order is consistent, such that two queries for the\nsame content (regardless of page size) yield annotations in the same order\nacross their respective streams of paginated responses. Caller must have\nREAD permission for the queried annotation sets.",
+ "httpMethod": "POST",
+ "id": "genomics.annotations.search",
+ "parameterOrder": [],
+ "parameters": {},
+ "path": "v1/annotations/search",
+ "request": {
+ "$ref": "SearchAnnotationsRequest"
+ },
+ "response": {
+ "$ref": "SearchAnnotationsResponse"
+ },
+ "scopes": [
+ "https://www.googleapis.com/auth/cloud-platform",
+ "https://www.googleapis.com/auth/genomics",
+ "https://www.googleapis.com/auth/genomics.readonly"
+ ]
+ },
+ "get": {
+ "description": "Gets an annotation. Caller must have READ permission\nfor the associated annotation set.",
+ "httpMethod": "GET",
+ "id": "genomics.annotations.get",
+ "parameterOrder": [
+ "annotationId"
+ ],
+ "parameters": {
+ "annotationId": {
+ "description": "The ID of the annotation to be retrieved.",
+ "location": "path",
+ "required": true,
+ "type": "string"
+ }
+ },
+ "path": "v1/annotations/{annotationId}",
+ "response": {
+ "$ref": "Annotation"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
@@ -1219,46 +1373,33 @@
"https://www.googleapis.com/auth/genomics.readonly"
]
},
- "setIamPolicy": {
- "description": "Sets the access control policy on the specified dataset. Replaces any\nexisting policy.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nSee <a href=\"/iam/docs/managing-policies#setting_a_policy\">Setting a\nPolicy</a> for more information.",
- "httpMethod": "POST",
- "id": "genomics.datasets.setIamPolicy",
+ "update": {
+ "description": "Updates an annotation. Caller must have\nWRITE permission for the associated dataset.",
+ "httpMethod": "PUT",
+ "id": "genomics.annotations.update",
"parameterOrder": [
- "resource"
+ "annotationId"
],
"parameters": {
- "resource": {
- "description": "REQUIRED: The resource for which policy is being specified. Format is\n`datasets/<dataset ID>`.",
+ "updateMask": {
+ "description": "An optional mask specifying which fields to update. Mutable fields are\nname,\nvariant,\ntranscript, and\ninfo. If unspecified, all mutable\nfields will be updated.",
+ "format": "google-fieldmask",
+ "location": "query",
+ "type": "string"
+ },
+ "annotationId": {
+ "description": "The ID of the annotation to be updated.",
"location": "path",
- "pattern": "^datasets/[^/]+$",
"required": true,
"type": "string"
}
},
- "path": "v1/{+resource}:setIamPolicy",
- "request": {
- "$ref": "SetIamPolicyRequest"
- },
- "response": {
- "$ref": "Policy"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics"
- ]
- },
- "create": {
- "description": "Creates a new dataset.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
- "httpMethod": "POST",
- "id": "genomics.datasets.create",
- "parameterOrder": [],
- "parameters": {},
- "path": "v1/datasets",
+ "path": "v1/annotations/{annotationId}",
"request": {
- "$ref": "Dataset"
+ "$ref": "Annotation"
},
"response": {
- "$ref": "Dataset"
+ "$ref": "Annotation"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
@@ -1269,24 +1410,6 @@
},
"variantsets": {
"methods": {
- "create": {
- "description": "Creates a new variant set.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThe provided variant set must have a valid `datasetId` set - all other\nfields are optional. Note that the `id` field will be ignored, as this is\nassigned by the server.",
- "httpMethod": "POST",
- "id": "genomics.variantsets.create",
- "parameterOrder": [],
- "parameters": {},
- "path": "v1/variantsets",
- "request": {
- "$ref": "VariantSet"
- },
- "response": {
- "$ref": "VariantSet"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics"
- ]
- },
"export": {
"description": "Exports variant set data to an external destination.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
"httpMethod": "POST",
@@ -1415,166 +1538,95 @@
"https://www.googleapis.com/auth/cloud-platform",
"https://www.googleapis.com/auth/genomics"
]
- }
- }
- },
- "annotations": {
- "methods": {
- "delete": {
- "description": "Deletes an annotation. Caller must have WRITE permission for\nthe associated annotation set.",
- "httpMethod": "DELETE",
- "id": "genomics.annotations.delete",
- "parameterOrder": [
- "annotationId"
- ],
- "parameters": {
- "annotationId": {
- "description": "The ID of the annotation to be deleted.",
- "location": "path",
- "required": true,
- "type": "string"
- }
- },
- "path": "v1/annotations/{annotationId}",
- "response": {
- "$ref": "Empty"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics"
- ]
},
"create": {
- "description": "Creates a new annotation. Caller must have WRITE permission\nfor the associated annotation set.\n\nThe following fields are required:\n\n* annotationSetId\n* referenceName or\n referenceId\n\n### Transcripts\n\nFor annotations of type TRANSCRIPT, the following fields of\ntranscript must be provided:\n\n* exons.start\n* exons.end\n\nAll other fields may be optionally specified, unless documented as being\nserver-generated (for example, the `id` field). The annotated\nrange must be no longer than 100Mbp (mega base pairs). See the\nAnnotation resource\nfor additional restrictions on each field.",
+ "description": "Creates a new variant set.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThe provided variant set must have a valid `datasetId` set - all other\nfields are optional. Note that the `id` field will be ignored, as this is\nassigned by the server.",
"httpMethod": "POST",
- "id": "genomics.annotations.create",
+ "id": "genomics.variantsets.create",
"parameterOrder": [],
"parameters": {},
- "path": "v1/annotations",
+ "path": "v1/variantsets",
"request": {
- "$ref": "Annotation"
+ "$ref": "VariantSet"
},
"response": {
- "$ref": "Annotation"
+ "$ref": "VariantSet"
},
"scopes": [
"https://www.googleapis.com/auth/cloud-platform",
"https://www.googleapis.com/auth/genomics"
]
- },
- "batchCreate": {
- "description": "Creates one or more new annotations atomically. All annotations must\nbelong to the same annotation set. Caller must have WRITE\npermission for this annotation set. For optimal performance, batch\npositionally adjacent annotations together.\n\nIf the request has a systemic issue, such as an attempt to write to\nan inaccessible annotation set, the entire RPC will fail accordingly. For\nlesser data issues, when possible an error will be isolated to the\ncorresponding batch entry in the response; the remaining well formed\nannotations will be created normally.\n\nFor details on the requirements for each individual annotation resource,\nsee\nCreateAnnotation.",
- "httpMethod": "POST",
- "id": "genomics.annotations.batchCreate",
- "parameterOrder": [],
- "parameters": {},
- "path": "v1/annotations:batchCreate",
- "request": {
- "$ref": "BatchCreateAnnotationsRequest"
- },
- "response": {
- "$ref": "BatchCreateAnnotationsResponse"
+ }
+ }
+ }
+ },
+ "revision": "20170322",
+ "rootUrl": "https://genomics.googleapis.com/",
+ "schemas": {
+ "ImportReadGroupSetsRequest": {
+ "description": "The read group set import request.",
+ "id": "ImportReadGroupSetsRequest",
+ "properties": {
+ "sourceUris": {
+ "description": "A list of URIs pointing at [BAM\nfiles](https://samtools.github.io/hts-specs/SAMv1.pdf)\nin Google Cloud Storage.\nThose URIs can include wildcards (*), but do not add or remove\nmatching files before import has completed.\n\nNote that Google Cloud Storage object listing is only eventually\nconsistent: files added may be not be immediately visible to\neveryone. Thus, if using a wildcard it is preferable not to start\nthe import immediately after the files are created.",
+ "items": {
+ "type": "string"
},
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics"
- ]
+ "type": "array"
},
- "search": {
- "description": "Searches for annotations that match the given criteria. Results are\nordered by genomic coordinate (by reference sequence, then position).\nAnnotations with equivalent genomic coordinates are returned in an\nunspecified order. This order is consistent, such that two queries for the\nsame content (regardless of page size) yield annotations in the same order\nacross their respective streams of paginated responses. Caller must have\nREAD permission for the queried annotation sets.",
- "httpMethod": "POST",
- "id": "genomics.annotations.search",
- "parameterOrder": [],
- "parameters": {},
- "path": "v1/annotations/search",
- "request": {
- "$ref": "SearchAnnotationsRequest"
- },
- "response": {
- "$ref": "SearchAnnotationsResponse"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics",
- "https://www.googleapis.com/auth/genomics.readonly"
- ]
+ "referenceSetId": {
+ "description": "The reference set to which the imported read group sets are aligned to, if\nany. The reference names of this reference set must be a superset of those\nfound in the imported file headers. If no reference set id is provided, a\nbest effort is made to associate with a matching reference set.",
+ "type": "string"
},
- "get": {
- "description": "Gets an annotation. Caller must have READ permission\nfor the associated annotation set.",
- "httpMethod": "GET",
- "id": "genomics.annotations.get",
- "parameterOrder": [
- "annotationId"
+ "partitionStrategy": {
+ "description": "The partition strategy describes how read groups are partitioned into read\ngroup sets.",
+ "enum": [
+ "PARTITION_STRATEGY_UNSPECIFIED",
+ "PER_FILE_PER_SAMPLE",
+ "MERGE_ALL"
],
- "parameters": {
- "annotationId": {
- "description": "The ID of the annotation to be retrieved.",
- "location": "path",
- "required": true,
- "type": "string"
- }
- },
- "path": "v1/annotations/{annotationId}",
- "response": {
- "$ref": "Annotation"
- },
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics",
- "https://www.googleapis.com/auth/genomics.readonly"
- ]
- },
- "update": {
- "description": "Updates an annotation. Caller must have\nWRITE permission for the associated dataset.",
- "httpMethod": "PUT",
- "id": "genomics.annotations.update",
- "parameterOrder": [
- "annotationId"
+ "enumDescriptions": [
+ "",
+ "In most cases, this strategy yields one read group set per file. This is\nthe default behavior.\n\nAllocate one read group set per file per sample. For BAM files, read\ngroups are considered to share a sample if they have identical sample\nnames. Furthermore, all reads for each file which do not belong to a read\ngroup, if any, will be grouped into a single read group set per-file.",
+ "Includes all read groups in all imported files into a single read group\nset. Requires that the headers for all imported files are equivalent. All\nreads which do not belong to a read group, if any, will be grouped into a\nseparate read group set."
],
- "parameters": {
- "updateMask": {
- "description": "An optional mask specifying which fields to update. Mutable fields are\nname,\nvariant,\ntranscript, and\ninfo. If unspecified, all mutable\nfields will be updated.",
- "format": "google-fieldmask",
- "location": "query",
- "type": "string"
- },
- "annotationId": {
- "description": "The ID of the annotation to be updated.",
- "location": "path",
- "required": true,
- "type": "string"
- }
- },
- "path": "v1/annotations/{annotationId}",
- "request": {
- "$ref": "Annotation"
- },
- "response": {
- "$ref": "Annotation"
+ "type": "string"
+ },
+ "datasetId": {
+ "description": "Required. The ID of the dataset these read group sets will belong to. The\ncaller must have WRITE permissions to this dataset.",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "Policy": {
+ "description": "Defines an Identity and Access Management (IAM) policy. It is used to\nspecify access control policies for Cloud Platform resources.\n\n\nA `Policy` consists of a list of `bindings`. A `Binding` binds a list of\n`members` to a `role`, where the members can be user accounts, Google groups,\nGoogle domains, and service accounts. A `role` is a named list of permissions\ndefined by IAM.\n\n**Example**\n\n {\n \"bindings\": [\n {\n \"role\": \"roles/owner\",\n \"members\": [\n \"user:mike@example.com\",\n \"group:admins@example.com\",\n \"domain:google.com\",\n \"serviceAccount:my-other-app@appspot.gserviceaccount.com\",\n ]\n },\n {\n \"role\": \"roles/viewer\",\n \"members\": [\"user:sean@example.com\"]\n }\n ]\n }\n\nFor a description of IAM and its features, see the\n[IAM developer's guide](https://cloud.google.com/iam).",
+ "id": "Policy",
+ "properties": {
+ "bindings": {
+ "description": "Associates a list of `members` to a `role`.\nMultiple `bindings` must not be specified for the same `role`.\n`bindings` with no members will result in an error.",
+ "items": {
+ "$ref": "Binding"
},
- "scopes": [
- "https://www.googleapis.com/auth/cloud-platform",
- "https://www.googleapis.com/auth/genomics"
- ]
+ "type": "array"
+ },
+ "etag": {
+ "description": "`etag` is used for optimistic concurrency control as a way to help\nprevent simultaneous updates of a policy from overwriting each other.\nIt is strongly suggested that systems make use of the `etag` in the\nread-modify-write cycle to perform policy updates in order to avoid race\nconditions: An `etag` is returned in the response to `getIamPolicy`, and\nsystems are expected to put that etag in the request to `setIamPolicy` to\nensure that their change will be applied to the same version of the policy.\n\nIf no `etag` is provided in the call to `setIamPolicy`, then the existing\npolicy is overwritten blindly.",
+ "format": "byte",
+ "type": "string"
+ },
+ "version": {
+ "description": "Version of the `Policy`. The default version is 0.",
+ "format": "int32",
+ "type": "integer"
}
- }
- }
- },
- "revision": "20170302",
- "rootUrl": "https://genomics.googleapis.com/",
- "schemas": {
+ },
+ "type": "object"
+ },
"Annotation": {
"description": "An annotation describes a region of reference genome. The value of an\nannotation may be one of several canonical types, supplemented by arbitrary\ninfo tags. An annotation is not inherently associated with a specific\nsample or individual (though a client could choose to use annotations in\nthis way). Example canonical annotation types are `GENE` and\n`VARIANT`.",
"id": "Annotation",
"properties": {
- "id": {
- "description": "The server-generated annotation ID, unique across all annotations.",
- "type": "string"
- },
- "referenceId": {
- "description": "The ID of the Google Genomics reference associated with this range.",
- "type": "string"
- },
"reverseStrand": {
"description": "Whether this range refers to the reverse strand, as opposed to the forward\nstrand. Note that regardless of this field, the start/end position of the\nrange always refer to the forward strand.",
"type": "boolean"
@@ -1636,6 +1688,14 @@
"variant": {
"$ref": "VariantAnnotation",
"description": "A variant annotation, which describes the effect of a variant on the\ngenome, the coding sequence, and/or higher level consequences at the\norganism level e.g. pathogenicity. This field is only set for annotations\nof type `VARIANT`."
+ },
+ "id": {
+ "description": "The server-generated annotation ID, unique across all annotations.",
+ "type": "string"
+ },
+ "referenceId": {
+ "description": "The ID of the Google Genomics reference associated with this range.",
+ "type": "string"
}
},
"type": "object"
@@ -1650,18 +1710,6 @@
"description": "The read search request.",
"id": "SearchReadsRequest",
"properties": {
- "readGroupIds": {
- "description": "The IDs of the read groups within which to search for reads. All specified\nread groups must belong to the same read group sets. Must specify one of\n`readGroupSetIds` or `readGroupIds`.",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "end": {
- "description": "The end position of the range on the reference, 0-based exclusive. If\nspecified, `referenceName` must also be specified.",
- "format": "int64",
- "type": "string"
- },
"pageToken": {
"description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
"type": "string"
@@ -1686,17 +1734,18 @@
"type": "string"
},
"type": "array"
- }
- },
- "type": "object"
- },
- "RuntimeMetadata": {
- "description": "Runtime metadata that will be populated in the\nruntimeMetadata\nfield of the Operation associated with a RunPipeline execution.",
- "id": "RuntimeMetadata",
- "properties": {
- "computeEngine": {
- "$ref": "ComputeEngine",
- "description": "Execution information specific to Google Compute Engine."
+ },
+ "readGroupIds": {
+ "description": "The IDs of the read groups within which to search for reads. All specified\nread groups must belong to the same read group sets. Must specify one of\n`readGroupSetIds` or `readGroupIds`.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "end": {
+ "description": "The end position of the range on the reference, 0-based exclusive. If\nspecified, `referenceName` must also be specified.",
+ "format": "int64",
+ "type": "string"
}
},
"type": "object"
@@ -1705,6 +1754,18 @@
"description": "This resource represents a long-running operation that is the result of a\nnetwork API call.",
"id": "Operation",
"properties": {
+ "metadata": {
+ "additionalProperties": {
+ "description": "Properties of the object. Contains field @type with type URL.",
+ "type": "any"
+ },
+ "description": "An OperationMetadata object. This will always be returned with the Operation.",
+ "type": "object"
+ },
+ "done": {
+ "description": "If the value is `false`, it means the operation is still in progress.\nIf true, the operation is completed, and either `error` or `response` is\navailable.",
+ "type": "boolean"
+ },
"response": {
"additionalProperties": {
"description": "Properties of the object. Contains field @type with type URL.",
@@ -1720,18 +1781,17 @@
"error": {
"$ref": "Status",
"description": "The error result of the operation in case of failure or cancellation."
- },
- "metadata": {
- "additionalProperties": {
- "description": "Properties of the object. Contains field @type with type URL.",
- "type": "any"
- },
- "description": "An OperationMetadata object. This will always be returned with the Operation.",
- "type": "object"
- },
- "done": {
- "description": "If the value is `false`, it means the operation is still in progress.\nIf true, the operation is completed, and either `error` or `response` is\navailable.",
- "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "RuntimeMetadata": {
+ "description": "Runtime metadata that will be populated in the\nruntimeMetadata\nfield of the Operation associated with a RunPipeline execution.",
+ "id": "RuntimeMetadata",
+ "properties": {
+ "computeEngine": {
+ "$ref": "ComputeEngine",
+ "description": "Execution information specific to Google Compute Engine."
}
},
"type": "object"
@@ -1754,6 +1814,24 @@
"description": "A call represents the determination of genotype with respect to a particular\nvariant. It may include associated information such as quality and phasing.\nFor example, a call might assign a probability of 0.32 to the occurrence of\na SNP named rs1234 in a call set with the name NA12345.",
"id": "VariantCall",
"properties": {
+ "phaseset": {
+ "description": "If this field is present, this variant call's genotype ordering implies\nthe phase of the bases and is consistent with any other variant calls in\nthe same reference sequence which have the same phaseset value.\nWhen importing data from VCF, if the genotype data was phased but no\nphase set was specified this field will be set to `*`.",
+ "type": "string"
+ },
+ "info": {
+ "additionalProperties": {
+ "items": {
+ "type": "any"
+ },
+ "type": "array"
+ },
+ "description": "A map of additional variant call information. This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).",
+ "type": "object"
+ },
+ "callSetName": {
+ "description": "The name of the call set this variant call belongs to.",
+ "type": "string"
+ },
"genotypeLikelihood": {
"description": "The genotype likelihoods for this variant call. Each array entry\nrepresents how likely a specific genotype is for this call. The value\nordering is defined by the GL tag in the VCF spec.\nIf Phred-scaled genotype likelihood scores (PL) are available and\nlog10(P) genotype likelihood scores (GL) are not, PL scores are converted\nto GL scores. If both are available, PL scores are stored in `info`.",
"items": {
@@ -1773,24 +1851,6 @@
"type": "integer"
},
"type": "array"
- },
- "phaseset": {
- "description": "If this field is present, this variant call's genotype ordering implies\nthe phase of the bases and is consistent with any other variant calls in\nthe same reference sequence which have the same phaseset value.\nWhen importing data from VCF, if the genotype data was phased but no\nphase set was specified this field will be set to `*`.",
- "type": "string"
- },
- "info": {
- "additionalProperties": {
- "items": {
- "type": "any"
- },
- "type": "array"
- },
- "description": "A map of additional variant call information. This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).",
- "type": "object"
- },
- "callSetName": {
- "description": "The name of the call set this variant call belongs to.",
- "type": "string"
}
},
"type": "object"
@@ -1859,6 +1919,11 @@
},
"type": "object"
},
+ "UndeleteDatasetRequest": {
+ "id": "UndeleteDatasetRequest",
+ "properties": {},
+ "type": "object"
+ },
"Binding": {
"description": "Associates `members` with a `role`.",
"id": "Binding",
@@ -1877,19 +1942,10 @@
},
"type": "object"
},
- "UndeleteDatasetRequest": {
- "id": "UndeleteDatasetRequest",
- "properties": {},
- "type": "object"
- },
"Range": {
"description": "A 0-based half-open genomic coordinate range for search requests.",
"id": "Range",
"properties": {
- "referenceName": {
- "description": "The reference sequence name, for example `chr1`,\n`1`, or `chrX`.",
- "type": "string"
- },
"start": {
"description": "The start position of the range on the reference, 0-based inclusive.",
"format": "int64",
@@ -1899,6 +1955,10 @@
"description": "The end position of the range on the reference, 0-based exclusive.",
"format": "int64",
"type": "string"
+ },
+ "referenceName": {
+ "description": "The reference sequence name, for example `chr1`,\n`1`, or `chrX`.",
+ "type": "string"
}
},
"type": "object"
@@ -1907,10 +1967,6 @@
"description": "A variant set is a collection of call sets and variants. It contains summary\nstatistics of those contents. A variant set belongs to a dataset.\n\nFor more genomics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
"id": "VariantSet",
"properties": {
- "datasetId": {
- "description": "The dataset to which this variant set belongs.",
- "type": "string"
- },
"name": {
"description": "User-specified, mutable name.",
"type": "string"
@@ -1940,21 +1996,9 @@
"description": {
"description": "A textual description of this variant set.",
"type": "string"
- }
- },
- "type": "object"
- },
- "ReferenceBound": {
- "description": "ReferenceBound records an upper bound for the starting coordinate of\nvariants in a particular reference.",
- "id": "ReferenceBound",
- "properties": {
- "upperBound": {
- "description": "An upper bound (inclusive) on the starting coordinate of any\nvariant in the reference sequence.",
- "format": "int64",
- "type": "string"
},
- "referenceName": {
- "description": "The name of the reference associated with this reference bound.",
+ "datasetId": {
+ "description": "The dataset to which this variant set belongs.",
"type": "string"
}
},
@@ -1973,18 +2017,34 @@
},
"type": "object"
},
- "ListOperationsResponse": {
- "description": "The response message for Operations.ListOperations.",
- "id": "ListOperationsResponse",
+ "ReferenceBound": {
+ "description": "ReferenceBound records an upper bound for the starting coordinate of\nvariants in a particular reference.",
+ "id": "ReferenceBound",
+ "properties": {
+ "referenceName": {
+ "description": "The name of the reference associated with this reference bound.",
+ "type": "string"
+ },
+ "upperBound": {
+ "description": "An upper bound (inclusive) on the starting coordinate of any\nvariant in the reference sequence.",
+ "format": "int64",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "SearchCallSetsResponse": {
+ "description": "The call set search response.",
+ "id": "SearchCallSetsResponse",
"properties": {
"nextPageToken": {
- "description": "The standard List next-page token.",
+ "description": "The continuation token, which is used to page through large result sets.\nProvide this value in a subsequent request to return the next page of\nresults. This field will be empty if there aren't any additional results.",
"type": "string"
},
- "operations": {
- "description": "A list of operations that matches the specified filter in the request.",
+ "callSets": {
+ "description": "The list of matching call sets.",
"items": {
- "$ref": "Operation"
+ "$ref": "CallSet"
},
"type": "array"
}
@@ -1995,11 +2055,6 @@
"description": "A variant represents a change in DNA sequence relative to a reference\nsequence. For example, a variant could represent a SNP or an insertion.\nVariants belong to a variant set.\n\nFor more genomics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nEach of the calls on a variant represent a determination of genotype with\nrespect to that variant. For example, a call might assign probability of 0.32\nto the occurrence of a SNP named rs1234 in a sample named NA12345. A call\nbelongs to a call set, which contains related calls typically from one\nsample.",
"id": "Variant",
"properties": {
- "start": {
- "description": "The position at which this variant occurs (0-based).\nThis corresponds to the first base of the string of reference bases.",
- "format": "int64",
- "type": "string"
- },
"quality": {
"description": "A measure of how likely this variant is to be real.\nA higher value is better.",
"format": "double",
@@ -2045,11 +2100,6 @@
},
"type": "array"
},
- "end": {
- "description": "The end position (0-based) of this variant. This corresponds to the first\nbase after the last base in the reference allele. So, the length of\nthe reference allele is (end - start). This is useful for variants\nthat don't explicitly give alternate bases, for example large deletions.",
- "format": "int64",
- "type": "string"
- },
"filter": {
"description": "A list of filters (normally quality filters) this variant has failed.\n`PASS` indicates this variant has passed all filters.",
"items": {
@@ -2057,6 +2107,11 @@
},
"type": "array"
},
+ "end": {
+ "description": "The end position (0-based) of this variant. This corresponds to the first\nbase after the last base in the reference allele. So, the length of\nthe reference allele is (end - start). This is useful for variants\nthat don't explicitly give alternate bases, for example large deletions.",
+ "format": "int64",
+ "type": "string"
+ },
"calls": {
"description": "The variant calls for this particular variant. Each one represents the\ndetermination of genotype with respect to this variant.",
"items": {
@@ -2068,77 +2123,29 @@
"description": "The date this variant was created, in milliseconds from the epoch.",
"format": "int64",
"type": "string"
- }
- },
- "type": "object"
- },
- "SearchCallSetsResponse": {
- "description": "The call set search response.",
- "id": "SearchCallSetsResponse",
- "properties": {
- "nextPageToken": {
- "description": "The continuation token, which is used to page through large result sets.\nProvide this value in a subsequent request to return the next page of\nresults. This field will be empty if there aren't any additional results.",
- "type": "string"
},
- "callSets": {
- "description": "The list of matching call sets.",
- "items": {
- "$ref": "CallSet"
- },
- "type": "array"
+ "start": {
+ "description": "The position at which this variant occurs (0-based).\nThis corresponds to the first base of the string of reference bases.",
+ "format": "int64",
+ "type": "string"
}
},
"type": "object"
},
- "SearchVariantsRequest": {
- "description": "The variant search request.",
- "id": "SearchVariantsRequest",
+ "ListOperationsResponse": {
+ "description": "The response message for Operations.ListOperations.",
+ "id": "ListOperationsResponse",
"properties": {
- "referenceName": {
- "description": "Required. Only return variants in this reference sequence.",
- "type": "string"
- },
- "variantSetIds": {
- "description": "At most one variant set ID must be provided. Only variants from this\nvariant set will be returned. If omitted, a call set id must be included in\nthe request.",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "end": {
- "description": "The end of the window, 0-based exclusive. If unspecified or 0, defaults to\nthe length of the reference.",
- "format": "int64",
- "type": "string"
- },
- "maxCalls": {
- "description": "The maximum number of calls to return in a single page. Note that this\nlimit may be exceeded in the event that a matching variant contains more\ncalls than the requested maximum. If unspecified, defaults to 5000. The\nmaximum value is 10000.",
- "format": "int32",
- "type": "integer"
- },
- "pageToken": {
- "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
+ "nextPageToken": {
+ "description": "The standard List next-page token.",
"type": "string"
},
- "pageSize": {
- "description": "The maximum number of variants to return in a single page. If unspecified,\ndefaults to 5000. The maximum value is 10000.",
- "format": "int32",
- "type": "integer"
- },
- "callSetIds": {
- "description": "Only return variant calls which belong to call sets with these ids.\nLeaving this blank returns all variant calls. If a variant has no\ncalls belonging to any of these call sets, it won't be returned at all.",
+ "operations": {
+ "description": "A list of operations that matches the specified filter in the request.",
"items": {
- "type": "string"
+ "$ref": "Operation"
},
"type": "array"
- },
- "start": {
- "description": "The beginning of the window (0-based, inclusive) for which\noverlapping variants should be returned. If unspecified, defaults to 0.",
- "format": "int64",
- "type": "string"
- },
- "variantName": {
- "description": "Only return variants which have exactly this name.",
- "type": "string"
}
},
"type": "object"
@@ -2147,14 +2154,6 @@
"description": "Metadata describing an Operation.",
"id": "OperationMetadata",
"properties": {
- "projectId": {
- "description": "The Google Cloud Project in which the job is scoped.",
- "type": "string"
- },
- "clientId": {
- "description": "This field is deprecated. Use `labels` instead. Optionally provided by the\ncaller when submitting the request that creates the operation.",
- "type": "string"
- },
"events": {
"description": "Optional event messages that were generated during the job's execution.\nThis also contains any warnings that were generated during import\nor export.",
"items": {
@@ -2199,21 +2198,75 @@
},
"description": "Optionally provided by the caller when submitting the request that creates\nthe operation.",
"type": "object"
+ },
+ "projectId": {
+ "description": "The Google Cloud Project in which the job is scoped.",
+ "type": "string"
+ },
+ "clientId": {
+ "description": "This field is deprecated. Use `labels` instead. Optionally provided by the\ncaller when submitting the request that creates the operation.",
+ "type": "string"
}
},
"type": "object"
},
- "SearchReadGroupSetsRequest": {
- "description": "The read group set search request.",
- "id": "SearchReadGroupSetsRequest",
+ "SearchVariantsRequest": {
+ "description": "The variant search request.",
+ "id": "SearchVariantsRequest",
"properties": {
- "datasetIds": {
- "description": "Restricts this query to read group sets within the given datasets. At least\none ID must be provided.",
+ "pageToken": {
+ "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
+ "type": "string"
+ },
+ "maxCalls": {
+ "description": "The maximum number of calls to return in a single page. Note that this\nlimit may be exceeded in the event that a matching variant contains more\ncalls than the requested maximum. If unspecified, defaults to 5000. The\nmaximum value is 10000.",
+ "format": "int32",
+ "type": "integer"
+ },
+ "pageSize": {
+ "description": "The maximum number of variants to return in a single page. If unspecified,\ndefaults to 5000. The maximum value is 10000.",
+ "format": "int32",
+ "type": "integer"
+ },
+ "callSetIds": {
+ "description": "Only return variant calls which belong to call sets with these ids.\nLeaving this blank returns all variant calls. If a variant has no\ncalls belonging to any of these call sets, it won't be returned at all.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "variantName": {
+ "description": "Only return variants which have exactly this name.",
+ "type": "string"
+ },
+ "start": {
+ "description": "The beginning of the window (0-based, inclusive) for which\noverlapping variants should be returned. If unspecified, defaults to 0.",
+ "format": "int64",
+ "type": "string"
+ },
+ "referenceName": {
+ "description": "Required. Only return variants in this reference sequence.",
+ "type": "string"
+ },
+ "variantSetIds": {
+ "description": "At most one variant set ID must be provided. Only variants from this\nvariant set will be returned. If omitted, a call set id must be included in\nthe request.",
"items": {
"type": "string"
},
"type": "array"
},
+ "end": {
+ "description": "The end of the window, 0-based exclusive. If unspecified or 0, defaults to\nthe length of the reference.",
+ "format": "int64",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "SearchReadGroupSetsRequest": {
+ "description": "The read group set search request.",
+ "id": "SearchReadGroupSetsRequest",
+ "properties": {
"name": {
"description": "Only return read group sets for which a substring of the name matches this\nstring.",
"type": "string"
@@ -2226,6 +2279,13 @@
"description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 256. The maximum value is 1024.",
"format": "int32",
"type": "integer"
+ },
+ "datasetIds": {
+ "description": "Restricts this query to read group sets within the given datasets. At least\none ID must be provided.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
}
},
"type": "object"
@@ -2250,25 +2310,25 @@
"ClinicalCondition": {
"id": "ClinicalCondition",
"properties": {
- "omimId": {
- "description": "The OMIM id for this condition.\nSearch for these IDs at http://omim.org/",
+ "conceptId": {
+ "description": "The MedGen concept id associated with this gene.\nSearch for these IDs at http://www.ncbi.nlm.nih.gov/medgen/",
"type": "string"
},
- "externalIds": {
- "description": "The set of external IDs for this condition.",
+ "names": {
+ "description": "A set of names for the condition.",
"items": {
- "$ref": "ExternalId"
+ "type": "string"
},
"type": "array"
},
- "conceptId": {
- "description": "The MedGen concept id associated with this gene.\nSearch for these IDs at http://www.ncbi.nlm.nih.gov/medgen/",
+ "omimId": {
+ "description": "The OMIM id for this condition.\nSearch for these IDs at http://omim.org/",
"type": "string"
},
- "names": {
- "description": "A set of names for the condition.",
+ "externalIds": {
+ "description": "The set of external IDs for this condition.",
"items": {
- "type": "string"
+ "$ref": "ExternalId"
},
"type": "array"
}
@@ -2375,25 +2435,42 @@
},
"type": "object"
},
- "SearchVariantSetsRequest": {
- "description": "The search variant sets request.",
- "id": "SearchVariantSetsRequest",
+ "Reference": {
+ "description": "A reference is a canonical assembled DNA sequence, intended to act as a\nreference coordinate space for other genomic annotations. A single reference\nmight represent the human chromosome 1 or mitochandrial DNA, for instance. A\nreference belongs to one or more reference sets.\n\nFor more genomics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
+ "id": "Reference",
"properties": {
- "datasetIds": {
- "description": "Exactly one dataset ID must be provided here. Only variant sets which\nbelong to this dataset will be returned.",
+ "name": {
+ "description": "The name of this reference, for example `22`.",
+ "type": "string"
+ },
+ "md5checksum": {
+ "description": "MD5 of the upper-case sequence excluding all whitespace characters (this\nis equivalent to SQ:M5 in SAM). This value is represented in lower case\nhexadecimal format.",
+ "type": "string"
+ },
+ "id": {
+ "description": "The server-generated reference ID, unique across all references.",
+ "type": "string"
+ },
+ "length": {
+ "description": "The length of this reference's sequence.",
+ "format": "int64",
+ "type": "string"
+ },
+ "sourceAccessions": {
+ "description": "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally\nwith a version number, for example `GCF_000001405.26`.",
"items": {
"type": "string"
},
"type": "array"
},
- "pageToken": {
- "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
- "type": "string"
- },
- "pageSize": {
- "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024.",
+ "ncbiTaxonId": {
+ "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.",
"format": "int32",
"type": "integer"
+ },
+ "sourceUri": {
+ "description": "The URI from which the sequence was obtained. Typically specifies a FASTA\nformat file.",
+ "type": "string"
}
},
"type": "object"
@@ -2432,14 +2509,14 @@
],
"type": "string"
},
- "value": {
- "description": "The value field for simple metadata",
- "type": "string"
- },
"id": {
"description": "User-provided ID field, not enforced by this API.\nTwo or more pieces of structured metadata with identical\nid and key fields are considered equivalent.",
"type": "string"
},
+ "value": {
+ "description": "The value field for simple metadata",
+ "type": "string"
+ },
"number": {
"description": "The number of values that can be included in a field described by this\nmetadata.",
"type": "string"
@@ -2455,42 +2532,25 @@
},
"type": "object"
},
- "Reference": {
- "description": "A reference is a canonical assembled DNA sequence, intended to act as a\nreference coordinate space for other genomic annotations. A single reference\nmight represent the human chromosome 1 or mitochandrial DNA, for instance. A\nreference belongs to one or more reference sets.\n\nFor more genomics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
- "id": "Reference",
+ "SearchVariantSetsRequest": {
+ "description": "The search variant sets request.",
+ "id": "SearchVariantSetsRequest",
"properties": {
- "ncbiTaxonId": {
- "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.",
- "format": "int32",
- "type": "integer"
- },
- "sourceUri": {
- "description": "The URI from which the sequence was obtained. Typically specifies a FASTA\nformat file.",
- "type": "string"
- },
- "name": {
- "description": "The name of this reference, for example `22`.",
- "type": "string"
- },
- "md5checksum": {
- "description": "MD5 of the upper-case sequence excluding all whitespace characters (this\nis equivalent to SQ:M5 in SAM). This value is represented in lower case\nhexadecimal format.",
- "type": "string"
- },
- "id": {
- "description": "The server-generated reference ID, unique across all references.",
- "type": "string"
- },
- "length": {
- "description": "The length of this reference's sequence.",
- "format": "int64",
- "type": "string"
- },
- "sourceAccessions": {
- "description": "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally\nwith a version number, for example `GCF_000001405.26`.",
+ "datasetIds": {
+ "description": "Exactly one dataset ID must be provided here. Only variant sets which\nbelong to this dataset will be returned.",
"items": {
"type": "string"
},
"type": "array"
+ },
+ "pageToken": {
+ "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
+ "type": "string"
+ },
+ "pageSize": {
+ "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024.",
+ "format": "int32",
+ "type": "integer"
}
},
"type": "object"
@@ -2542,10 +2602,6 @@
"MergeVariantsRequest": {
"id": "MergeVariantsRequest",
"properties": {
- "variantSetId": {
- "description": "The destination variant set.",
- "type": "string"
- },
"variants": {
"description": "The variants to be merged with existing variants.",
"items": {
@@ -2564,6 +2620,10 @@
},
"description": "A mapping between info field keys and the InfoMergeOperations to\nbe performed on them.",
"type": "object"
+ },
+ "variantSetId": {
+ "description": "The destination variant set.",
+ "type": "string"
}
},
"type": "object"
@@ -2572,6 +2632,14 @@
"description": "A read alignment describes a linear alignment of a string of DNA to a\nreference sequence, in addition to metadata\nabout the fragment (the molecule of DNA sequenced) and the read (the bases\nwhich were read by the sequencer). A read is equivalent to a line in a SAM\nfile. A read belongs to exactly one read group and exactly one\nread group set.\n\nFor more genomics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\n### Reverse-stranded reads\n\nMapped reads (reads having a non-null `alignment`) can be aligned to either\nthe forward or the reverse strand of their associated reference. Strandedness\nof a mapped read is encoded by `alignment.position.reverseStrand`.\n\nIf we consider the reference to be a forward-stranded coordinate space of\n`[0, reference.length)` with `0` as the left-most position and\n`reference.length` as the right-most position, reads are always aligned left\nto right. That is, `alignment.position.position` always refers to the\nleft-most reference coordinate and `alignment.cigar` describes the alignment\nof this read to the reference from left to right. All per-base fields such as\n`alignedSequence` and `alignedQuality` share this same left-to-right\norientation; this is true of reads which are aligned to either strand. For\nreverse-stranded reads, this means that `alignedSequence` is the reverse\ncomplement of the bases that were originally reported by the sequencing\nmachine.\n\n### Generating a reference-aligned sequence string\n\nWhen interacting with mapped reads, it's often useful to produce a string\nrepresenting the local alignment of the read to reference. The following\npseudocode demonstrates one way of doing this:\n\n out = \"\"\n offset = 0\n for c in read.alignment.cigar {\n switch c.operation {\n case \"ALIGNMENT_MATCH\", \"SEQUENCE_MATCH\", \"SEQUENCE_MISMATCH\":\n out += read.alignedSequence[offset:offset+c.operationLength]\n offset += c.operationLength\n break\n case \"CLIP_SOFT\", \"INSERT\":\n offset += c.operationLength\n break\n case \"PAD\":\n out += repeat(\"*\", c.operationLength)\n break\n case \"DELETE\":\n out += repeat(\"-\", c.operationLength)\n break\n case \"SKIP\":\n out += repeat(\" \", c.operationLength)\n break\n case \"CLIP_HARD\":\n break\n }\n }\n return out\n\n### Converting to SAM's CIGAR string\n\nThe following pseudocode generates a SAM CIGAR string from the\n`cigar` field. Note that this is a lossy conversion\n(`cigar.referenceSequence` is lost).\n\n cigarMap = {\n \"ALIGNMENT_MATCH\": \"M\",\n \"INSERT\": \"I\",\n \"DELETE\": \"D\",\n \"SKIP\": \"N\",\n \"CLIP_SOFT\": \"S\",\n \"CLIP_HARD\": \"H\",\n \"PAD\": \"P\",\n \"SEQUENCE_MATCH\": \"=\",\n \"SEQUENCE_MISMATCH\": \"X\",\n }\n cigarStr = \"\"\n for c in read.alignment.cigar {\n cigarStr += c.operationLength + cigarMap[c.operation]\n }\n return cigarStr",
"id": "Read",
"properties": {
+ "fragmentName": {
+ "description": "The fragment name. Equivalent to QNAME (query template name) in SAM.",
+ "type": "string"
+ },
+ "readGroupSetId": {
+ "description": "The ID of the read group set this read belongs to. A read belongs to\nexactly one read group set.",
+ "type": "string"
+ },
"duplicateFragment": {
"description": "The fragment is a PCR or optical duplicate (SAM flag 0x400).",
"type": "boolean"
@@ -2644,14 +2712,6 @@
"secondaryAlignment": {
"description": "Whether this alignment is secondary. Equivalent to SAM flag 0x100.\nA secondary alignment represents an alternative to the primary alignment\nfor this read. Aligners may return secondary alignments if a read can map\nambiguously to multiple coordinates in the genome. By convention, each read\nhas one and only one alignment where both `secondaryAlignment`\nand `supplementaryAlignment` are false.",
"type": "boolean"
- },
- "fragmentName": {
- "description": "The fragment name. Equivalent to QNAME (query template name) in SAM.",
- "type": "string"
- },
- "readGroupSetId": {
- "description": "The ID of the read group set this read belongs to. A read belongs to\nexactly one read group set.",
- "type": "string"
}
},
"type": "object"
@@ -2716,26 +2776,10 @@
},
"type": "object"
},
- "ReferenceSet": {
- "description": "A reference set is a set of references which typically comprise a reference\nassembly for a species, such as `GRCh38` which is representative\nof the human genome. A reference set defines a common coordinate space for\ncomparing reference-aligned experimental data. A reference set contains 1 or\nmore references.\n\nFor more genomics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
- "id": "ReferenceSet",
- "properties": {
- "md5checksum": {
- "description": "Order-independent MD5 checksum which identifies this reference set. The\nchecksum is computed by sorting all lower case hexidecimal string\n`reference.md5checksum` (for all reference in this set) in\nascending lexicographic order, concatenating, and taking the MD5 of that\nvalue. The resulting value is represented in lower case hexadecimal format.",
- "type": "string"
- },
- "assemblyId": {
- "description": "Public id of this reference set, such as `GRCh37`.",
- "type": "string"
- },
- "id": {
- "description": "The server-generated reference set ID, unique across all reference sets.",
- "type": "string"
- },
- "description": {
- "description": "Free text description of this reference set.",
- "type": "string"
- },
+ "ReferenceSet": {
+ "description": "A reference set is a set of references which typically comprise a reference\nassembly for a species, such as `GRCh38` which is representative\nof the human genome. A reference set defines a common coordinate space for\ncomparing reference-aligned experimental data. A reference set contains 1 or\nmore references.\n\nFor more genomics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
+ "id": "ReferenceSet",
+ "properties": {
"sourceAccessions": {
"description": "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally\nwith a version number, for example `NC_000001.11`.",
"items": {
@@ -2743,6 +2787,10 @@
},
"type": "array"
},
+ "description": {
+ "description": "Free text description of this reference set.",
+ "type": "string"
+ },
"sourceUri": {
"description": "The URI from which the references were obtained.",
"type": "string"
@@ -2758,6 +2806,18 @@
"type": "string"
},
"type": "array"
+ },
+ "assemblyId": {
+ "description": "Public id of this reference set, such as `GRCh37`.",
+ "type": "string"
+ },
+ "md5checksum": {
+ "description": "Order-independent MD5 checksum which identifies this reference set. The\nchecksum is computed by sorting all lower case hexidecimal string\n`reference.md5checksum` (for all reference in this set) in\nascending lexicographic order, concatenating, and taking the MD5 of that\nvalue. The resulting value is represented in lower case hexadecimal format.",
+ "type": "string"
+ },
+ "id": {
+ "description": "The server-generated reference set ID, unique across all reference sets.",
+ "type": "string"
}
},
"type": "object"
@@ -2788,22 +2848,6 @@
"description": "An annotation set is a logical grouping of annotations that share consistent\ntype information and provenance. Examples of annotation sets include 'all\ngenes from refseq', and 'all variant annotations from ClinVar'.",
"id": "AnnotationSet",
"properties": {
- "sourceUri": {
- "description": "The source URI describing the file from which this annotation set was\ngenerated, if any.",
- "type": "string"
- },
- "datasetId": {
- "description": "The dataset to which this annotation set belongs.",
- "type": "string"
- },
- "name": {
- "description": "The display name for this annotation set.",
- "type": "string"
- },
- "referenceSetId": {
- "description": "The ID of the reference set that defines the coordinate space for this\nset's annotations.",
- "type": "string"
- },
"info": {
"additionalProperties": {
"items": {
@@ -2835,6 +2879,22 @@
"id": {
"description": "The server-generated annotation set ID, unique across all annotation sets.",
"type": "string"
+ },
+ "datasetId": {
+ "description": "The dataset to which this annotation set belongs.",
+ "type": "string"
+ },
+ "sourceUri": {
+ "description": "The source URI describing the file from which this annotation set was\ngenerated, if any.",
+ "type": "string"
+ },
+ "name": {
+ "description": "The display name for this annotation set.",
+ "type": "string"
+ },
+ "referenceSetId": {
+ "description": "The ID of the reference set that defines the coordinate space for this\nset's annotations.",
+ "type": "string"
}
},
"type": "object"
@@ -2842,6 +2902,10 @@
"Experiment": {
"id": "Experiment",
"properties": {
+ "sequencingCenter": {
+ "description": "The sequencing center used as part of this experiment.",
+ "type": "string"
+ },
"platformUnit": {
"description": "The platform unit used as part of this experiment, for example\nflowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the\n@RG PU field in the SAM spec.",
"type": "string"
@@ -2853,10 +2917,6 @@
"instrumentModel": {
"description": "The instrument model used as part of this experiment. This maps to\nsequencing technology in the SAM spec.",
"type": "string"
- },
- "sequencingCenter": {
- "description": "The sequencing center used as part of this experiment.",
- "type": "string"
}
},
"type": "object"
@@ -2893,27 +2953,6 @@
},
"type": "object"
},
- "Exon": {
- "id": "Exon",
- "properties": {
- "start": {
- "description": "The start position of the exon on this annotation's reference sequence,\n0-based inclusive. Note that this is relative to the reference start, and\n**not** the containing annotation start.",
- "format": "int64",
- "type": "string"
- },
- "end": {
- "description": "The end position of the exon on this annotation's reference sequence,\n0-based exclusive. Note that this is relative to the reference start, and\n*not* the containing annotation start.",
- "format": "int64",
- "type": "string"
- },
- "frame": {
- "description": "The frame of this exon. Contains a value of 0, 1, or 2, which indicates\nthe offset of the first coding base of the exon within the reading frame\nof the coding DNA sequence, if any. This field is dependent on the\nstrandedness of this annotation (see\nAnnotation.reverse_strand).\nFor forward stranded annotations, this offset is relative to the\nexon.start. For reverse\nstrand annotations, this offset is relative to the\nexon.end `- 1`.\n\nUnset if this exon does not intersect the coding sequence. Upon creation\nof a transcript, the frame must be populated for all or none of the\ncoding exons.",
- "format": "int32",
- "type": "integer"
- }
- },
- "type": "object"
- },
"ExportReadGroupSetRequest": {
"description": "The read group set export request.",
"id": "ExportReadGroupSetRequest",
@@ -2936,10 +2975,35 @@
},
"type": "object"
},
+ "Exon": {
+ "id": "Exon",
+ "properties": {
+ "start": {
+ "description": "The start position of the exon on this annotation's reference sequence,\n0-based inclusive. Note that this is relative to the reference start, and\n**not** the containing annotation start.",
+ "format": "int64",
+ "type": "string"
+ },
+ "end": {
+ "description": "The end position of the exon on this annotation's reference sequence,\n0-based exclusive. Note that this is relative to the reference start, and\n*not* the containing annotation start.",
+ "format": "int64",
+ "type": "string"
+ },
+ "frame": {
+ "description": "The frame of this exon. Contains a value of 0, 1, or 2, which indicates\nthe offset of the first coding base of the exon within the reading frame\nof the coding DNA sequence, if any. This field is dependent on the\nstrandedness of this annotation (see\nAnnotation.reverse_strand).\nFor forward stranded annotations, this offset is relative to the\nexon.start. For reverse\nstrand annotations, this offset is relative to the\nexon.end `- 1`.\n\nUnset if this exon does not intersect the coding sequence. Upon creation\nof a transcript, the frame must be populated for all or none of the\ncoding exons.",
+ "format": "int32",
+ "type": "integer"
+ }
+ },
+ "type": "object"
+ },
"CallSet": {
"description": "A call set is a collection of variant calls, typically for one sample. It\nbelongs to a variant set.\n\nFor more genomics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
"id": "CallSet",
"properties": {
+ "sampleId": {
+ "description": "The sample ID this call set corresponds to.",
+ "type": "string"
+ },
"name": {
"description": "The call set name.",
"type": "string"
@@ -2969,10 +3033,6 @@
"description": "The date this call set was created in milliseconds from the epoch.",
"format": "int64",
"type": "string"
- },
- "sampleId": {
- "description": "The sample ID this call set corresponds to.",
- "type": "string"
}
},
"type": "object"
@@ -2998,18 +3058,6 @@
"description": "The variant data import request.",
"id": "ImportVariantsRequest",
"properties": {
- "infoMergeConfig": {
- "additionalProperties": {
- "enum": [
- "INFO_MERGE_OPERATION_UNSPECIFIED",
- "IGNORE_NEW",
- "MOVE_TO_CALLS"
- ],
- "type": "string"
- },
- "description": "A mapping between info field keys and the InfoMergeOperations to\nbe performed on them. This is plumbed down to the MergeVariantRequests\ngenerated by the resulting import job.",
- "type": "object"
- },
"variantSetId": {
"description": "Required. The variant set to which variant data should be imported.",
"type": "string"
@@ -3038,28 +3086,18 @@
"Complete Genomics masterVarBeta format. The masterVarBeta files may\nbe bzip2 compressed."
],
"type": "string"
- }
- },
- "type": "object"
- },
- "ListCoverageBucketsResponse": {
- "id": "ListCoverageBucketsResponse",
- "properties": {
- "nextPageToken": {
- "description": "The continuation token, which is used to page through large result sets.\nProvide this value in a subsequent request to return the next page of\nresults. This field will be empty if there aren't any additional results.",
- "type": "string"
- },
- "bucketWidth": {
- "description": "The length of each coverage bucket in base pairs. Note that buckets at the\nend of a reference sequence may be shorter. This value is omitted if the\nbucket width is infinity (the default behaviour, with no range or\n`targetBucketWidth`).",
- "format": "int64",
- "type": "string"
},
- "coverageBuckets": {
- "description": "The coverage buckets. The list of buckets is sparse; a bucket with 0\noverlapping reads is not returned. A bucket never crosses more than one\nreference sequence. Each bucket has width `bucketWidth`, unless\nits end is the end of the reference sequence.",
- "items": {
- "$ref": "CoverageBucket"
+ "infoMergeConfig": {
+ "additionalProperties": {
+ "enum": [
+ "INFO_MERGE_OPERATION_UNSPECIFIED",
+ "IGNORE_NEW",
+ "MOVE_TO_CALLS"
+ ],
+ "type": "string"
},
- "type": "array"
+ "description": "A mapping between info field keys and the InfoMergeOperations to\nbe performed on them. This is plumbed down to the MergeVariantRequests\ngenerated by the resulting import job.",
+ "type": "object"
}
},
"type": "object"
@@ -3067,6 +3105,74 @@
"VariantAnnotation": {
"id": "VariantAnnotation",
"properties": {
+ "type": {
+ "description": "Type has been adapted from ClinVar's list of variant types.",
+ "enum": [
+ "TYPE_UNSPECIFIED",
+ "TYPE_OTHER",
+ "INSERTION",
+ "DELETION",
+ "SUBSTITUTION",
+ "SNP",
+ "STRUCTURAL",
+ "CNV"
+ ],
+ "enumDescriptions": [
+ "",
+ "`TYPE_OTHER` should be used when no other Type will suffice.\nFurther explanation of the variant type may be included in the\ninfo field.",
+ "`INSERTION` indicates an insertion.",
+ "`DELETION` indicates a deletion.",
+ "`SUBSTITUTION` indicates a block substitution of\ntwo or more nucleotides.",
+ "`SNP` indicates a single nucleotide polymorphism.",
+ "`STRUCTURAL` indicates a large structural variant,\nincluding chromosomal fusions, inversions, etc.",
+ "`CNV` indicates a variation in copy number."
+ ],
+ "type": "string"
+ },
+ "alternateBases": {
+ "description": "The alternate allele for this variant. If multiple alternate alleles\nexist at this location, create a separate variant for each one, as they\nmay represent distinct conditions.",
+ "type": "string"
+ },
+ "geneId": {
+ "description": "Google annotation ID of the gene affected by this variant. This should\nbe provided when the variant is created.",
+ "type": "string"
+ },
+ "clinicalSignificance": {
+ "description": "Describes the clinical significance of a variant.\nIt is adapted from the ClinVar controlled vocabulary for clinical\nsignificance described at:\nhttp://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/",
+ "enum": [
+ "CLINICAL_SIGNIFICANCE_UNSPECIFIED",
+ "CLINICAL_SIGNIFICANCE_OTHER",
+ "UNCERTAIN",
+ "BENIGN",
+ "LIKELY_BENIGN",
+ "LIKELY_PATHOGENIC",
+ "PATHOGENIC",
+ "DRUG_RESPONSE",
+ "HISTOCOMPATIBILITY",
+ "CONFERS_SENSITIVITY",
+ "RISK_FACTOR",
+ "ASSOCIATION",
+ "PROTECTIVE",
+ "MULTIPLE_REPORTED"
+ ],
+ "enumDescriptions": [
+ "",
+ "`OTHER` should be used when no other clinical significance\nvalue will suffice.",
+ "",
+ "",
+ "",
+ "",
+ "",
+ "",
+ "",
+ "",
+ "",
+ "",
+ "",
+ "`MULTIPLE_REPORTED` should be used when multiple clinical\nsignficances are reported for a variant. The original clinical\nsignificance values may be provided in the `info` field."
+ ],
+ "type": "string"
+ },
"conditions": {
"description": "The set of conditions associated with this variant.\nA condition describes the way a variant influences human health.",
"items": {
@@ -3106,73 +3212,27 @@
"type": "string"
},
"type": "array"
+ }
+ },
+ "type": "object"
+ },
+ "ListCoverageBucketsResponse": {
+ "id": "ListCoverageBucketsResponse",
+ "properties": {
+ "coverageBuckets": {
+ "description": "The coverage buckets. The list of buckets is sparse; a bucket with 0\noverlapping reads is not returned. A bucket never crosses more than one\nreference sequence. Each bucket has width `bucketWidth`, unless\nits end is the end of the reference sequence.",
+ "items": {
+ "$ref": "CoverageBucket"
+ },
+ "type": "array"
},
- "type": {
- "description": "Type has been adapted from ClinVar's list of variant types.",
- "enum": [
- "TYPE_UNSPECIFIED",
- "TYPE_OTHER",
- "INSERTION",
- "DELETION",
- "SUBSTITUTION",
- "SNP",
- "STRUCTURAL",
- "CNV"
- ],
- "enumDescriptions": [
- "",
- "`TYPE_OTHER` should be used when no other Type will suffice.\nFurther explanation of the variant type may be included in the\ninfo field.",
- "`INSERTION` indicates an insertion.",
- "`DELETION` indicates a deletion.",
- "`SUBSTITUTION` indicates a block substitution of\ntwo or more nucleotides.",
- "`SNP` indicates a single nucleotide polymorphism.",
- "`STRUCTURAL` indicates a large structural variant,\nincluding chromosomal fusions, inversions, etc.",
- "`CNV` indicates a variation in copy number."
- ],
- "type": "string"
- },
- "alternateBases": {
- "description": "The alternate allele for this variant. If multiple alternate alleles\nexist at this location, create a separate variant for each one, as they\nmay represent distinct conditions.",
- "type": "string"
- },
- "geneId": {
- "description": "Google annotation ID of the gene affected by this variant. This should\nbe provided when the variant is created.",
+ "nextPageToken": {
+ "description": "The continuation token, which is used to page through large result sets.\nProvide this value in a subsequent request to return the next page of\nresults. This field will be empty if there aren't any additional results.",
"type": "string"
},
- "clinicalSignificance": {
- "description": "Describes the clinical significance of a variant.\nIt is adapted from the ClinVar controlled vocabulary for clinical\nsignificance described at:\nhttp://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/",
- "enum": [
- "CLINICAL_SIGNIFICANCE_UNSPECIFIED",
- "CLINICAL_SIGNIFICANCE_OTHER",
- "UNCERTAIN",
- "BENIGN",
- "LIKELY_BENIGN",
- "LIKELY_PATHOGENIC",
- "PATHOGENIC",
- "DRUG_RESPONSE",
- "HISTOCOMPATIBILITY",
- "CONFERS_SENSITIVITY",
- "RISK_FACTOR",
- "ASSOCIATION",
- "PROTECTIVE",
- "MULTIPLE_REPORTED"
- ],
- "enumDescriptions": [
- "",
- "`OTHER` should be used when no other clinical significance\nvalue will suffice.",
- "",
- "",
- "",
- "",
- "",
- "",
- "",
- "",
- "",
- "",
- "",
- "`MULTIPLE_REPORTED` should be used when multiple clinical\nsignficances are reported for a variant. The original clinical\nsignificance values may be provided in the `info` field."
- ],
+ "bucketWidth": {
+ "description": "The length of each coverage bucket in base pairs. Note that buckets at the\nend of a reference sequence may be shorter. This value is omitted if the\nbucket width is infinity (the default behaviour, with no range or\n`targetBucketWidth`).",
+ "format": "int64",
"type": "string"
}
},
@@ -3219,6 +3279,15 @@
"SearchAnnotationsRequest": {
"id": "SearchAnnotationsRequest",
"properties": {
+ "referenceId": {
+ "description": "The ID of the reference to query.",
+ "type": "string"
+ },
+ "end": {
+ "description": "The end position of the range on the reference, 0-based exclusive. If\nreferenceId or\nreferenceName\nmust be specified, Defaults to the length of the reference.",
+ "format": "int64",
+ "type": "string"
+ },
"pageToken": {
"description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
"type": "string"
@@ -3243,15 +3312,6 @@
"referenceName": {
"description": "The name of the reference to query, within the reference set associated\nwith this query.",
"type": "string"
- },
- "referenceId": {
- "description": "The ID of the reference to query.",
- "type": "string"
- },
- "end": {
- "description": "The end position of the range on the reference, 0-based exclusive. If\nreferenceId or\nreferenceName\nmust be specified, Defaults to the length of the reference.",
- "format": "int64",
- "type": "string"
}
},
"type": "object"
@@ -3333,6 +3393,15 @@
"SearchAnnotationSetsRequest": {
"id": "SearchAnnotationSetsRequest",
"properties": {
+ "pageToken": {
+ "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
+ "type": "string"
+ },
+ "pageSize": {
+ "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 128. The maximum value is 1024.",
+ "format": "int32",
+ "type": "integer"
+ },
"datasetIds": {
"description": "Required. The dataset IDs to search within. Caller must have `READ` access\nto these datasets.",
"items": {
@@ -3368,15 +3437,6 @@
"referenceSetId": {
"description": "If specified, only annotation sets associated with the given reference set\nare returned.",
"type": "string"
- },
- "pageToken": {
- "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
- "type": "string"
- },
- "pageSize": {
- "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 128. The maximum value is 1024.",
- "format": "int32",
- "type": "integer"
}
},
"type": "object"
@@ -3403,11 +3463,6 @@
"description": "A linear alignment can be represented by one CIGAR string. Describes the\nmapped position and local alignment of the read to the reference.",
"id": "LinearAlignment",
"properties": {
- "mappingQuality": {
- "description": "The mapping quality of this alignment. Represents how likely\nthe read maps to this position as opposed to other locations.\n\nSpecifically, this is -10 log10 Pr(mapping position is wrong), rounded to\nthe nearest integer.",
- "format": "int32",
- "type": "integer"
- },
"position": {
"$ref": "Position",
"description": "The position of this alignment."
@@ -3418,6 +3473,11 @@
"$ref": "CigarUnit"
},
"type": "array"
+ },
+ "mappingQuality": {
+ "description": "The mapping quality of this alignment. Represents how likely\nthe read maps to this position as opposed to other locations.\n\nSpecifically, this is -10 log10 Pr(mapping position is wrong), rounded to\nthe nearest integer.",
+ "format": "int32",
+ "type": "integer"
}
},
"type": "object"
@@ -3497,30 +3557,6 @@
"description": "A read group is all the data that's processed the same way by the sequencer.",
"id": "ReadGroup",
"properties": {
- "predictedInsertSize": {
- "description": "The predicted insert size of this read group. The insert size is the length\nthe sequenced DNA fragment from end-to-end, not including the adapters.",
- "format": "int32",
- "type": "integer"
- },
- "programs": {
- "description": "The programs used to generate this read group. Programs are always\nidentical for all read groups within a read group set. For this reason,\nonly the first read group in a returned set will have this field\npopulated.",
- "items": {
- "$ref": "Program"
- },
- "type": "array"
- },
- "description": {
- "description": "A free-form text description of this read group.",
- "type": "string"
- },
- "sampleId": {
- "description": "A client-supplied sample identifier for the reads in this read group.",
- "type": "string"
- },
- "datasetId": {
- "description": "The dataset to which this read group belongs.",
- "type": "string"
- },
"experiment": {
"$ref": "Experiment",
"description": "The experiment used to generate this read group."
@@ -3546,33 +3582,38 @@
"id": {
"description": "The server-generated read group ID, unique for all read groups.\nNote: This is different than the @RG ID field in the SAM spec. For that\nvalue, see name.",
"type": "string"
- }
- },
- "type": "object"
- },
- "ReadGroupSet": {
- "description": "A read group set is a logical collection of read groups, which are\ncollections of reads produced by a sequencer. A read group set typically\nmodels reads corresponding to one sample, sequenced one way, and aligned one\nway.\n\n* A read group set belongs to one dataset.\n* A read group belongs to one read group set.\n* A read belongs to one read group.\n\nFor more genomics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
- "id": "ReadGroupSet",
- "properties": {
- "readGroups": {
- "description": "The read groups in this set. There are typically 1-10 read groups in a read\ngroup set.",
+ },
+ "programs": {
+ "description": "The programs used to generate this read group. Programs are always\nidentical for all read groups within a read group set. For this reason,\nonly the first read group in a returned set will have this field\npopulated.",
"items": {
- "$ref": "ReadGroup"
+ "$ref": "Program"
},
"type": "array"
},
- "filename": {
- "description": "The filename of the original source file for this read group set, if any.",
- "type": "string"
+ "predictedInsertSize": {
+ "description": "The predicted insert size of this read group. The insert size is the length\nthe sequenced DNA fragment from end-to-end, not including the adapters.",
+ "format": "int32",
+ "type": "integer"
},
- "name": {
- "description": "The read group set name. By default this will be initialized to the sample\nname of the sequenced data contained in this set.",
+ "description": {
+ "description": "A free-form text description of this read group.",
"type": "string"
},
- "referenceSetId": {
- "description": "The reference set to which the reads in this read group set are aligned.",
+ "sampleId": {
+ "description": "A client-supplied sample identifier for the reads in this read group.",
"type": "string"
},
+ "datasetId": {
+ "description": "The dataset to which this read group belongs.",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "ReadGroupSet": {
+ "description": "A read group set is a logical collection of read groups, which are\ncollections of reads produced by a sequencer. A read group set typically\nmodels reads corresponding to one sample, sequenced one way, and aligned one\nway.\n\n* A read group set belongs to one dataset.\n* A read group belongs to one read group set.\n* A read belongs to one read group.\n\nFor more genomics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
+ "id": "ReadGroupSet",
+ "properties": {
"info": {
"additionalProperties": {
"items": {
@@ -3590,6 +3631,25 @@
"datasetId": {
"description": "The dataset to which this read group set belongs.",
"type": "string"
+ },
+ "readGroups": {
+ "description": "The read groups in this set. There are typically 1-10 read groups in a read\ngroup set.",
+ "items": {
+ "$ref": "ReadGroup"
+ },
+ "type": "array"
+ },
+ "filename": {
+ "description": "The filename of the original source file for this read group set, if any.",
+ "type": "string"
+ },
+ "name": {
+ "description": "The read group set name. By default this will be initialized to the sample\nname of the sequenced data contained in this set.",
+ "type": "string"
+ },
+ "referenceSetId": {
+ "description": "The reference set to which the reads in this read group set are aligned.",
+ "type": "string"
}
},
"type": "object"
@@ -3598,16 +3658,16 @@
"description": "The search variant sets response.",
"id": "SearchVariantSetsResponse",
"properties": {
- "nextPageToken": {
- "description": "The continuation token, which is used to page through large result sets.\nProvide this value in a subsequent request to return the next page of\nresults. This field will be empty if there aren't any additional results.",
- "type": "string"
- },
"variantSets": {
"description": "The variant sets belonging to the requested dataset.",
"items": {
"$ref": "VariantSet"
},
"type": "array"
+ },
+ "nextPageToken": {
+ "description": "The continuation token, which is used to page through large result sets.\nProvide this value in a subsequent request to return the next page of\nresults. This field will be empty if there aren't any additional results.",
+ "type": "string"
}
},
"type": "object"
@@ -3673,83 +3733,23 @@
"description": "The call set search request.",
"id": "SearchCallSetsRequest",
"properties": {
- "name": {
- "description": "Only return call sets for which a substring of the name matches this\nstring.",
- "type": "string"
- },
- "pageToken": {
- "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
- "type": "string"
- },
- "pageSize": {
- "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024.",
- "format": "int32",
- "type": "integer"
- },
"variantSetIds": {
"description": "Restrict the query to call sets within the given variant sets. At least one\nID must be provided.",
"items": {
"type": "string"
},
"type": "array"
- }
- },
- "type": "object"
- },
- "ImportReadGroupSetsRequest": {
- "description": "The read group set import request.",
- "id": "ImportReadGroupSetsRequest",
- "properties": {
- "sourceUris": {
- "description": "A list of URIs pointing at [BAM\nfiles](https://samtools.github.io/hts-specs/SAMv1.pdf)\nin Google Cloud Storage.\nThose URIs can include wildcards (*), but do not add or remove\nmatching files before import has completed.\n\nNote that Google Cloud Storage object listing is only eventually\nconsistent: files added may be not be immediately visible to\neveryone. Thus, if using a wildcard it is preferable not to start\nthe import immediately after the files are created.",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "referenceSetId": {
- "description": "The reference set to which the imported read group sets are aligned to, if\nany. The reference names of this reference set must be a superset of those\nfound in the imported file headers. If no reference set id is provided, a\nbest effort is made to associate with a matching reference set.",
- "type": "string"
- },
- "partitionStrategy": {
- "description": "The partition strategy describes how read groups are partitioned into read\ngroup sets.",
- "enum": [
- "PARTITION_STRATEGY_UNSPECIFIED",
- "PER_FILE_PER_SAMPLE",
- "MERGE_ALL"
- ],
- "enumDescriptions": [
- "",
- "In most cases, this strategy yields one read group set per file. This is\nthe default behavior.\n\nAllocate one read group set per file per sample. For BAM files, read\ngroups are considered to share a sample if they have identical sample\nnames. Furthermore, all reads for each file which do not belong to a read\ngroup, if any, will be grouped into a single read group set per-file.",
- "Includes all read groups in all imported files into a single read group\nset. Requires that the headers for all imported files are equivalent. All\nreads which do not belong to a read group, if any, will be grouped into a\nseparate read group set."
- ],
- "type": "string"
},
- "datasetId": {
- "description": "Required. The ID of the dataset these read group sets will belong to. The\ncaller must have WRITE permissions to this dataset.",
+ "name": {
+ "description": "Only return call sets for which a substring of the name matches this\nstring.",
"type": "string"
- }
- },
- "type": "object"
- },
- "Policy": {
- "description": "Defines an Identity and Access Management (IAM) policy. It is used to\nspecify access control policies for Cloud Platform resources.\n\n\nA `Policy` consists of a list of `bindings`. A `Binding` binds a list of\n`members` to a `role`, where the members can be user accounts, Google groups,\nGoogle domains, and service accounts. A `role` is a named list of permissions\ndefined by IAM.\n\n**Example**\n\n {\n \"bindings\": [\n {\n \"role\": \"roles/owner\",\n \"members\": [\n \"user:mike@example.com\",\n \"group:admins@example.com\",\n \"domain:google.com\",\n \"serviceAccount:my-other-app@appspot.gserviceaccount.com\",\n ]\n },\n {\n \"role\": \"roles/viewer\",\n \"members\": [\"user:sean@example.com\"]\n }\n ]\n }\n\nFor a description of IAM and its features, see the\n[IAM developer's guide](https://cloud.google.com/iam).",
- "id": "Policy",
- "properties": {
- "bindings": {
- "description": "Associates a list of `members` to a `role`.\nMultiple `bindings` must not be specified for the same `role`.\n`bindings` with no members will result in an error.",
- "items": {
- "$ref": "Binding"
- },
- "type": "array"
},
- "etag": {
- "description": "`etag` is used for optimistic concurrency control as a way to help\nprevent simultaneous updates of a policy from overwriting each other.\nIt is strongly suggested that systems make use of the `etag` in the\nread-modify-write cycle to perform policy updates in order to avoid race\nconditions: An `etag` is returned in the response to `getIamPolicy`, and\nsystems are expected to put that etag in the request to `setIamPolicy` to\nensure that their change will be applied to the same version of the policy.\n\nIf no `etag` is provided in the call to `setIamPolicy`, then the existing\npolicy is overwritten blindly.",
- "format": "byte",
+ "pageToken": {
+ "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
"type": "string"
},
- "version": {
- "description": "Version of the `Policy`. The default version is 0.",
+ "pageSize": {
+ "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024.",
"format": "int32",
"type": "integer"
}
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