| Index: discovery/googleapis/genomics__v1.json
|
| diff --git a/discovery/googleapis/genomics__v1.json b/discovery/googleapis/genomics__v1.json
|
| index d1fb6528d888765be44a0e2e0b17ef09f3a60034..83b77a41c848c9494df94f0d508577c3a293c29c 100644
|
| --- a/discovery/googleapis/genomics__v1.json
|
| +++ b/discovery/googleapis/genomics__v1.json
|
| @@ -36,6 +36,38 @@
|
| "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",
|
| + "type": "string"
|
| + },
|
| + "prettyPrint": {
|
| + "default": "true",
|
| + "description": "Returns response with indentations and line breaks.",
|
| + "location": "query",
|
| + "type": "boolean"
|
| + },
|
| "fields": {
|
| "description": "Selector specifying which fields to include in a partial response.",
|
| "location": "query",
|
| @@ -46,6 +78,11 @@
|
| "location": "query",
|
| "type": "string"
|
| },
|
| + "callback": {
|
| + "description": "JSONP",
|
| + "location": "query",
|
| + "type": "string"
|
| + },
|
| "$.xgafv": {
|
| "description": "V1 error format.",
|
| "enum": [
|
| @@ -59,11 +96,6 @@
|
| "location": "query",
|
| "type": "string"
|
| },
|
| - "callback": {
|
| - "description": "JSONP",
|
| - "location": "query",
|
| - "type": "string"
|
| - },
|
| "alt": {
|
| "default": "json",
|
| "description": "Data format for response.",
|
| @@ -80,99 +112,56 @@
|
| "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"
|
| },
|
| - "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"
|
| - },
|
| - "oauth_token": {
|
| - "description": "OAuth 2.0 token for the current user.",
|
| - "location": "query",
|
| - "type": "string"
|
| - },
|
| - "bearer_token": {
|
| - "description": "OAuth bearer token.",
|
| - "location": "query",
|
| - "type": "string"
|
| - },
|
| - "upload_protocol": {
|
| - "description": "Upload protocol for media (e.g. \"raw\", \"multipart\").",
|
| + "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"
|
| - },
|
| - "prettyPrint": {
|
| - "default": "true",
|
| - "description": "Returns response with indentations and line breaks.",
|
| - "location": "query",
|
| - "type": "boolean"
|
| }
|
| },
|
| "protocol": "rest",
|
| "resources": {
|
| - "variants": {
|
| + "operations": {
|
| "methods": {
|
| - "search": {
|
| - "description": "Gets a list of variants matching the criteria.\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\nImplements\n[GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).",
|
| - "httpMethod": "POST",
|
| - "id": "genomics.variants.search",
|
| - "parameterOrder": [],
|
| - "parameters": {},
|
| - "path": "v1/variants/search",
|
| - "request": {
|
| - "$ref": "SearchVariantsRequest"
|
| - },
|
| - "response": {
|
| - "$ref": "SearchVariantsResponse"
|
| - },
|
| - "scopes": [
|
| - "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/genomics",
|
| - "https://www.googleapis.com/auth/genomics.readonly"
|
| - ]
|
| - },
|
| - "patch": {
|
| - "description": "Updates a variant.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis method supports patch semantics. Returns the modified variant without\nits calls.",
|
| - "httpMethod": "PATCH",
|
| - "id": "genomics.variants.patch",
|
| + "list": {
|
| + "description": "Lists operations that match the specified filter in the request.",
|
| + "httpMethod": "GET",
|
| + "id": "genomics.operations.list",
|
| "parameterOrder": [
|
| - "variantId"
|
| + "name"
|
| ],
|
| "parameters": {
|
| - "variantId": {
|
| - "description": "The ID of the variant to be updated.",
|
| + "name": {
|
| + "description": "The name of the operation collection.",
|
| "location": "path",
|
| + "pattern": "^operations$",
|
| "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",
|
| + "pageToken": {
|
| + "description": "The standard list page token.",
|
| + "location": "query",
|
| + "type": "string"
|
| + },
|
| + "pageSize": {
|
| + "description": "The maximum number of results to return. If unspecified, defaults to\n256. The maximum value is 2048.",
|
| + "format": "int32",
|
| + "location": "query",
|
| + "type": "integer"
|
| + },
|
| + "filter": {
|
| + "description": "A string for filtering Operations.\nThe following filter fields are supported:\n\n* projectId: Required. Corresponds to\n OperationMetadata.projectId.\n* createTime: 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: 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:\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/variants/{variantId}",
|
| - "request": {
|
| - "$ref": "Variant"
|
| - },
|
| + "path": "v1/{+name}",
|
| "response": {
|
| - "$ref": "Variant"
|
| + "$ref": "ListOperationsResponse"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -180,39 +169,49 @@
|
| ]
|
| },
|
| "get": {
|
| - "description": "Gets a variant by ID.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| + "description": "Gets the latest state of a long-running operation. Clients can use this\nmethod to poll the operation result at intervals as recommended by the API\nservice.",
|
| "httpMethod": "GET",
|
| - "id": "genomics.variants.get",
|
| + "id": "genomics.operations.get",
|
| "parameterOrder": [
|
| - "variantId"
|
| + "name"
|
| ],
|
| "parameters": {
|
| - "variantId": {
|
| - "description": "The ID of the variant.",
|
| + "name": {
|
| + "description": "The name of the operation resource.",
|
| "location": "path",
|
| + "pattern": "^operations/.+$",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/variants/{variantId}",
|
| + "path": "v1/{+name}",
|
| "response": {
|
| - "$ref": "Variant"
|
| + "$ref": "Operation"
|
| },
|
| "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"
|
| ]
|
| },
|
| - "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.",
|
| + "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.variants.merge",
|
| - "parameterOrder": [],
|
| - "parameters": {},
|
| - "path": "v1/variants:merge",
|
| + "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": "MergeVariantsRequest"
|
| + "$ref": "CancelOperationRequest"
|
| },
|
| "response": {
|
| "$ref": "Empty"
|
| @@ -221,88 +220,94 @@
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| "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.",
|
| + }
|
| + }
|
| + },
|
| + "referencesets": {
|
| + "methods": {
|
| + "search": {
|
| + "description": "Searches for reference sets 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.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)",
|
| "httpMethod": "POST",
|
| - "id": "genomics.variants.import",
|
| + "id": "genomics.referencesets.search",
|
| "parameterOrder": [],
|
| "parameters": {},
|
| - "path": "v1/variants:import",
|
| + "path": "v1/referencesets/search",
|
| "request": {
|
| - "$ref": "ImportVariantsRequest"
|
| + "$ref": "SearchReferenceSetsRequest"
|
| },
|
| "response": {
|
| - "$ref": "Operation"
|
| + "$ref": "SearchReferenceSetsResponse"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/devstorage.read_write",
|
| - "https://www.googleapis.com/auth/genomics"
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| ]
|
| },
|
| - "delete": {
|
| - "description": "Deletes 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)",
|
| - "httpMethod": "DELETE",
|
| - "id": "genomics.variants.delete",
|
| + "get": {
|
| + "description": "Gets a reference set.\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.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).",
|
| + "httpMethod": "GET",
|
| + "id": "genomics.referencesets.get",
|
| "parameterOrder": [
|
| - "variantId"
|
| + "referenceSetId"
|
| ],
|
| "parameters": {
|
| - "variantId": {
|
| - "description": "The ID of the variant to be deleted.",
|
| + "referenceSetId": {
|
| + "description": "The ID of the reference set.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/variants/{variantId}",
|
| + "path": "v1/referencesets/{referenceSetId}",
|
| "response": {
|
| - "$ref": "Empty"
|
| + "$ref": "ReferenceSet"
|
| },
|
| "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"
|
| ]
|
| - },
|
| - "create": {
|
| - "description": "Creates a new 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)",
|
| + }
|
| + }
|
| + },
|
| + "readgroupsets": {
|
| + "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.variants.create",
|
| + "id": "genomics.readgroupsets.import",
|
| "parameterOrder": [],
|
| "parameters": {},
|
| - "path": "v1/variants",
|
| + "path": "v1/readgroupsets:import",
|
| "request": {
|
| - "$ref": "Variant"
|
| + "$ref": "ImportReadGroupSetsRequest"
|
| },
|
| "response": {
|
| - "$ref": "Variant"
|
| + "$ref": "Operation"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| + "https://www.googleapis.com/auth/devstorage.read_write",
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| - }
|
| - }
|
| - },
|
| - "annotationsets": {
|
| - "methods": {
|
| + },
|
| "delete": {
|
| - "description": "Deletes an annotation set. Caller must have WRITE permission\nfor the associated annotation set.",
|
| + "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.annotationsets.delete",
|
| + "id": "genomics.readgroupsets.delete",
|
| "parameterOrder": [
|
| - "annotationSetId"
|
| + "readGroupSetId"
|
| ],
|
| "parameters": {
|
| - "annotationSetId": {
|
| - "description": "The ID of the annotation set to be deleted.",
|
| - "location": "path",
|
| + "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/annotationsets/{annotationSetId}",
|
| + "path": "v1/readgroupsets/{readGroupSetId}",
|
| "response": {
|
| "$ref": "Empty"
|
| },
|
| @@ -311,142 +316,104 @@
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| },
|
| - "search": {
|
| - "description": "Searches for annotation sets that match the given criteria. Annotation sets\nare returned in an unspecified order. This order is consistent, such that\ntwo queries for the same content (regardless of page size) yield annotation\nsets in the same order across their respective streams of paginated\nresponses. Caller must have READ permission for the queried datasets.",
|
| + "export": {
|
| + "description": "Exports a read group set to a BAM file in Google Cloud Storage.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nNote that currently there may be some differences between exported BAM\nfiles and the original BAM file at the time of import. See\nImportReadGroupSets\nfor caveats.",
|
| "httpMethod": "POST",
|
| - "id": "genomics.annotationsets.search",
|
| - "parameterOrder": [],
|
| - "parameters": {},
|
| - "path": "v1/annotationsets/search",
|
| - "request": {
|
| - "$ref": "SearchAnnotationSetsRequest"
|
| - },
|
| - "response": {
|
| - "$ref": "SearchAnnotationSetsResponse"
|
| - },
|
| - "scopes": [
|
| - "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/genomics",
|
| - "https://www.googleapis.com/auth/genomics.readonly"
|
| - ]
|
| - },
|
| - "get": {
|
| - "description": "Gets an annotation set. Caller must have READ permission for\nthe associated dataset.",
|
| - "httpMethod": "GET",
|
| - "id": "genomics.annotationsets.get",
|
| - "parameterOrder": [
|
| - "annotationSetId"
|
| - ],
|
| - "parameters": {
|
| - "annotationSetId": {
|
| - "description": "The ID of the annotation set to be retrieved.",
|
| - "location": "path",
|
| - "required": true,
|
| - "type": "string"
|
| - }
|
| - },
|
| - "path": "v1/annotationsets/{annotationSetId}",
|
| - "response": {
|
| - "$ref": "AnnotationSet"
|
| - },
|
| - "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 set. The update must respect all mutability\nrestrictions and other invariants described on the annotation set resource.\nCaller must have WRITE permission for the associated dataset.",
|
| - "httpMethod": "PUT",
|
| - "id": "genomics.annotationsets.update",
|
| + "id": "genomics.readgroupsets.export",
|
| "parameterOrder": [
|
| - "annotationSetId"
|
| + "readGroupSetId"
|
| ],
|
| "parameters": {
|
| - "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.",
|
| + "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/annotationsets/{annotationSetId}",
|
| + "path": "v1/readgroupsets/{readGroupSetId}:export",
|
| "request": {
|
| - "$ref": "AnnotationSet"
|
| + "$ref": "ExportReadGroupSetRequest"
|
| },
|
| "response": {
|
| - "$ref": "AnnotationSet"
|
| + "$ref": "Operation"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| + "https://www.googleapis.com/auth/devstorage.read_write",
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| },
|
| - "create": {
|
| - "description": "Creates a new annotation set. Caller must have WRITE permission for the\nassociated dataset.\n\nThe following fields are required:\n\n * datasetId\n * referenceSetId\n\nAll other fields may be optionally specified, unless documented as being\nserver-generated (for example, the `id` field).",
|
| + "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).",
|
| "httpMethod": "POST",
|
| - "id": "genomics.annotationsets.create",
|
| + "id": "genomics.readgroupsets.search",
|
| "parameterOrder": [],
|
| "parameters": {},
|
| - "path": "v1/annotationsets",
|
| + "path": "v1/readgroupsets/search",
|
| "request": {
|
| - "$ref": "AnnotationSet"
|
| + "$ref": "SearchReadGroupSetsRequest"
|
| },
|
| "response": {
|
| - "$ref": "AnnotationSet"
|
| + "$ref": "SearchReadGroupSetsResponse"
|
| },
|
| "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"
|
| ]
|
| - }
|
| - }
|
| - },
|
| - "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",
|
| + },
|
| + "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": [
|
| + "readGroupSetId"
|
| + ],
|
| + "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.",
|
| + "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/readgroupsets/{readGroupSetId}",
|
| "request": {
|
| - "$ref": "SearchReferencesRequest"
|
| + "$ref": "ReadGroupSet"
|
| },
|
| "response": {
|
| - "$ref": "SearchReferencesResponse"
|
| + "$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"
|
| ]
|
| },
|
| "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).",
|
| + "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.references.get",
|
| + "id": "genomics.readgroupsets.get",
|
| "parameterOrder": [
|
| - "referenceId"
|
| + "readGroupSetId"
|
| ],
|
| "parameters": {
|
| - "referenceId": {
|
| - "description": "The ID of the reference.",
|
| + "readGroupSetId": {
|
| + "description": "The ID of the read group set.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/references/{referenceId}",
|
| + "path": "v1/readgroupsets/{readGroupSetId}",
|
| "response": {
|
| - "$ref": "Reference"
|
| + "$ref": "ReadGroupSet"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -456,36 +423,41 @@
|
| }
|
| },
|
| "resources": {
|
| - "bases": {
|
| + "coveragebuckets": {
|
| "methods": {
|
| "list": {
|
| - "description": "Lists the bases in a reference, optionally restricted to a range.\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.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).",
|
| + "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.references.bases.list",
|
| + "id": "genomics.readgroupsets.coveragebuckets.list",
|
| "parameterOrder": [
|
| - "referenceId"
|
| + "readGroupSetId"
|
| ],
|
| "parameters": {
|
| - "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",
|
| + "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": "integer"
|
| + "type": "string"
|
| },
|
| - "start": {
|
| - "description": "The start position (0-based) of this query. Defaults to 0.",
|
| + "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"
|
| },
|
| - "referenceId": {
|
| - "description": "The ID of the reference.",
|
| + "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 (0-based, exclusive) of this query. Defaults to the length\nof this reference.",
|
| + "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"
|
| @@ -494,11 +466,17 @@
|
| "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/references/{referenceId}/bases",
|
| + "path": "v1/readgroupsets/{readGroupSetId}/coveragebuckets",
|
| "response": {
|
| - "$ref": "ListBasesResponse"
|
| + "$ref": "ListCoverageBucketsResponse"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -510,194 +488,181 @@
|
| }
|
| }
|
| },
|
| - "datasets": {
|
| + "reads": {
|
| "methods": {
|
| - "testIamPermissions": {
|
| - "description": "Returns permissions that a caller has on the specified resource.\nSee <a href=\"/iam/docs/managing-policies#testing_permissions\">Testing\nPermissions</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)",
|
| + "search": {
|
| + "description": "Gets a list of reads for one or more read group sets.\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\nReads search operates over a genomic coordinate space of reference sequence\n& position defined over the reference sequences to which the requested\nread group sets are aligned.\n\nIf a target positional range is specified, search returns all reads whose\nalignment to the reference genome overlap the range. A query which\nspecifies only read group set IDs yields all reads in those read group\nsets, including unmapped reads.\n\nAll reads returned (including reads on subsequent pages) are ordered by\ngenomic coordinate (by reference sequence, then position). Reads with\nequivalent genomic coordinates are returned in an unspecified order. This\norder is consistent, such that two queries for the same content (regardless\nof page size) yield reads in the same order across their respective streams\nof paginated responses.\n\nImplements\n[GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).",
|
| "httpMethod": "POST",
|
| - "id": "genomics.datasets.testIamPermissions",
|
| + "id": "genomics.reads.search",
|
| + "parameterOrder": [],
|
| + "parameters": {},
|
| + "path": "v1/reads/search",
|
| + "request": {
|
| + "$ref": "SearchReadsRequest"
|
| + },
|
| + "response": {
|
| + "$ref": "SearchReadsResponse"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/cloud-platform",
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| + ]
|
| + }
|
| + }
|
| + },
|
| + "callsets": {
|
| + "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": [
|
| - "resource"
|
| + "callSetId"
|
| ],
|
| "parameters": {
|
| - "resource": {
|
| - "description": "REQUIRED: The resource for which policy is being specified. Format is\n`datasets/<dataset ID>`.",
|
| + "callSetId": {
|
| + "description": "The ID of the call set to be updated.",
|
| "location": "path",
|
| - "pattern": "^datasets/[^/]+$",
|
| "required": true,
|
| "type": "string"
|
| + },
|
| + "updateMask": {
|
| + "description": "An optional mask specifying which fields to update. At this time, the only\nmutable field is name. The only\nacceptable value is \"name\". If unspecified, all mutable fields will be\nupdated.",
|
| + "format": "google-fieldmask",
|
| + "location": "query",
|
| + "type": "string"
|
| }
|
| },
|
| - "path": "v1/{+resource}:testIamPermissions",
|
| + "path": "v1/callsets/{callSetId}",
|
| "request": {
|
| - "$ref": "TestIamPermissionsRequest"
|
| + "$ref": "CallSet"
|
| },
|
| "response": {
|
| - "$ref": "TestIamPermissionsResponse"
|
| + "$ref": "CallSet"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| },
|
| - "delete": {
|
| - "description": "Deletes a dataset and all of its contents (all read group sets,\nreference sets, variant sets, call sets, annotation sets, etc.)\nThis is reversible (up to one week after the deletion) via\nthe\ndatasets.undelete\noperation.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| - "httpMethod": "DELETE",
|
| - "id": "genomics.datasets.delete",
|
| + "get": {
|
| + "description": "Gets a call set by ID.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| + "httpMethod": "GET",
|
| + "id": "genomics.callsets.get",
|
| "parameterOrder": [
|
| - "datasetId"
|
| + "callSetId"
|
| ],
|
| "parameters": {
|
| - "datasetId": {
|
| - "description": "The ID of the dataset to be deleted.",
|
| + "callSetId": {
|
| + "description": "The ID of the call set.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/datasets/{datasetId}",
|
| + "path": "v1/callsets/{callSetId}",
|
| "response": {
|
| - "$ref": "Empty"
|
| + "$ref": "CallSet"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/genomics"
|
| - ]
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| + ]
|
| },
|
| - "list": {
|
| - "description": "Lists datasets within a project.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| - "httpMethod": "GET",
|
| - "id": "genomics.datasets.list",
|
| + "create": {
|
| + "description": "Creates a new call set.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.callsets.create",
|
| "parameterOrder": [],
|
| - "parameters": {
|
| - "pageSize": {
|
| - "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 50. The maximum value is 1024.",
|
| - "format": "int32",
|
| - "location": "query",
|
| - "type": "integer"
|
| - },
|
| - "projectId": {
|
| - "description": "Required. The Google Cloud project ID to list datasets for.",
|
| - "location": "query",
|
| - "type": "string"
|
| - },
|
| - "pageToken": {
|
| - "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
|
| - "location": "query",
|
| - "type": "string"
|
| - }
|
| + "parameters": {},
|
| + "path": "v1/callsets",
|
| + "request": {
|
| + "$ref": "CallSet"
|
| },
|
| - "path": "v1/datasets",
|
| "response": {
|
| - "$ref": "ListDatasetsResponse"
|
| + "$ref": "CallSet"
|
| },
|
| "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"
|
| ]
|
| },
|
| - "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",
|
| + "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",
|
| "parameterOrder": [
|
| - "resource"
|
| + "callSetId"
|
| ],
|
| "parameters": {
|
| - "resource": {
|
| - "description": "REQUIRED: The resource for which policy is being specified. Format is\n`datasets/<dataset ID>`.",
|
| + "callSetId": {
|
| + "description": "The ID of the call set to be deleted.",
|
| "location": "path",
|
| - "pattern": "^datasets/[^/]+$",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/{+resource}:setIamPolicy",
|
| - "request": {
|
| - "$ref": "SetIamPolicyRequest"
|
| - },
|
| + "path": "v1/callsets/{callSetId}",
|
| "response": {
|
| - "$ref": "Policy"
|
| + "$ref": "Empty"
|
| },
|
| "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)",
|
| + "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).",
|
| "httpMethod": "POST",
|
| - "id": "genomics.datasets.create",
|
| + "id": "genomics.callsets.search",
|
| "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"
|
| - ]
|
| - },
|
| - "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/[^/]+$",
|
| - "required": true,
|
| - "type": "string"
|
| - }
|
| - },
|
| - "path": "v1/{+resource}:getIamPolicy",
|
| + "path": "v1/callsets/search",
|
| "request": {
|
| - "$ref": "GetIamPolicyRequest"
|
| + "$ref": "SearchCallSetsRequest"
|
| },
|
| "response": {
|
| - "$ref": "Policy"
|
| + "$ref": "SearchCallSetsResponse"
|
| },
|
| "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"
|
| ]
|
| - },
|
| + }
|
| + }
|
| + },
|
| + "variants": {
|
| + "methods": {
|
| "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.",
|
| + "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.datasets.patch",
|
| + "id": "genomics.variants.patch",
|
| "parameterOrder": [
|
| - "datasetId"
|
| + "variantId"
|
| ],
|
| "parameters": {
|
| - "datasetId": {
|
| - "description": "The ID of the dataset to be updated.",
|
| + "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, the only\nmutable field is name. The only\nacceptable value is \"name\". If unspecified, all mutable fields will be\nupdated.",
|
| + "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/datasets/{datasetId}",
|
| + "path": "v1/variants/{variantId}",
|
| "request": {
|
| - "$ref": "Dataset"
|
| + "$ref": "Variant"
|
| },
|
| "response": {
|
| - "$ref": "Dataset"
|
| + "$ref": "Variant"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -705,23 +670,23 @@
|
| ]
|
| },
|
| "get": {
|
| - "description": "Gets a dataset by ID.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| + "description": "Gets a variant by ID.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| "httpMethod": "GET",
|
| - "id": "genomics.datasets.get",
|
| + "id": "genomics.variants.get",
|
| "parameterOrder": [
|
| - "datasetId"
|
| + "variantId"
|
| ],
|
| "parameters": {
|
| - "datasetId": {
|
| - "description": "The ID of the dataset.",
|
| + "variantId": {
|
| + "description": "The ID of the variant.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/datasets/{datasetId}",
|
| + "path": "v1/variants/{variantId}",
|
| "response": {
|
| - "$ref": "Dataset"
|
| + "$ref": "Variant"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -729,168 +694,221 @@
|
| "https://www.googleapis.com/auth/genomics.readonly"
|
| ]
|
| },
|
| - "undelete": {
|
| - "description": "Undeletes a dataset by restoring a dataset which was deleted via this API.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis operation is only possible for a week after the deletion occurred.",
|
| + "import": {
|
| + "description": "Creates variant data by asynchronously importing the provided information.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThe variants for import will be merged with any existing variant that\nmatches its reference sequence, start, end, reference bases, and\nalternative bases. If no such variant exists, a new one will be created.\n\nWhen variants are merged, the call information from the new variant\nis added to the existing variant, and Variant info fields are merged\nas specified in\ninfoMergeConfig.\nAs a special case, for single-sample VCF files, QUAL and FILTER fields will\nbe moved to the call level; these are sometimes interpreted in a\ncall-specific context.\nImported VCF headers are appended to the metadata already in a variant set.",
|
| "httpMethod": "POST",
|
| - "id": "genomics.datasets.undelete",
|
| + "id": "genomics.variants.import",
|
| + "parameterOrder": [],
|
| + "parameters": {},
|
| + "path": "v1/variants:import",
|
| + "request": {
|
| + "$ref": "ImportVariantsRequest"
|
| + },
|
| + "response": {
|
| + "$ref": "Operation"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/cloud-platform",
|
| + "https://www.googleapis.com/auth/devstorage.read_write",
|
| + "https://www.googleapis.com/auth/genomics"
|
| + ]
|
| + },
|
| + "delete": {
|
| + "description": "Deletes a variant.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| + "httpMethod": "DELETE",
|
| + "id": "genomics.variants.delete",
|
| "parameterOrder": [
|
| - "datasetId"
|
| + "variantId"
|
| ],
|
| "parameters": {
|
| - "datasetId": {
|
| - "description": "The ID of the dataset to be undeleted.",
|
| + "variantId": {
|
| + "description": "The ID of the variant to be deleted.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/datasets/{datasetId}:undelete",
|
| + "path": "v1/variants/{variantId}",
|
| + "response": {
|
| + "$ref": "Empty"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/cloud-platform",
|
| + "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.",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.variants.merge",
|
| + "parameterOrder": [],
|
| + "parameters": {},
|
| + "path": "v1/variants:merge",
|
| "request": {
|
| - "$ref": "UndeleteDatasetRequest"
|
| + "$ref": "MergeVariantsRequest"
|
| },
|
| "response": {
|
| - "$ref": "Dataset"
|
| + "$ref": "Empty"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| - }
|
| - }
|
| - },
|
| - "annotations": {
|
| - "methods": {
|
| + },
|
| + "create": {
|
| + "description": "Creates a new 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)",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.variants.create",
|
| + "parameterOrder": [],
|
| + "parameters": {},
|
| + "path": "v1/variants",
|
| + "request": {
|
| + "$ref": "Variant"
|
| + },
|
| + "response": {
|
| + "$ref": "Variant"
|
| + },
|
| + "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.",
|
| + "description": "Gets a list of variants matching the criteria.\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\nImplements\n[GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).",
|
| "httpMethod": "POST",
|
| - "id": "genomics.annotations.search",
|
| + "id": "genomics.variants.search",
|
| "parameterOrder": [],
|
| "parameters": {},
|
| - "path": "v1/annotations/search",
|
| + "path": "v1/variants/search",
|
| "request": {
|
| - "$ref": "SearchAnnotationsRequest"
|
| + "$ref": "SearchVariantsRequest"
|
| },
|
| "response": {
|
| - "$ref": "SearchAnnotationsResponse"
|
| + "$ref": "SearchVariantsResponse"
|
| },
|
| "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",
|
| + }
|
| + }
|
| + },
|
| + "annotationsets": {
|
| + "methods": {
|
| + "delete": {
|
| + "description": "Deletes an annotation set. Caller must have WRITE permission\nfor the associated annotation set.",
|
| + "httpMethod": "DELETE",
|
| + "id": "genomics.annotationsets.delete",
|
| "parameterOrder": [
|
| - "annotationId"
|
| + "annotationSetId"
|
| ],
|
| "parameters": {
|
| - "annotationId": {
|
| - "description": "The ID of the annotation to be retrieved.",
|
| + "annotationSetId": {
|
| + "description": "The ID of the annotation set to be deleted.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/annotations/{annotationId}",
|
| + "path": "v1/annotationsets/{annotationSetId}",
|
| "response": {
|
| - "$ref": "Annotation"
|
| + "$ref": "Empty"
|
| },
|
| "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"
|
| ]
|
| },
|
| - "update": {
|
| - "description": "Updates an annotation. Caller must have\nWRITE permission for the associated dataset.",
|
| - "httpMethod": "PUT",
|
| - "id": "genomics.annotations.update",
|
| - "parameterOrder": [
|
| - "annotationId"
|
| - ],
|
| - "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}",
|
| + "search": {
|
| + "description": "Searches for annotation sets that match the given criteria. Annotation sets\nare returned in an unspecified order. This order is consistent, such that\ntwo queries for the same content (regardless of page size) yield annotation\nsets in the same order across their respective streams of paginated\nresponses. Caller must have READ permission for the queried datasets.",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.annotationsets.search",
|
| + "parameterOrder": [],
|
| + "parameters": {},
|
| + "path": "v1/annotationsets/search",
|
| "request": {
|
| - "$ref": "Annotation"
|
| + "$ref": "SearchAnnotationSetsRequest"
|
| },
|
| "response": {
|
| - "$ref": "Annotation"
|
| + "$ref": "SearchAnnotationSetsResponse"
|
| },
|
| "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"
|
| ]
|
| },
|
| - "delete": {
|
| - "description": "Deletes an annotation. Caller must have WRITE permission for\nthe associated annotation set.",
|
| - "httpMethod": "DELETE",
|
| - "id": "genomics.annotations.delete",
|
| + "get": {
|
| + "description": "Gets an annotation set. Caller must have READ permission for\nthe associated dataset.",
|
| + "httpMethod": "GET",
|
| + "id": "genomics.annotationsets.get",
|
| "parameterOrder": [
|
| - "annotationId"
|
| + "annotationSetId"
|
| ],
|
| "parameters": {
|
| - "annotationId": {
|
| - "description": "The ID of the annotation to be deleted.",
|
| + "annotationSetId": {
|
| + "description": "The ID of the annotation set to be retrieved.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/annotations/{annotationId}",
|
| + "path": "v1/annotationsets/{annotationSetId}",
|
| "response": {
|
| - "$ref": "Empty"
|
| + "$ref": "AnnotationSet"
|
| },
|
| "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"
|
| ]
|
| },
|
| - "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",
|
| + "update": {
|
| + "description": "Updates an annotation set. The update must respect all mutability\nrestrictions and other invariants described on the annotation set resource.\nCaller must have WRITE permission for the associated dataset.",
|
| + "httpMethod": "PUT",
|
| + "id": "genomics.annotationsets.update",
|
| + "parameterOrder": [
|
| + "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"
|
| + }
|
| + },
|
| + "path": "v1/annotationsets/{annotationSetId}",
|
| "request": {
|
| - "$ref": "Annotation"
|
| + "$ref": "AnnotationSet"
|
| },
|
| "response": {
|
| - "$ref": "Annotation"
|
| + "$ref": "AnnotationSet"
|
| },
|
| "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.",
|
| + "create": {
|
| + "description": "Creates a new annotation set. Caller must have WRITE permission for the\nassociated dataset.\n\nThe following fields are required:\n\n * datasetId\n * referenceSetId\n\nAll other fields may be optionally specified, unless documented as being\nserver-generated (for example, the `id` field).",
|
| "httpMethod": "POST",
|
| - "id": "genomics.annotations.batchCreate",
|
| + "id": "genomics.annotationsets.create",
|
| "parameterOrder": [],
|
| "parameters": {},
|
| - "path": "v1/annotations:batchCreate",
|
| + "path": "v1/annotationsets",
|
| "request": {
|
| - "$ref": "BatchCreateAnnotationsRequest"
|
| + "$ref": "AnnotationSet"
|
| },
|
| "response": {
|
| - "$ref": "BatchCreateAnnotationsResponse"
|
| + "$ref": "AnnotationSet"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -899,91 +917,189 @@
|
| }
|
| }
|
| },
|
| - "variantsets": {
|
| + "references": {
|
| "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.",
|
| + "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.variantsets.create",
|
| + "id": "genomics.references.search",
|
| "parameterOrder": [],
|
| "parameters": {},
|
| - "path": "v1/variantsets",
|
| + "path": "v1/references/search",
|
| "request": {
|
| - "$ref": "VariantSet"
|
| + "$ref": "SearchReferencesRequest"
|
| },
|
| "response": {
|
| - "$ref": "VariantSet"
|
| + "$ref": "SearchReferencesResponse"
|
| },
|
| "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"
|
| ]
|
| },
|
| - "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)",
|
| + "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",
|
| + "id": "genomics.references.get",
|
| + "parameterOrder": [
|
| + "referenceId"
|
| + ],
|
| + "parameters": {
|
| + "referenceId": {
|
| + "description": "The ID of the reference.",
|
| + "location": "path",
|
| + "required": true,
|
| + "type": "string"
|
| + }
|
| + },
|
| + "path": "v1/references/{referenceId}",
|
| + "response": {
|
| + "$ref": "Reference"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/cloud-platform",
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| + ]
|
| + }
|
| + },
|
| + "resources": {
|
| + "bases": {
|
| + "methods": {
|
| + "list": {
|
| + "description": "Lists the bases in a reference, optionally restricted to a range.\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.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).",
|
| + "httpMethod": "GET",
|
| + "id": "genomics.references.bases.list",
|
| + "parameterOrder": [
|
| + "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",
|
| + "location": "query",
|
| + "type": "string"
|
| + },
|
| + "referenceId": {
|
| + "description": "The ID of the reference.",
|
| + "location": "path",
|
| + "required": true,
|
| + "type": "string"
|
| + },
|
| + "end": {
|
| + "description": "The end position (0-based, exclusive) of this query. Defaults to the length\nof this reference.",
|
| + "format": "int64",
|
| + "location": "query",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "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.variantsets.export",
|
| + "id": "genomics.datasets.getIamPolicy",
|
| "parameterOrder": [
|
| - "variantSetId"
|
| + "resource"
|
| ],
|
| "parameters": {
|
| - "variantSetId": {
|
| - "description": "Required. The ID of the variant set that contains variant data which\nshould be exported. The caller must have READ access to this variant set.",
|
| + "resource": {
|
| + "description": "REQUIRED: The resource for which policy is being specified. Format is\n`datasets/<dataset ID>`.",
|
| "location": "path",
|
| + "pattern": "^datasets/[^/]+$",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/variantsets/{variantSetId}:export",
|
| + "path": "v1/{+resource}:getIamPolicy",
|
| "request": {
|
| - "$ref": "ExportVariantSetRequest"
|
| + "$ref": "GetIamPolicyRequest"
|
| },
|
| "response": {
|
| - "$ref": "Operation"
|
| + "$ref": "Policy"
|
| },
|
| "scopes": [
|
| - "https://www.googleapis.com/auth/bigquery",
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| },
|
| - "search": {
|
| - "description": "Returns a list of all variant sets matching search criteria.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).",
|
| - "httpMethod": "POST",
|
| - "id": "genomics.variantsets.search",
|
| - "parameterOrder": [],
|
| - "parameters": {},
|
| - "path": "v1/variantsets/search",
|
| + "patch": {
|
| + "description": "Updates a dataset.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis method supports patch semantics.",
|
| + "httpMethod": "PATCH",
|
| + "id": "genomics.datasets.patch",
|
| + "parameterOrder": [
|
| + "datasetId"
|
| + ],
|
| + "parameters": {
|
| + "datasetId": {
|
| + "description": "The ID of the dataset to be updated.",
|
| + "location": "path",
|
| + "required": true,
|
| + "type": "string"
|
| + },
|
| + "updateMask": {
|
| + "description": "An optional mask specifying which fields to update. At this time, the only\nmutable field is name. The only\nacceptable value is \"name\". If unspecified, all mutable fields will be\nupdated.",
|
| + "format": "google-fieldmask",
|
| + "location": "query",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "path": "v1/datasets/{datasetId}",
|
| "request": {
|
| - "$ref": "SearchVariantSetsRequest"
|
| + "$ref": "Dataset"
|
| },
|
| "response": {
|
| - "$ref": "SearchVariantSetsResponse"
|
| + "$ref": "Dataset"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/genomics",
|
| - "https://www.googleapis.com/auth/genomics.readonly"
|
| + "https://www.googleapis.com/auth/genomics"
|
| ]
|
| },
|
| "get": {
|
| - "description": "Gets a variant set by ID.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| + "description": "Gets a dataset by ID.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| "httpMethod": "GET",
|
| - "id": "genomics.variantsets.get",
|
| + "id": "genomics.datasets.get",
|
| "parameterOrder": [
|
| - "variantSetId"
|
| + "datasetId"
|
| ],
|
| "parameters": {
|
| - "variantSetId": {
|
| - "description": "Required. The ID of the variant set.",
|
| + "datasetId": {
|
| + "description": "The ID of the dataset.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/variantsets/{variantSetId}",
|
| + "path": "v1/datasets/{datasetId}",
|
| "response": {
|
| - "$ref": "VariantSet"
|
| + "$ref": "Dataset"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -991,87 +1107,77 @@
|
| "https://www.googleapis.com/auth/genomics.readonly"
|
| ]
|
| },
|
| - "patch": {
|
| - "description": "Updates a variant set using patch semantics.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| - "httpMethod": "PATCH",
|
| - "id": "genomics.variantsets.patch",
|
| + "undelete": {
|
| + "description": "Undeletes a dataset by restoring a dataset which was deleted via this API.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis operation is only possible for a week after the deletion occurred.",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.datasets.undelete",
|
| "parameterOrder": [
|
| - "variantSetId"
|
| + "datasetId"
|
| ],
|
| "parameters": {
|
| - "updateMask": {
|
| - "description": "An optional mask specifying which fields to update. Supported fields:\n\n* metadata.\n* name.\n* description.\n\nLeaving `updateMask` unset is equivalent to specifying all mutable\nfields.",
|
| - "format": "google-fieldmask",
|
| - "location": "query",
|
| - "type": "string"
|
| - },
|
| - "variantSetId": {
|
| - "description": "The ID of the variant to be updated (must already exist).",
|
| + "datasetId": {
|
| + "description": "The ID of the dataset to be undeleted.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/variantsets/{variantSetId}",
|
| + "path": "v1/datasets/{datasetId}:undelete",
|
| "request": {
|
| - "$ref": "VariantSet"
|
| + "$ref": "UndeleteDatasetRequest"
|
| },
|
| "response": {
|
| - "$ref": "VariantSet"
|
| + "$ref": "Dataset"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| },
|
| - "delete": {
|
| - "description": "Deletes a variant set including all variants, call sets, and calls within.\nThis is not reversible.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| - "httpMethod": "DELETE",
|
| - "id": "genomics.variantsets.delete",
|
| + "testIamPermissions": {
|
| + "description": "Returns permissions that a caller has on the specified resource.\nSee <a href=\"/iam/docs/managing-policies#testing_permissions\">Testing\nPermissions</a> for more information.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.datasets.testIamPermissions",
|
| "parameterOrder": [
|
| - "variantSetId"
|
| + "resource"
|
| ],
|
| "parameters": {
|
| - "variantSetId": {
|
| - "description": "The ID of the variant set to be deleted.",
|
| + "resource": {
|
| + "description": "REQUIRED: The resource for which policy is being specified. Format is\n`datasets/<dataset ID>`.",
|
| "location": "path",
|
| + "pattern": "^datasets/[^/]+$",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/variantsets/{variantSetId}",
|
| + "path": "v1/{+resource}:testIamPermissions",
|
| + "request": {
|
| + "$ref": "TestIamPermissionsRequest"
|
| + },
|
| "response": {
|
| - "$ref": "Empty"
|
| + "$ref": "TestIamPermissionsResponse"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| - }
|
| - }
|
| - },
|
| - "operations": {
|
| - "methods": {
|
| - "cancel": {
|
| - "description": "Starts asynchronous cancellation on a long-running operation. The server makes a best effort to cancel the operation, but success is not guaranteed. Clients may use Operations.GetOperation or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite cancellation.",
|
| - "httpMethod": "POST",
|
| - "id": "genomics.operations.cancel",
|
| + },
|
| + "delete": {
|
| + "description": "Deletes a dataset and all of its contents (all read group sets,\nreference sets, variant sets, call sets, annotation sets, etc.)\nThis is reversible (up to one week after the deletion) via\nthe\ndatasets.undelete\noperation.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| + "httpMethod": "DELETE",
|
| + "id": "genomics.datasets.delete",
|
| "parameterOrder": [
|
| - "name"
|
| + "datasetId"
|
| ],
|
| "parameters": {
|
| - "name": {
|
| - "description": "The name of the operation resource to be cancelled.",
|
| + "datasetId": {
|
| + "description": "The ID of the dataset to be deleted.",
|
| "location": "path",
|
| - "pattern": "^operations/.+$",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/{+name}:cancel",
|
| - "request": {
|
| - "$ref": "CancelOperationRequest"
|
| - },
|
| + "path": "v1/datasets/{datasetId}",
|
| "response": {
|
| "$ref": "Empty"
|
| },
|
| @@ -1081,65 +1187,78 @@
|
| ]
|
| },
|
| "list": {
|
| - "description": "Lists operations that match the specified filter in the request.",
|
| + "description": "Lists datasets within a project.\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": "GET",
|
| - "id": "genomics.operations.list",
|
| - "parameterOrder": [
|
| - "name"
|
| - ],
|
| + "id": "genomics.datasets.list",
|
| + "parameterOrder": [],
|
| "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 results to return. If unspecified, defaults to\n256. The maximum value is 2048.",
|
| + "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 50. The maximum value is 1024.",
|
| "format": "int32",
|
| "location": "query",
|
| "type": "integer"
|
| },
|
| - "filter": {
|
| - "description": "A string for filtering Operations.\nThe following filter fields are supported:\n\n* projectId: Required. Corresponds to\n OperationMetadata.projectId.\n* createTime: 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: 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:\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",
|
| - "pattern": "^operations$",
|
| - "required": true,
|
| - "type": "string"
|
| - },
|
| - "pageToken": {
|
| - "description": "The standard list page token.",
|
| + "projectId": {
|
| + "description": "Required. The Google Cloud project ID to list datasets for.",
|
| "location": "query",
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/{+name}",
|
| + "path": "v1/datasets",
|
| "response": {
|
| - "$ref": "ListOperationsResponse"
|
| + "$ref": "ListDatasetsResponse"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/genomics"
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| ]
|
| },
|
| - "get": {
|
| - "description": "Gets the latest state of a long-running operation. Clients can use this\nmethod to poll the operation result at intervals as recommended by the API\nservice.",
|
| - "httpMethod": "GET",
|
| - "id": "genomics.operations.get",
|
| + "setIamPolicy": {
|
| + "description": "Sets the access control policy on the specified dataset. Replaces any\nexisting policy.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nSee <a href=\"/iam/docs/managing-policies#setting_a_policy\">Setting a\nPolicy</a> for more information.",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.datasets.setIamPolicy",
|
| "parameterOrder": [
|
| - "name"
|
| + "resource"
|
| ],
|
| "parameters": {
|
| - "name": {
|
| - "description": "The name of the operation resource.",
|
| + "resource": {
|
| + "description": "REQUIRED: The resource for which policy is being specified. Format is\n`datasets/<dataset ID>`.",
|
| "location": "path",
|
| - "pattern": "^operations/.+$",
|
| + "pattern": "^datasets/[^/]+$",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/{+name}",
|
| + "path": "v1/{+resource}:setIamPolicy",
|
| + "request": {
|
| + "$ref": "SetIamPolicyRequest"
|
| + },
|
| "response": {
|
| - "$ref": "Operation"
|
| + "$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",
|
| + "request": {
|
| + "$ref": "Dataset"
|
| + },
|
| + "response": {
|
| + "$ref": "Dataset"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -1148,96 +1267,66 @@
|
| }
|
| }
|
| },
|
| - "referencesets": {
|
| + "variantsets": {
|
| "methods": {
|
| - "search": {
|
| - "description": "Searches for reference sets 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.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)",
|
| + "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.referencesets.search",
|
| + "id": "genomics.variantsets.create",
|
| "parameterOrder": [],
|
| "parameters": {},
|
| - "path": "v1/referencesets/search",
|
| + "path": "v1/variantsets",
|
| "request": {
|
| - "$ref": "SearchReferenceSetsRequest"
|
| + "$ref": "VariantSet"
|
| },
|
| "response": {
|
| - "$ref": "SearchReferenceSetsResponse"
|
| + "$ref": "VariantSet"
|
| },
|
| "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"
|
| ]
|
| },
|
| - "get": {
|
| - "description": "Gets a reference set.\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.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).",
|
| - "httpMethod": "GET",
|
| - "id": "genomics.referencesets.get",
|
| - "parameterOrder": [
|
| - "referenceSetId"
|
| - ],
|
| - "parameters": {
|
| - "referenceSetId": {
|
| - "description": "The ID of the reference set.",
|
| - "location": "path",
|
| - "required": true,
|
| - "type": "string"
|
| - }
|
| - },
|
| - "path": "v1/referencesets/{referenceSetId}",
|
| - "response": {
|
| - "$ref": "ReferenceSet"
|
| - },
|
| - "scopes": [
|
| - "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/genomics",
|
| - "https://www.googleapis.com/auth/genomics.readonly"
|
| - ]
|
| - }
|
| - }
|
| - },
|
| - "readgroupsets": {
|
| - "methods": {
|
| "export": {
|
| - "description": "Exports a read group set to a BAM file in Google Cloud Storage.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nNote that currently there may be some differences between exported BAM\nfiles and the original BAM file at the time of import. See\nImportReadGroupSets\nfor caveats.",
|
| + "description": "Exports variant set data to an external destination.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| "httpMethod": "POST",
|
| - "id": "genomics.readgroupsets.export",
|
| + "id": "genomics.variantsets.export",
|
| "parameterOrder": [
|
| - "readGroupSetId"
|
| + "variantSetId"
|
| ],
|
| "parameters": {
|
| - "readGroupSetId": {
|
| - "description": "Required. The ID of the read group set to export. The caller must have\nREAD access to this read group set.",
|
| + "variantSetId": {
|
| + "description": "Required. The ID of the variant set that contains variant data which\nshould be exported. The caller must have READ access to this variant set.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/readgroupsets/{readGroupSetId}:export",
|
| + "path": "v1/variantsets/{variantSetId}:export",
|
| "request": {
|
| - "$ref": "ExportReadGroupSetRequest"
|
| + "$ref": "ExportVariantSetRequest"
|
| },
|
| "response": {
|
| "$ref": "Operation"
|
| },
|
| "scopes": [
|
| + "https://www.googleapis.com/auth/bigquery",
|
| "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": "Returns a list of all variant sets matching search criteria.\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\nImplements\n[GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).",
|
| "httpMethod": "POST",
|
| - "id": "genomics.readgroupsets.search",
|
| + "id": "genomics.variantsets.search",
|
| "parameterOrder": [],
|
| "parameters": {},
|
| - "path": "v1/readgroupsets/search",
|
| + "path": "v1/variantsets/search",
|
| "request": {
|
| - "$ref": "SearchReadGroupSetsRequest"
|
| + "$ref": "SearchVariantSetsRequest"
|
| },
|
| "response": {
|
| - "$ref": "SearchReadGroupSetsResponse"
|
| + "$ref": "SearchVariantSetsResponse"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -1246,32 +1335,32 @@
|
| ]
|
| },
|
| "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 variant set using patch semantics.\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": "PATCH",
|
| - "id": "genomics.readgroupsets.patch",
|
| + "id": "genomics.variantsets.patch",
|
| "parameterOrder": [
|
| - "readGroupSetId"
|
| + "variantSetId"
|
| ],
|
| "parameters": {
|
| + "variantSetId": {
|
| + "description": "The ID of the variant to be updated (must already exist).",
|
| + "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. Supported fields:\n\n* metadata.\n* name.\n* description.\n\nLeaving `updateMask` unset is equivalent to specifying all mutable\nfields.",
|
| "format": "google-fieldmask",
|
| "location": "query",
|
| "type": "string"
|
| - },
|
| - "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"
|
| }
|
| },
|
| - "path": "v1/readgroupsets/{readGroupSetId}",
|
| + "path": "v1/variantsets/{variantSetId}",
|
| "request": {
|
| - "$ref": "ReadGroupSet"
|
| + "$ref": "VariantSet"
|
| },
|
| "response": {
|
| - "$ref": "ReadGroupSet"
|
| + "$ref": "VariantSet"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -1279,23 +1368,23 @@
|
| ]
|
| },
|
| "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 variant set by ID.\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": "GET",
|
| - "id": "genomics.readgroupsets.get",
|
| + "id": "genomics.variantsets.get",
|
| "parameterOrder": [
|
| - "readGroupSetId"
|
| + "variantSetId"
|
| ],
|
| "parameters": {
|
| - "readGroupSetId": {
|
| - "description": "The ID of the read group set.",
|
| + "variantSetId": {
|
| + "description": "Required. The ID of the variant set.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/readgroupsets/{readGroupSetId}",
|
| + "path": "v1/variantsets/{variantSetId}",
|
| "response": {
|
| - "$ref": "ReadGroupSet"
|
| + "$ref": "VariantSet"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -1303,41 +1392,50 @@
|
| "https://www.googleapis.com/auth/genomics.readonly"
|
| ]
|
| },
|
| - "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": {
|
| - "$ref": "ImportReadGroupSetsRequest"
|
| + "delete": {
|
| + "description": "Deletes a variant set including all variants, call sets, and calls within.\nThis is not reversible.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| + "httpMethod": "DELETE",
|
| + "id": "genomics.variantsets.delete",
|
| + "parameterOrder": [
|
| + "variantSetId"
|
| + ],
|
| + "parameters": {
|
| + "variantSetId": {
|
| + "description": "The ID of the variant set to be deleted.",
|
| + "location": "path",
|
| + "required": true,
|
| + "type": "string"
|
| + }
|
| },
|
| + "path": "v1/variantsets/{variantSetId}",
|
| "response": {
|
| - "$ref": "Operation"
|
| + "$ref": "Empty"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/devstorage.read_write",
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| - },
|
| + }
|
| + }
|
| + },
|
| + "annotations": {
|
| + "methods": {
|
| "delete": {
|
| - "description": "Deletes a read group set.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| + "description": "Deletes an annotation. Caller must have WRITE permission for\nthe associated annotation set.",
|
| "httpMethod": "DELETE",
|
| - "id": "genomics.readgroupsets.delete",
|
| + "id": "genomics.annotations.delete",
|
| "parameterOrder": [
|
| - "readGroupSetId"
|
| + "annotationId"
|
| ],
|
| "parameters": {
|
| - "readGroupSetId": {
|
| - "description": "The ID of the read group set to be deleted. The caller must have WRITE\npermissions to the dataset associated with this read group set.",
|
| + "annotationId": {
|
| + "description": "The ID of the annotation to be deleted.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/readgroupsets/{readGroupSetId}",
|
| + "path": "v1/annotations/{annotationId}",
|
| "response": {
|
| "$ref": "Empty"
|
| },
|
| @@ -1345,169 +1443,80 @@
|
| "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": {
|
| - "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"
|
| - },
|
| - "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"
|
| - }
|
| - },
|
| - "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": {
|
| - "methods": {
|
| - "search": {
|
| - "description": "Gets a list of reads for one or more read group sets.\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\nReads search operates over a genomic coordinate space of reference sequence\n& position defined over the reference sequences to which the requested\nread group sets are aligned.\n\nIf a target positional range is specified, search returns all reads whose\nalignment to the reference genome overlap the range. A query which\nspecifies only read group set IDs yields all reads in those read group\nsets, including unmapped reads.\n\nAll reads returned (including reads on subsequent pages) are ordered by\ngenomic coordinate (by reference sequence, then position). Reads with\nequivalent genomic coordinates are returned in an unspecified order. This\norder is consistent, such that two queries for the same content (regardless\nof page size) yield reads in the same order across their respective streams\nof paginated responses.\n\nImplements\n[GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).",
|
| + },
|
| + "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.reads.search",
|
| + "id": "genomics.annotations.create",
|
| "parameterOrder": [],
|
| "parameters": {},
|
| - "path": "v1/reads/search",
|
| + "path": "v1/annotations",
|
| "request": {
|
| - "$ref": "SearchReadsRequest"
|
| + "$ref": "Annotation"
|
| },
|
| "response": {
|
| - "$ref": "SearchReadsResponse"
|
| + "$ref": "Annotation"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/genomics",
|
| - "https://www.googleapis.com/auth/genomics.readonly"
|
| + "https://www.googleapis.com/auth/genomics"
|
| ]
|
| - }
|
| - }
|
| - },
|
| - "callsets": {
|
| - "methods": {
|
| - "search": {
|
| - "description": "Gets a list of call sets matching the criteria.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).",
|
| + },
|
| + "batchCreate": {
|
| + "description": "Creates one or more new annotations atomically. All annotations must\nbelong to the same annotation set. Caller must have WRITE\npermission for this annotation set. For optimal performance, batch\npositionally adjacent annotations together.\n\nIf the request has a systemic issue, such as an attempt to write to\nan inaccessible annotation set, the entire RPC will fail accordingly. For\nlesser data issues, when possible an error will be isolated to the\ncorresponding batch entry in the response; the remaining well formed\nannotations will be created normally.\n\nFor details on the requirements for each individual annotation resource,\nsee\nCreateAnnotation.",
|
| "httpMethod": "POST",
|
| - "id": "genomics.callsets.search",
|
| + "id": "genomics.annotations.batchCreate",
|
| "parameterOrder": [],
|
| "parameters": {},
|
| - "path": "v1/callsets/search",
|
| + "path": "v1/annotations:batchCreate",
|
| "request": {
|
| - "$ref": "SearchCallSetsRequest"
|
| + "$ref": "BatchCreateAnnotationsRequest"
|
| },
|
| "response": {
|
| - "$ref": "SearchCallSetsResponse"
|
| + "$ref": "BatchCreateAnnotationsResponse"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/genomics",
|
| - "https://www.googleapis.com/auth/genomics.readonly"
|
| + "https://www.googleapis.com/auth/genomics"
|
| ]
|
| },
|
| - "patch": {
|
| - "description": "Updates a call set.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis method supports patch semantics.",
|
| - "httpMethod": "PATCH",
|
| - "id": "genomics.callsets.patch",
|
| - "parameterOrder": [
|
| - "callSetId"
|
| - ],
|
| - "parameters": {
|
| - "updateMask": {
|
| - "description": "An optional mask specifying which fields to update. At this time, the only\nmutable field is name. The only\nacceptable value is \"name\". If unspecified, all mutable fields will be\nupdated.",
|
| - "format": "google-fieldmask",
|
| - "location": "query",
|
| - "type": "string"
|
| - },
|
| - "callSetId": {
|
| - "description": "The ID of the call set to be updated.",
|
| - "location": "path",
|
| - "required": true,
|
| - "type": "string"
|
| - }
|
| - },
|
| - "path": "v1/callsets/{callSetId}",
|
| + "search": {
|
| + "description": "Searches for annotations that match the given criteria. Results are\nordered by genomic coordinate (by reference sequence, then position).\nAnnotations with equivalent genomic coordinates are returned in an\nunspecified order. This order is consistent, such that two queries for the\nsame content (regardless of page size) yield annotations in the same order\nacross their respective streams of paginated responses. Caller must have\nREAD permission for the queried annotation sets.",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.annotations.search",
|
| + "parameterOrder": [],
|
| + "parameters": {},
|
| + "path": "v1/annotations/search",
|
| "request": {
|
| - "$ref": "CallSet"
|
| + "$ref": "SearchAnnotationsRequest"
|
| },
|
| "response": {
|
| - "$ref": "CallSet"
|
| + "$ref": "SearchAnnotationsResponse"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/genomics"
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| ]
|
| },
|
| "get": {
|
| - "description": "Gets a call set by ID.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| + "description": "Gets an annotation. Caller must have READ permission\nfor the associated annotation set.",
|
| "httpMethod": "GET",
|
| - "id": "genomics.callsets.get",
|
| + "id": "genomics.annotations.get",
|
| "parameterOrder": [
|
| - "callSetId"
|
| + "annotationId"
|
| ],
|
| "parameters": {
|
| - "callSetId": {
|
| - "description": "The ID of the call set.",
|
| + "annotationId": {
|
| + "description": "The ID of the annotation to be retrieved.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/callsets/{callSetId}",
|
| + "path": "v1/annotations/{annotationId}",
|
| "response": {
|
| - "$ref": "CallSet"
|
| + "$ref": "Annotation"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -1515,42 +1524,33 @@
|
| "https://www.googleapis.com/auth/genomics.readonly"
|
| ]
|
| },
|
| - "create": {
|
| - "description": "Creates a new call set.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| - "httpMethod": "POST",
|
| - "id": "genomics.callsets.create",
|
| - "parameterOrder": [],
|
| - "parameters": {},
|
| - "path": "v1/callsets",
|
| - "request": {
|
| - "$ref": "CallSet"
|
| - },
|
| - "response": {
|
| - "$ref": "CallSet"
|
| - },
|
| - "scopes": [
|
| - "https://www.googleapis.com/auth/cloud-platform",
|
| - "https://www.googleapis.com/auth/genomics"
|
| - ]
|
| - },
|
| - "delete": {
|
| - "description": "Deletes a call set.\n\nFor the definitions of call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| - "httpMethod": "DELETE",
|
| - "id": "genomics.callsets.delete",
|
| + "update": {
|
| + "description": "Updates an annotation. Caller must have\nWRITE permission for the associated dataset.",
|
| + "httpMethod": "PUT",
|
| + "id": "genomics.annotations.update",
|
| "parameterOrder": [
|
| - "callSetId"
|
| + "annotationId"
|
| ],
|
| "parameters": {
|
| - "callSetId": {
|
| - "description": "The ID of the call set to be deleted.",
|
| + "updateMask": {
|
| + "description": "An optional mask specifying which fields to update. Mutable fields are\nname,\nvariant,\ntranscript, and\ninfo. If unspecified, all mutable\nfields will be updated.",
|
| + "format": "google-fieldmask",
|
| + "location": "query",
|
| + "type": "string"
|
| + },
|
| + "annotationId": {
|
| + "description": "The ID of the annotation to be updated.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "v1/callsets/{callSetId}",
|
| + "path": "v1/annotations/{annotationId}",
|
| + "request": {
|
| + "$ref": "Annotation"
|
| + },
|
| "response": {
|
| - "$ref": "Empty"
|
| + "$ref": "Annotation"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/cloud-platform",
|
| @@ -1560,99 +1560,21 @@
|
| }
|
| }
|
| },
|
| - "revision": "20170209",
|
| + "revision": "20170302",
|
| "rootUrl": "https://genomics.googleapis.com/",
|
| "schemas": {
|
| - "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": {
|
| - "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"
|
| - },
|
| - "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"
|
| - }
|
| - },
|
| - "type": "object"
|
| - },
|
| - "CancelOperationRequest": {
|
| - "description": "The request message for Operations.CancelOperation.",
|
| - "id": "CancelOperationRequest",
|
| - "properties": {},
|
| - "type": "object"
|
| - },
|
| - "SearchReadsRequest": {
|
| - "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"
|
| - },
|
| - "pageSize": {
|
| - "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 256. The maximum value is 2048.",
|
| - "format": "int32",
|
| - "type": "integer"
|
| - },
|
| - "start": {
|
| - "description": "The start position of the range on the reference, 0-based inclusive. If\nspecified, `referenceName` must also be specified.",
|
| - "format": "int64",
|
| - "type": "string"
|
| - },
|
| - "referenceName": {
|
| - "description": "The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to\n`*`, only unmapped reads are returned. If unspecified, all reads (mapped\nand unmapped) are returned.",
|
| - "type": "string"
|
| - },
|
| - "readGroupSetIds": {
|
| - "description": "The IDs of the read groups sets within which to search for reads. All\nspecified read group sets must be aligned against a common set of reference\nsequences; this defines the genomic coordinates for the query. Must specify\none of `readGroupSetIds` or `readGroupIds`.",
|
| - "items": {
|
| - "type": "string"
|
| - },
|
| - "type": "array"
|
| - }
|
| - },
|
| - "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": {
|
| - "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"
|
| },
|
| - "id": {
|
| - "description": "The server-generated annotation ID, unique across all annotations.",
|
| - "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"
|
| @@ -1661,6 +1583,16 @@
|
| "description": "The display name corresponding to the reference specified by\n`referenceId`, for example `chr1`, `1`, or `chrX`.",
|
| "type": "string"
|
| },
|
| + "info": {
|
| + "additionalProperties": {
|
| + "items": {
|
| + "type": "any"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "description": "A map of additional read alignment information. This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).",
|
| + "type": "object"
|
| + },
|
| "type": {
|
| "description": "The data type for this annotation. Must match the containing annotation\nset's type.",
|
| "enum": [
|
| @@ -1679,37 +1611,92 @@
|
| ],
|
| "type": "string"
|
| },
|
| - "info": {
|
| - "additionalProperties": {
|
| - "items": {
|
| - "type": "any"
|
| - },
|
| - "type": "array"
|
| + "end": {
|
| + "description": "The end position of the range on the reference, 0-based exclusive.",
|
| + "format": "int64",
|
| + "type": "string"
|
| + },
|
| + "transcript": {
|
| + "$ref": "Transcript",
|
| + "description": "A transcript value represents the assertion that a particular region of\nthe reference genome may be transcribed as RNA. An alternative splicing\npattern would be represented as a separate transcript object. This field\nis only set for annotations of type `TRANSCRIPT`."
|
| + },
|
| + "start": {
|
| + "description": "The start position of the range on the reference, 0-based inclusive.",
|
| + "format": "int64",
|
| + "type": "string"
|
| + },
|
| + "annotationSetId": {
|
| + "description": "The annotation set to which this annotation belongs.",
|
| + "type": "string"
|
| + },
|
| + "name": {
|
| + "description": "The display name of this annotation.",
|
| + "type": "string"
|
| + },
|
| + "variant": {
|
| + "$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`."
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "CancelOperationRequest": {
|
| + "description": "The request message for Operations.CancelOperation.",
|
| + "id": "CancelOperationRequest",
|
| + "properties": {},
|
| + "type": "object"
|
| + },
|
| + "SearchReadsRequest": {
|
| + "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"
|
| },
|
| - "description": "A map of additional read alignment information. This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).",
|
| - "type": "object"
|
| + "type": "array"
|
| },
|
| "end": {
|
| - "description": "The end position of the range on the reference, 0-based exclusive.",
|
| + "description": "The end position of the range on the reference, 0-based exclusive. If\nspecified, `referenceName` must also be specified.",
|
| "format": "int64",
|
| "type": "string"
|
| },
|
| - "transcript": {
|
| - "$ref": "Transcript",
|
| - "description": "A transcript value represents the assertion that a particular region of\nthe reference genome may be transcribed as RNA. An alternative splicing\npattern would be represented as a separate transcript object. This field\nis only set for annotations of type `TRANSCRIPT`."
|
| + "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 256. The maximum value is 2048.",
|
| + "format": "int32",
|
| + "type": "integer"
|
| },
|
| "start": {
|
| - "description": "The start position of the range on the reference, 0-based inclusive.",
|
| + "description": "The start position of the range on the reference, 0-based inclusive. If\nspecified, `referenceName` must also be specified.",
|
| "format": "int64",
|
| "type": "string"
|
| },
|
| - "annotationSetId": {
|
| - "description": "The annotation set to which this annotation belongs.",
|
| + "referenceName": {
|
| + "description": "The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to\n`*`, only unmapped reads are returned. If unspecified, all reads (mapped\nand unmapped) are returned.",
|
| "type": "string"
|
| },
|
| - "name": {
|
| - "description": "The display name of this annotation.",
|
| - "type": "string"
|
| + "readGroupSetIds": {
|
| + "description": "The IDs of the read groups sets within which to search for reads. All\nspecified read group sets must be aligned against a common set of reference\nsequences; this defines the genomic coordinates for the query. Must specify\none of `readGroupSetIds` or `readGroupIds`.",
|
| + "items": {
|
| + "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."
|
| }
|
| },
|
| "type": "object"
|
| @@ -1718,10 +1705,6 @@
|
| "description": "This resource represents a long-running operation that is the result of a\nnetwork API call.",
|
| "id": "Operation",
|
| "properties": {
|
| - "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.",
|
| @@ -1745,17 +1728,10 @@
|
| },
|
| "description": "An OperationMetadata object. This will always be returned with the Operation.",
|
| "type": "object"
|
| - }
|
| - },
|
| - "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."
|
| + },
|
| + "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"
|
| @@ -1778,24 +1754,6 @@
|
| "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": {
|
| @@ -1815,6 +1773,24 @@
|
| "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"
|
| @@ -1883,33 +1859,37 @@
|
| },
|
| "type": "object"
|
| },
|
| - "UndeleteDatasetRequest": {
|
| - "id": "UndeleteDatasetRequest",
|
| - "properties": {},
|
| - "type": "object"
|
| - },
|
| "Binding": {
|
| "description": "Associates `members` with a `role`.",
|
| "id": "Binding",
|
| "properties": {
|
| + "role": {
|
| + "description": "Role that is assigned to `members`.\nFor example, `roles/viewer`, `roles/editor`, or `roles/owner`.\nRequired",
|
| + "type": "string"
|
| + },
|
| "members": {
|
| "description": "Specifies the identities requesting access for a Cloud Platform resource.\n`members` can have the following values:\n\n* `allUsers`: A special identifier that represents anyone who is\n on the internet; with or without a Google account.\n\n* `allAuthenticatedUsers`: A special identifier that represents anyone\n who is authenticated with a Google account or a service account.\n\n* `user:{emailid}`: An email address that represents a specific Google\n account. For example, `alice@gmail.com` or `joe@example.com`.\n\n\n* `serviceAccount:{emailid}`: An email address that represents a service\n account. For example, `my-other-app@appspot.gserviceaccount.com`.\n\n* `group:{emailid}`: An email address that represents a Google group.\n For example, `admins@example.com`.\n\n* `domain:{domain}`: A Google Apps domain name that represents all the\n users of that domain. For example, `google.com` or `example.com`.\n\n",
|
| "items": {
|
| "type": "string"
|
| },
|
| "type": "array"
|
| - },
|
| - "role": {
|
| - "description": "Role that is assigned to `members`.\nFor example, `roles/viewer`, `roles/editor`, or `roles/owner`.\nRequired",
|
| - "type": "string"
|
| }
|
| },
|
| "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",
|
| @@ -1919,10 +1899,6 @@
|
| "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"
|
| @@ -1931,10 +1907,6 @@
|
| "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": {
|
| - "description": {
|
| - "description": "A textual description of this variant set.",
|
| - "type": "string"
|
| - },
|
| "datasetId": {
|
| "description": "The dataset to which this variant set belongs.",
|
| "type": "string"
|
| @@ -1964,6 +1936,10 @@
|
| "id": {
|
| "description": "The server-generated variant set ID, unique across all variant sets.",
|
| "type": "string"
|
| + },
|
| + "description": {
|
| + "description": "A textual description of this variant set.",
|
| + "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| @@ -1997,20 +1973,20 @@
|
| },
|
| "type": "object"
|
| },
|
| - "SearchCallSetsResponse": {
|
| - "description": "The call set search response.",
|
| - "id": "SearchCallSetsResponse",
|
| + "ListOperationsResponse": {
|
| + "description": "The response message for Operations.ListOperations.",
|
| + "id": "ListOperationsResponse",
|
| "properties": {
|
| - "callSets": {
|
| - "description": "The list of matching call sets.",
|
| + "nextPageToken": {
|
| + "description": "The standard List next-page token.",
|
| + "type": "string"
|
| + },
|
| + "operations": {
|
| + "description": "A list of operations that matches the specified filter in the request.",
|
| "items": {
|
| - "$ref": "CallSet"
|
| + "$ref": "Operation"
|
| },
|
| "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"
|
| @@ -2019,6 +1995,20 @@
|
| "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",
|
| + "type": "number"
|
| + },
|
| + "id": {
|
| + "description": "The server-generated variant ID, unique across all variants.",
|
| + "type": "string"
|
| + },
|
| "variantSetId": {
|
| "description": "The ID of the variant set this variant belongs to.",
|
| "type": "string"
|
| @@ -2041,15 +2031,15 @@
|
| "description": "The reference bases for this variant. They start at the given\nposition.",
|
| "type": "string"
|
| },
|
| - "names": {
|
| - "description": "Names for the variant, for example a RefSNP ID.",
|
| + "alternateBases": {
|
| + "description": "The bases that appear instead of the reference bases.",
|
| "items": {
|
| "type": "string"
|
| },
|
| "type": "array"
|
| },
|
| - "alternateBases": {
|
| - "description": "The bases that appear instead of the reference bases.",
|
| + "names": {
|
| + "description": "Names for the variant, for example a RefSNP ID.",
|
| "items": {
|
| "type": "string"
|
| },
|
| @@ -2070,106 +2060,32 @@
|
| "calls": {
|
| "description": "The variant calls for this particular variant. Each one represents the\ndetermination of genotype with respect to this variant.",
|
| "items": {
|
| - "$ref": "VariantCall"
|
| - },
|
| - "type": "array"
|
| - },
|
| - "created": {
|
| - "description": "The date this variant was created, in milliseconds from the epoch.",
|
| - "format": "int64",
|
| - "type": "string"
|
| - },
|
| - "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",
|
| - "type": "number"
|
| - },
|
| - "id": {
|
| - "description": "The server-generated variant ID, unique across all variants.",
|
| - "type": "string"
|
| - }
|
| - },
|
| - "type": "object"
|
| - },
|
| - "ListOperationsResponse": {
|
| - "description": "The response message for Operations.ListOperations.",
|
| - "id": "ListOperationsResponse",
|
| - "properties": {
|
| - "nextPageToken": {
|
| - "description": "The standard List next-page token.",
|
| - "type": "string"
|
| - },
|
| - "operations": {
|
| - "description": "A list of operations that matches the specified filter in the request.",
|
| - "items": {
|
| - "$ref": "Operation"
|
| - },
|
| - "type": "array"
|
| - }
|
| - },
|
| - "type": "object"
|
| - },
|
| - "OperationMetadata": {
|
| - "description": "Metadata describing an Operation.",
|
| - "id": "OperationMetadata",
|
| - "properties": {
|
| - "projectId": {
|
| - "description": "The Google Cloud Project in which the job is scoped.",
|
| - "type": "string"
|
| - },
|
| - "clientId": {
|
| - "description": "This field is deprecated. Use `labels` instead. Optionally provided by the\ncaller when submitting the request that creates the operation.",
|
| - "type": "string"
|
| - },
|
| - "endTime": {
|
| - "description": "The time at which the job stopped running.",
|
| - "format": "google-datetime",
|
| - "type": "string"
|
| - },
|
| - "events": {
|
| - "description": "Optional event messages that were generated during the job's execution.\nThis also contains any warnings that were generated during import\nor export.",
|
| - "items": {
|
| - "$ref": "OperationEvent"
|
| - },
|
| - "type": "array"
|
| - },
|
| - "startTime": {
|
| - "description": "The time at which the job began to run.",
|
| - "format": "google-datetime",
|
| - "type": "string"
|
| - },
|
| - "request": {
|
| - "additionalProperties": {
|
| - "description": "Properties of the object. Contains field @type with type URL.",
|
| - "type": "any"
|
| - },
|
| - "description": "The original request that started the operation. Note that this will be in\ncurrent version of the API. If the operation was started with v1beta2 API\nand a GetOperation is performed on v1 API, a v1 request will be returned.",
|
| - "type": "object"
|
| - },
|
| - "runtimeMetadata": {
|
| - "additionalProperties": {
|
| - "description": "Properties of the object. Contains field @type with type URL.",
|
| - "type": "any"
|
| - },
|
| - "description": "Runtime metadata on this Operation.",
|
| - "type": "object"
|
| - },
|
| - "labels": {
|
| - "additionalProperties": {
|
| - "type": "string"
|
| + "$ref": "VariantCall"
|
| },
|
| - "description": "Optionally provided by the caller when submitting the request that creates\nthe operation.",
|
| - "type": "object"
|
| + "type": "array"
|
| },
|
| - "createTime": {
|
| - "description": "The time at which the job was submitted to the Genomics service.",
|
| - "format": "google-datetime",
|
| + "created": {
|
| + "description": "The date this variant was created, in milliseconds from the epoch.",
|
| + "format": "int64",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "SearchCallSetsResponse": {
|
| + "description": "The call set search response.",
|
| + "id": "SearchCallSetsResponse",
|
| + "properties": {
|
| + "nextPageToken": {
|
| + "description": "The continuation token, which is used to page through large result sets.\nProvide this value in a subsequent request to return the next page of\nresults. This field will be empty if there aren't any additional results.",
|
| "type": "string"
|
| + },
|
| + "callSets": {
|
| + "description": "The list of matching call sets.",
|
| + "items": {
|
| + "$ref": "CallSet"
|
| + },
|
| + "type": "array"
|
| }
|
| },
|
| "type": "object"
|
| @@ -2227,10 +2143,77 @@
|
| },
|
| "type": "object"
|
| },
|
| + "OperationMetadata": {
|
| + "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": {
|
| + "$ref": "OperationEvent"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "endTime": {
|
| + "description": "The time at which the job stopped running.",
|
| + "format": "google-datetime",
|
| + "type": "string"
|
| + },
|
| + "startTime": {
|
| + "description": "The time at which the job began to run.",
|
| + "format": "google-datetime",
|
| + "type": "string"
|
| + },
|
| + "request": {
|
| + "additionalProperties": {
|
| + "description": "Properties of the object. Contains field @type with type URL.",
|
| + "type": "any"
|
| + },
|
| + "description": "The original request that started the operation. Note that this will be in\ncurrent version of the API. If the operation was started with v1beta2 API\nand a GetOperation is performed on v1 API, a v1 request will be returned.",
|
| + "type": "object"
|
| + },
|
| + "runtimeMetadata": {
|
| + "additionalProperties": {
|
| + "description": "Properties of the object. Contains field @type with type URL.",
|
| + "type": "any"
|
| + },
|
| + "description": "Runtime metadata on this Operation.",
|
| + "type": "object"
|
| + },
|
| + "createTime": {
|
| + "description": "The time at which the job was submitted to the Genomics service.",
|
| + "format": "google-datetime",
|
| + "type": "string"
|
| + },
|
| + "labels": {
|
| + "additionalProperties": {
|
| + "type": "string"
|
| + },
|
| + "description": "Optionally provided by the caller when submitting the request that creates\nthe operation.",
|
| + "type": "object"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| "SearchReadGroupSetsRequest": {
|
| "description": "The read group set search request.",
|
| "id": "SearchReadGroupSetsRequest",
|
| "properties": {
|
| + "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"
|
| + },
|
| "name": {
|
| "description": "Only return read group sets for which a substring of the name matches this\nstring.",
|
| "type": "string"
|
| @@ -2243,13 +2226,6 @@
|
| "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"
|
| @@ -2257,16 +2233,16 @@
|
| "SearchAnnotationsResponse": {
|
| "id": "SearchAnnotationsResponse",
|
| "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"
|
| + },
|
| "annotations": {
|
| "description": "The matching annotations.",
|
| "items": {
|
| "$ref": "Annotation"
|
| },
|
| "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"
|
| @@ -2274,25 +2250,25 @@
|
| "ClinicalCondition": {
|
| "id": "ClinicalCondition",
|
| "properties": {
|
| - "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"
|
| + "$ref": "ExternalId"
|
| },
|
| "type": "array"
|
| },
|
| - "omimId": {
|
| - "description": "The OMIM id for this condition.\nSearch for these IDs at http://omim.org/",
|
| + "conceptId": {
|
| + "description": "The MedGen concept id associated with this gene.\nSearch for these IDs at http://www.ncbi.nlm.nih.gov/medgen/",
|
| "type": "string"
|
| },
|
| - "externalIds": {
|
| - "description": "The set of external IDs for this condition.",
|
| + "names": {
|
| + "description": "A set of names for the condition.",
|
| "items": {
|
| - "$ref": "ExternalId"
|
| + "type": "string"
|
| },
|
| "type": "array"
|
| }
|
| @@ -2303,16 +2279,16 @@
|
| "description": "The read search response.",
|
| "id": "SearchReadsResponse",
|
| "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"
|
| - },
|
| "alignments": {
|
| "description": "The list of matching alignments sorted by mapped genomic coordinate,\nif any, ascending in position within the same reference. Unmapped reads,\nwhich have no position, are returned contiguously and are sorted in\nascending lexicographic order by fragment name.",
|
| "items": {
|
| "$ref": "Read"
|
| },
|
| "type": "array"
|
| + },
|
| + "nextPageToken": {
|
| + "description": "The continuation token, which is used to page through large result sets.\nProvide this value in a subsequent request to return the next page of\nresults. This field will be empty if there aren't any additional results.",
|
| + "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| @@ -2320,10 +2296,6 @@
|
| "Program": {
|
| "id": "Program",
|
| "properties": {
|
| - "name": {
|
| - "description": "The display name of the program. This is typically the colloquial name of\nthe tool used, for example 'bwa' or 'picard'.",
|
| - "type": "string"
|
| - },
|
| "commandLine": {
|
| "description": "The command line used to run this program.",
|
| "type": "string"
|
| @@ -2339,22 +2311,10 @@
|
| "version": {
|
| "description": "The version of the program run.",
|
| "type": "string"
|
| - }
|
| - },
|
| - "type": "object"
|
| - },
|
| - "CoverageBucket": {
|
| - "description": "A bucket over which read coverage has been precomputed. A bucket corresponds\nto a specific range of the reference sequence.",
|
| - "id": "CoverageBucket",
|
| - "properties": {
|
| - "meanCoverage": {
|
| - "description": "The average number of reads which are aligned to each individual\nreference base in this bucket.",
|
| - "format": "float",
|
| - "type": "number"
|
| },
|
| - "range": {
|
| - "$ref": "Range",
|
| - "description": "The genomic coordinate range spanned by this bucket."
|
| + "name": {
|
| + "description": "The display name of the program. This is typically the colloquial name of\nthe tool used, for example 'bwa' or 'picard'.",
|
| + "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| @@ -2363,10 +2323,6 @@
|
| "description": "Describes a Compute Engine resource that is being managed by a running\npipeline.",
|
| "id": "ComputeEngine",
|
| "properties": {
|
| - "instanceName": {
|
| - "description": "The instance on which the operation is running.",
|
| - "type": "string"
|
| - },
|
| "zone": {
|
| "description": "The availability zone in which the instance resides.",
|
| "type": "string"
|
| @@ -2381,6 +2337,26 @@
|
| "type": "string"
|
| },
|
| "type": "array"
|
| + },
|
| + "instanceName": {
|
| + "description": "The instance on which the operation is running.",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "CoverageBucket": {
|
| + "description": "A bucket over which read coverage has been precomputed. A bucket corresponds\nto a specific range of the reference sequence.",
|
| + "id": "CoverageBucket",
|
| + "properties": {
|
| + "meanCoverage": {
|
| + "description": "The average number of reads which are aligned to each individual\nreference base in this bucket.",
|
| + "format": "float",
|
| + "type": "number"
|
| + },
|
| + "range": {
|
| + "$ref": "Range",
|
| + "description": "The genomic coordinate range spanned by this bucket."
|
| }
|
| },
|
| "type": "object"
|
| @@ -2399,42 +2375,25 @@
|
| },
|
| "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": {
|
| - "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"
|
| },
|
| - "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.",
|
| + "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"
|
| },
|
| - "name": {
|
| - "description": "The name of this reference, for example `22`.",
|
| - "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"
|
| @@ -2443,10 +2402,6 @@
|
| "description": "Metadata describes a single piece of variant call metadata.\nThese data include a top level key and either a single value string (value)\nor a list of key-value pairs (info.)\nValue and info are mutually exclusive.",
|
| "id": "VariantSetMetadata",
|
| "properties": {
|
| - "description": {
|
| - "description": "A textual description of this metadata.",
|
| - "type": "string"
|
| - },
|
| "info": {
|
| "additionalProperties": {
|
| "items": {
|
| @@ -2477,40 +2432,61 @@
|
| ],
|
| "type": "string"
|
| },
|
| - "number": {
|
| - "description": "The number of values that can be included in a field described by this\nmetadata.",
|
| + "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"
|
| + },
|
| + "number": {
|
| + "description": "The number of values that can be included in a field described by this\nmetadata.",
|
| + "type": "string"
|
| + },
|
| + "key": {
|
| + "description": "The top-level key.",
|
| + "type": "string"
|
| + },
|
| + "description": {
|
| + "description": "A textual description of this metadata.",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "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",
|
| + "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"
|
| },
|
| - "value": {
|
| - "description": "The value field for simple metadata",
|
| + "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": "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.",
|
| + "description": "The server-generated reference ID, unique across all references.",
|
| "type": "string"
|
| },
|
| - "key": {
|
| - "description": "The top-level key.",
|
| - "type": "string"
|
| - }
|
| - },
|
| - "type": "object"
|
| - },
|
| - "SearchVariantSetsRequest": {
|
| - "description": "The search variant sets request.",
|
| - "id": "SearchVariantSetsRequest",
|
| - "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.",
|
| + "length": {
|
| + "description": "The length of this reference's sequence.",
|
| + "format": "int64",
|
| "type": "string"
|
| },
|
| - "pageSize": {
|
| - "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024.",
|
| - "format": "int32",
|
| - "type": "integer"
|
| - },
|
| - "datasetIds": {
|
| - "description": "Exactly one dataset ID must be provided here. Only variant sets which\nbelong to this dataset will be returned.",
|
| + "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"
|
| },
|
| @@ -2522,6 +2498,17 @@
|
| "SearchReferenceSetsRequest": {
|
| "id": "SearchReferenceSetsRequest",
|
| "properties": {
|
| + "accessions": {
|
| + "description": "If present, return reference sets for which a prefix of any of\nsourceAccessions\nmatch any of these strings. Accession numbers typically have a main number\nand a version, for example `NC_000001.11`.",
|
| + "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. The maximum value is 4096.",
|
| "format": "int32",
|
| @@ -2537,17 +2524,6 @@
|
| "type": "string"
|
| },
|
| "type": "array"
|
| - },
|
| - "accessions": {
|
| - "description": "If present, return reference sets for which a prefix of any of\nsourceAccessions\nmatch any of these strings. Accession numbers typically have a main number\nand a version, for example `NC_000001.11`.",
|
| - "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"
|
| }
|
| },
|
| "type": "object"
|
| @@ -2566,18 +2542,6 @@
|
| "MergeVariantsRequest": {
|
| "id": "MergeVariantsRequest",
|
| "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.",
|
| - "type": "object"
|
| - },
|
| "variantSetId": {
|
| "description": "The destination variant set.",
|
| "type": "string"
|
| @@ -2588,23 +2552,18 @@
|
| "$ref": "Variant"
|
| },
|
| "type": "array"
|
| - }
|
| - },
|
| - "type": "object"
|
| - },
|
| - "BatchCreateAnnotationsRequest": {
|
| - "id": "BatchCreateAnnotationsRequest",
|
| - "properties": {
|
| - "annotations": {
|
| - "description": "The annotations to be created. At most 4096 can be specified in a single\nrequest.",
|
| - "items": {
|
| - "$ref": "Annotation"
|
| - },
|
| - "type": "array"
|
| },
|
| - "requestId": {
|
| - "description": "A unique request ID which enables the server to detect duplicated requests.\nIf provided, duplicated requests will result in the same response; if not\nprovided, duplicated requests may result in duplicated data. For a given\nannotation set, callers should not reuse `request_id`s when writing\ndifferent batches of annotations - behavior in this case is undefined.\nA common approach is to use a UUID. For batch jobs where worker crashes are\na possibility, consider using some unique variant of a worker or run ID.",
|
| - "type": "string"
|
| + "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.",
|
| + "type": "object"
|
| }
|
| },
|
| "type": "object"
|
| @@ -2613,6 +2572,23 @@
|
| "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": {
|
| + "duplicateFragment": {
|
| + "description": "The fragment is a PCR or optical duplicate (SAM flag 0x400).",
|
| + "type": "boolean"
|
| + },
|
| + "readNumber": {
|
| + "description": "The read number in sequencing. 0-based and less than numberReads. This\nfield replaces SAM flag 0x40 and 0x80.",
|
| + "format": "int32",
|
| + "type": "integer"
|
| + },
|
| + "alignedSequence": {
|
| + "description": "The bases of the read sequence contained in this alignment record,\n**without CIGAR operations applied** (equivalent to SEQ in SAM).\n`alignedSequence` and `alignedQuality` may be\nshorter than the full read sequence and quality. This will occur if the\nalignment is part of a chimeric alignment, or if the read was trimmed. When\nthis occurs, the CIGAR for this read will begin/end with a hard clip\noperator that will indicate the length of the excised sequence.",
|
| + "type": "string"
|
| + },
|
| + "readGroupId": {
|
| + "description": "The ID of the read group this read belongs to. A read belongs to exactly\none read group. This is a server-generated ID which is distinct from SAM's\nRG tag (for that value, see\nReadGroup.name).",
|
| + "type": "string"
|
| + },
|
| "nextMatePosition": {
|
| "$ref": "Position",
|
| "description": "The mapping of the primary alignment of the\n`(readNumber+1)%numberReads` read in the fragment. It replaces\nmate position and mate strand in SAM."
|
| @@ -2656,15 +2632,15 @@
|
| "$ref": "LinearAlignment",
|
| "description": "The linear alignment for this alignment record. This field is null for\nunmapped reads."
|
| },
|
| - "id": {
|
| - "description": "The server-generated read ID, unique across all reads. This is different\nfrom the `fragmentName`.",
|
| - "type": "string"
|
| - },
|
| "numberReads": {
|
| "description": "The number of reads in the fragment (extension to SAM flag 0x1).",
|
| "format": "int32",
|
| "type": "integer"
|
| },
|
| + "id": {
|
| + "description": "The server-generated read ID, unique across all reads. This is different\nfrom the `fragmentName`.",
|
| + "type": "string"
|
| + },
|
| "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"
|
| @@ -2676,69 +2652,23 @@
|
| "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"
|
| - },
|
| - "readNumber": {
|
| - "description": "The read number in sequencing. 0-based and less than numberReads. This\nfield replaces SAM flag 0x40 and 0x80.",
|
| - "format": "int32",
|
| - "type": "integer"
|
| - },
|
| - "readGroupId": {
|
| - "description": "The ID of the read group this read belongs to. A read belongs to exactly\none read group. This is a server-generated ID which is distinct from SAM's\nRG tag (for that value, see\nReadGroup.name).",
|
| - "type": "string"
|
| - },
|
| - "alignedSequence": {
|
| - "description": "The bases of the read sequence contained in this alignment record,\n**without CIGAR operations applied** (equivalent to SEQ in SAM).\n`alignedSequence` and `alignedQuality` may be\nshorter than the full read sequence and quality. This will occur if the\nalignment is part of a chimeric alignment, or if the read was trimmed. When\nthis occurs, the CIGAR for this read will begin/end with a hard clip\noperator that will indicate the length of the excised sequence.",
|
| - "type": "string"
|
| }
|
| },
|
| "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",
|
| + "BatchCreateAnnotationsRequest": {
|
| + "id": "BatchCreateAnnotationsRequest",
|
| "properties": {
|
| - "referenceIds": {
|
| - "description": "The IDs of the reference objects that are part of this set.\n`Reference.md5checksum` must be unique within this set.",
|
| - "items": {
|
| - "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"
|
| - },
|
| - "description": {
|
| - "description": "Free text description of this reference set.",
|
| + "requestId": {
|
| + "description": "A unique request ID which enables the server to detect duplicated requests.\nIf provided, duplicated requests will result in the same response; if not\nprovided, duplicated requests may result in duplicated data. For a given\nannotation set, callers should not reuse `request_id`s when writing\ndifferent batches of annotations - behavior in this case is undefined.\nA common approach is to use a UUID. For batch jobs where worker crashes are\na possibility, consider using some unique variant of a worker or run ID.",
|
| "type": "string"
|
| },
|
| - "sourceAccessions": {
|
| - "description": "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally\nwith a version number, for example `NC_000001.11`.",
|
| + "annotations": {
|
| + "description": "The annotations to be created. At most 4096 can be specified in a single\nrequest.",
|
| "items": {
|
| - "type": "string"
|
| + "$ref": "Annotation"
|
| },
|
| "type": "array"
|
| - },
|
| - "ncbiTaxonId": {
|
| - "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)\nindicating the species which this reference set is intended to model. Note\nthat contained references may specify a different `ncbiTaxonId`, as\nassemblies may contain reference sequences which do not belong to the\nmodeled species, for example EBV in a human reference genome.",
|
| - "format": "int32",
|
| - "type": "integer"
|
| - },
|
| - "sourceUri": {
|
| - "description": "The URI from which the references were obtained.",
|
| - "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| @@ -2786,10 +2716,60 @@
|
| },
|
| "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"
|
| + },
|
| + "sourceAccessions": {
|
| + "description": "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally\nwith a version number, for example `NC_000001.11`.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "sourceUri": {
|
| + "description": "The URI from which the references were obtained.",
|
| + "type": "string"
|
| + },
|
| + "ncbiTaxonId": {
|
| + "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)\nindicating the species which this reference set is intended to model. Note\nthat contained references may specify a different `ncbiTaxonId`, as\nassemblies may contain reference sequences which do not belong to the\nmodeled species, for example EBV in a human reference genome.",
|
| + "format": "int32",
|
| + "type": "integer"
|
| + },
|
| + "referenceIds": {
|
| + "description": "The IDs of the reference objects that are part of this set.\n`Reference.md5checksum` must be unique within this set.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| "Transcript": {
|
| "description": "A transcript represents the assertion that a particular region of the\nreference genome may be transcribed as RNA.",
|
| "id": "Transcript",
|
| "properties": {
|
| + "geneId": {
|
| + "description": "The annotation ID of the gene from which this transcript is transcribed.",
|
| + "type": "string"
|
| + },
|
| "exons": {
|
| "description": "The <a href=\"http://en.wikipedia.org/wiki/Exon\">exons</a> that compose\nthis transcript. This field should be unset for genomes where transcript\nsplicing does not occur, for example prokaryotes.\n\nIntrons are regions of the transcript that are not included in the\nspliced RNA product. Though not explicitly modeled here, intron ranges can\nbe deduced; all regions of this transcript that are not exons are introns.\n\nExonic sequences do not necessarily code for a translational product\n(amino acids). Only the regions of exons bounded by the\ncodingSequence correspond\nto coding DNA sequence.\n\nExons are ordered by start position and may not overlap.",
|
| "items": {
|
| @@ -2800,10 +2780,6 @@
|
| "codingSequence": {
|
| "$ref": "CodingSequence",
|
| "description": "The range of the coding sequence for this transcript, if any. To determine\nthe exact ranges of coding sequence, intersect this range with those of the\nexons, if any. If there are any\nexons, the\ncodingSequence must start\nand end within them.\n\nNote that in some cases, the reference genome will not exactly match the\nobserved mRNA transcript e.g. due to variance in the source genome from\nreference. In these cases,\nexon.frame will not necessarily\nmatch the expected reference reading frame and coding exon reference bases\ncannot necessarily be concatenated to produce the original transcript mRNA."
|
| - },
|
| - "geneId": {
|
| - "description": "The annotation ID of the gene from which this transcript is transcribed.",
|
| - "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| @@ -2812,14 +2788,14 @@
|
| "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": {
|
| - "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"
|
| },
|
| + "datasetId": {
|
| + "description": "The dataset to which this annotation set belongs.",
|
| + "type": "string"
|
| + },
|
| "name": {
|
| "description": "The display name for this annotation set.",
|
| "type": "string"
|
| @@ -2828,6 +2804,16 @@
|
| "description": "The ID of the reference set that defines the coordinate space for this\nset's annotations.",
|
| "type": "string"
|
| },
|
| + "info": {
|
| + "additionalProperties": {
|
| + "items": {
|
| + "type": "any"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "description": "A map of additional read alignment information. This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).",
|
| + "type": "object"
|
| + },
|
| "type": {
|
| "description": "The type of annotations contained within this set.",
|
| "enum": [
|
| @@ -2846,16 +2832,6 @@
|
| ],
|
| "type": "string"
|
| },
|
| - "info": {
|
| - "additionalProperties": {
|
| - "items": {
|
| - "type": "any"
|
| - },
|
| - "type": "array"
|
| - },
|
| - "description": "A map of additional read alignment information. This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).",
|
| - "type": "object"
|
| - },
|
| "id": {
|
| "description": "The server-generated annotation set ID, unique across all annotation sets.",
|
| "type": "string"
|
| @@ -2917,28 +2893,6 @@
|
| },
|
| "type": "object"
|
| },
|
| - "ExportReadGroupSetRequest": {
|
| - "description": "The read group set export request.",
|
| - "id": "ExportReadGroupSetRequest",
|
| - "properties": {
|
| - "projectId": {
|
| - "description": "Required. The Google Cloud project ID that owns this\nexport. The caller must have WRITE access to this project.",
|
| - "type": "string"
|
| - },
|
| - "exportUri": {
|
| - "description": "Required. A Google Cloud Storage URI for the exported BAM file.\nThe currently authenticated user must have write access to the new file.\nAn error will be returned if the URI already contains data.",
|
| - "type": "string"
|
| - },
|
| - "referenceNames": {
|
| - "description": "The reference names to export. If this is not specified, all reference\nsequences, including unmapped reads, are exported.\nUse `*` to export only unmapped reads.",
|
| - "items": {
|
| - "type": "string"
|
| - },
|
| - "type": "array"
|
| - }
|
| - },
|
| - "type": "object"
|
| - },
|
| "Exon": {
|
| "id": "Exon",
|
| "properties": {
|
| @@ -2960,10 +2914,36 @@
|
| },
|
| "type": "object"
|
| },
|
| + "ExportReadGroupSetRequest": {
|
| + "description": "The read group set export request.",
|
| + "id": "ExportReadGroupSetRequest",
|
| + "properties": {
|
| + "exportUri": {
|
| + "description": "Required. A Google Cloud Storage URI for the exported BAM file.\nThe currently authenticated user must have write access to the new file.\nAn error will be returned if the URI already contains data.",
|
| + "type": "string"
|
| + },
|
| + "referenceNames": {
|
| + "description": "The reference names to export. If this is not specified, all reference\nsequences, including unmapped reads, are exported.\nUse `*` to export only unmapped reads.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "projectId": {
|
| + "description": "Required. The Google Cloud project ID that owns this\nexport. The caller must have WRITE access to this project.",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "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": {
|
| + "name": {
|
| + "description": "The call set name.",
|
| + "type": "string"
|
| + },
|
| "info": {
|
| "additionalProperties": {
|
| "items": {
|
| @@ -2993,10 +2973,6 @@
|
| "sampleId": {
|
| "description": "The sample ID this call set corresponds to.",
|
| "type": "string"
|
| - },
|
| - "name": {
|
| - "description": "The call set name.",
|
| - "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| @@ -3066,6 +3042,28 @@
|
| },
|
| "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"
|
| + },
|
| + "type": "array"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| "VariantAnnotation": {
|
| "id": "VariantAnnotation",
|
| "properties": {
|
| @@ -3180,28 +3178,6 @@
|
| },
|
| "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"
|
| - },
|
| - "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"
|
| - }
|
| - },
|
| - "type": "object"
|
| - },
|
| "ExportVariantSetRequest": {
|
| "description": "The variant data export request.",
|
| "id": "ExportVariantSetRequest",
|
| @@ -3243,11 +3219,6 @@
|
| "SearchAnnotationsRequest": {
|
| "id": "SearchAnnotationsRequest",
|
| "properties": {
|
| - "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"
|
| @@ -3276,6 +3247,11 @@
|
| "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"
|
| @@ -3304,32 +3280,29 @@
|
| "CodingSequence": {
|
| "id": "CodingSequence",
|
| "properties": {
|
| - "end": {
|
| - "description": "The end of the coding sequence on this annotation's reference sequence,\n0-based exclusive. Note that this position is relative to the reference\nstart, and *not* the containing annotation start.",
|
| + "start": {
|
| + "description": "The start of the coding sequence on this annotation's reference sequence,\n0-based inclusive. Note that this position is relative to the reference\nstart, and *not* the containing annotation start.",
|
| "format": "int64",
|
| "type": "string"
|
| },
|
| - "start": {
|
| - "description": "The start of the coding sequence on this annotation's reference sequence,\n0-based inclusive. Note that this position is relative to the reference\nstart, and *not* the containing annotation start.",
|
| + "end": {
|
| + "description": "The end of the coding sequence on this annotation's reference sequence,\n0-based exclusive. Note that this position is relative to the reference\nstart, and *not* the containing annotation start.",
|
| "format": "int64",
|
| "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| },
|
| - "SearchReferencesResponse": {
|
| - "id": "SearchReferencesResponse",
|
| + "TestIamPermissionsResponse": {
|
| + "description": "Response message for `TestIamPermissions` method.",
|
| + "id": "TestIamPermissionsResponse",
|
| "properties": {
|
| - "references": {
|
| - "description": "The matching references.",
|
| + "permissions": {
|
| + "description": "A subset of `TestPermissionsRequest.permissions` that the caller is\nallowed.",
|
| "items": {
|
| - "$ref": "Reference"
|
| + "type": "string"
|
| },
|
| "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"
|
| @@ -3340,16 +3313,19 @@
|
| "properties": {},
|
| "type": "object"
|
| },
|
| - "TestIamPermissionsResponse": {
|
| - "description": "Response message for `TestIamPermissions` method.",
|
| - "id": "TestIamPermissionsResponse",
|
| + "SearchReferencesResponse": {
|
| + "id": "SearchReferencesResponse",
|
| "properties": {
|
| - "permissions": {
|
| - "description": "A subset of `TestPermissionsRequest.permissions` that the caller is\nallowed.",
|
| + "references": {
|
| + "description": "The matching references.",
|
| "items": {
|
| - "type": "string"
|
| + "$ref": "Reference"
|
| },
|
| "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"
|
| @@ -3357,15 +3333,6 @@
|
| "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": {
|
| @@ -3401,6 +3368,15 @@
|
| "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"
|
| @@ -3409,16 +3385,16 @@
|
| "description": "The read group set search response.",
|
| "id": "SearchReadGroupSetsResponse",
|
| "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"
|
| - },
|
| "readGroupSets": {
|
| "description": "The list of matching read group sets.",
|
| "items": {
|
| "$ref": "ReadGroupSet"
|
| },
|
| "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"
|
| @@ -3483,6 +3459,10 @@
|
| "description": "A Dataset is a collection of genomic data.\n\nFor more genomics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
|
| "id": "Dataset",
|
| "properties": {
|
| + "name": {
|
| + "description": "The dataset name.",
|
| + "type": "string"
|
| + },
|
| "projectId": {
|
| "description": "The Google Cloud project ID that this dataset belongs to.",
|
| "type": "string"
|
| @@ -3495,10 +3475,6 @@
|
| "description": "The time this dataset was created, in seconds from the epoch.",
|
| "format": "google-datetime",
|
| "type": "string"
|
| - },
|
| - "name": {
|
| - "description": "The dataset name.",
|
| - "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| @@ -3578,14 +3554,6 @@
|
| "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": {
|
| - "datasetId": {
|
| - "description": "The dataset to which this read group set belongs.",
|
| - "type": "string"
|
| - },
|
| - "filename": {
|
| - "description": "The filename of the original source file for this read group set, if any.",
|
| - "type": "string"
|
| - },
|
| "readGroups": {
|
| "description": "The read groups in this set. There are typically 1-10 read groups in a read\ngroup set.",
|
| "items": {
|
| @@ -3593,6 +3561,10 @@
|
| },
|
| "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"
|
| @@ -3614,6 +3586,10 @@
|
| "id": {
|
| "description": "The server-generated read group set ID, unique for all read group sets.",
|
| "type": "string"
|
| + },
|
| + "datasetId": {
|
| + "description": "The dataset to which this read group set belongs.",
|
| + "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| @@ -3622,16 +3598,16 @@
|
| "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": {
|
| "$ref": "VariantSet"
|
| },
|
| "type": "array"
|
| - },
|
| - "nextPageToken": {
|
| - "description": "The continuation token, which is used to page through large result sets.\nProvide this value in a subsequent request to return the next page of\nresults. This field will be empty if there aren't any additional results.",
|
| - "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| @@ -3679,16 +3655,16 @@
|
| "SearchReferenceSetsResponse": {
|
| "id": "SearchReferenceSetsResponse",
|
| "properties": {
|
| + "nextPageToken": {
|
| + "description": "The continuation token, which is used to page through large result sets.\nProvide this value in a subsequent request to return the next page of\nresults. This field will be empty if there aren't any additional results.",
|
| + "type": "string"
|
| + },
|
| "referenceSets": {
|
| "description": "The matching references sets.",
|
| "items": {
|
| "$ref": "ReferenceSet"
|
| },
|
| "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"
|
| @@ -3724,6 +3700,13 @@
|
| "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"
|
| @@ -3745,13 +3728,30 @@
|
| "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"
|
| - },
|
| - "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.",
|
| + }
|
| + },
|
| + "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": {
|
| - "type": "string"
|
| + "$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",
|
| + "type": "string"
|
| + },
|
| + "version": {
|
| + "description": "Version of the `Policy`. The default version is 0.",
|
| + "format": "int32",
|
| + "type": "integer"
|
| }
|
| },
|
| "type": "object"
|
|
|
Chromium Code Reviews
Issue 2734843002:
Api-roll 46: 2017-03-06 (Closed)
