| Index: discovery/googleapis_beta/genomics__v1beta2.json
|
| diff --git a/discovery/googleapis_beta/genomics__v1beta.json b/discovery/googleapis_beta/genomics__v1beta2.json
|
| similarity index 61%
|
| copy from discovery/googleapis_beta/genomics__v1beta.json
|
| copy to discovery/googleapis_beta/genomics__v1beta2.json
|
| index 18b851ac696b6e928f260f49ef1783c7bc7f2a05..425b981703d0c5e52cd5eb1609ae57543722622a 100644
|
| --- a/discovery/googleapis_beta/genomics__v1beta.json
|
| +++ b/discovery/googleapis_beta/genomics__v1beta2.json
|
| @@ -17,18 +17,18 @@
|
| }
|
| }
|
| },
|
| - "basePath": "/genomics/v1beta/",
|
| - "baseUrl": "https://www.googleapis.com/genomics/v1beta/",
|
| + "basePath": "/genomics/v1beta2/",
|
| + "baseUrl": "https://www.googleapis.com/genomics/v1beta2/",
|
| "batchPath": "batch",
|
| "description": "Provides access to Genomics data.",
|
| "discoveryVersion": "v1",
|
| - "documentationLink": "https://developers.google.com/genomics/v1beta/reference",
|
| - "etag": "\"l66ggWbucbkBw9Lpos72oziyefE/QFkFkv2LMi0ob1p4dyYfQYJIVYc\"",
|
| + "documentationLink": "https://developers.google.com/genomics/v1beta2/reference",
|
| + "etag": "\"l66ggWbucbkBw9Lpos72oziyefE/EKP2HqTiCFaMtGY4TKqgoDAIFBQ\"",
|
| "icons": {
|
| "x16": "http://www.google.com/images/icons/product/search-16.gif",
|
| "x32": "http://www.google.com/images/icons/product/search-32.gif"
|
| },
|
| - "id": "genomics:v1beta",
|
| + "id": "genomics:v1beta2",
|
| "kind": "discovery#restDescription",
|
| "name": "genomics",
|
| "ownerDomain": "google.com",
|
| @@ -80,46 +80,6 @@
|
| },
|
| "protocol": "rest",
|
| "resources": {
|
| - "beacons": {
|
| - "methods": {
|
| - "get": {
|
| - "description": "This is an experimental API that provides a Global Alliance for Genomics and Health Beacon. It may change at any time.",
|
| - "httpMethod": "GET",
|
| - "id": "genomics.beacons.get",
|
| - "parameterOrder": [
|
| - "variantSetId"
|
| - ],
|
| - "parameters": {
|
| - "allele": {
|
| - "description": "Required. The allele to look for ('A', 'C', 'G' or 'T').",
|
| - "location": "query",
|
| - "type": "string"
|
| - },
|
| - "position": {
|
| - "description": "Required. The 0-based position to query.",
|
| - "format": "int64",
|
| - "location": "query",
|
| - "type": "string"
|
| - },
|
| - "referenceName": {
|
| - "description": "Required. The reference to query over.",
|
| - "location": "query",
|
| - "type": "string"
|
| - },
|
| - "variantSetId": {
|
| - "description": "The ID of the variant set to query over. It must be public. Private variant sets will return an unauthorized exception.",
|
| - "location": "path",
|
| - "required": true,
|
| - "type": "string"
|
| - }
|
| - },
|
| - "path": "beacons/{variantSetId}",
|
| - "response": {
|
| - "$ref": "Beacon"
|
| - }
|
| - }
|
| - }
|
| - },
|
| "callsets": {
|
| "methods": {
|
| "create": {
|
| @@ -146,7 +106,7 @@
|
| ],
|
| "parameters": {
|
| "callSetId": {
|
| - "description": "The ID of the callset to be deleted.",
|
| + "description": "The ID of the call set to be deleted.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| @@ -166,7 +126,7 @@
|
| ],
|
| "parameters": {
|
| "callSetId": {
|
| - "description": "The ID of the callset.",
|
| + "description": "The ID of the call set.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| @@ -190,7 +150,7 @@
|
| ],
|
| "parameters": {
|
| "callSetId": {
|
| - "description": "The ID of the callset to be updated.",
|
| + "description": "The ID of the call set to be updated.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| @@ -208,7 +168,7 @@
|
| ]
|
| },
|
| "search": {
|
| - "description": "Gets a list of call sets matching the criteria.",
|
| + "description": "Gets a list of call sets matching the criteria.\n\nImplements GlobalAllianceApi.searchCallSets.",
|
| "httpMethod": "POST",
|
| "id": "genomics.callsets.search",
|
| "path": "callsets/search",
|
| @@ -232,7 +192,7 @@
|
| ],
|
| "parameters": {
|
| "callSetId": {
|
| - "description": "The ID of the callset to be updated.",
|
| + "description": "The ID of the call set to be updated.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| @@ -317,19 +277,19 @@
|
| "httpMethod": "GET",
|
| "id": "genomics.datasets.list",
|
| "parameters": {
|
| - "maxResults": {
|
| + "pageSize": {
|
| "default": "50",
|
| "description": "The maximum number of results returned by this request.",
|
| - "format": "uint64",
|
| + "format": "int32",
|
| "location": "query",
|
| - "type": "string"
|
| + "type": "integer"
|
| },
|
| "pageToken": {
|
| "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
|
| "location": "query",
|
| "type": "string"
|
| },
|
| - "projectId": {
|
| + "projectNumber": {
|
| "description": "Only return datasets which belong to this Google Developers Console project. Only accepts project numbers. Returns all public projects if no project number is specified.",
|
| "format": "int64",
|
| "location": "query",
|
| @@ -510,58 +470,68 @@
|
| }
|
| }
|
| },
|
| - "reads": {
|
| + "readgroupsets": {
|
| "methods": {
|
| - "search": {
|
| - "description": "Gets a list of reads for one or more readsets. Reads search operates over a genomic coordinate space of reference sequence & position defined over the reference sequences to which the requested readsets are aligned. If a target positional range is specified, search returns all reads whose alignment to the reference genome overlap the range. A query which specifies only readset IDs yields all reads in those readsets, including unmapped reads. All reads returned (including reads on subsequent pages) are ordered by genomic coordinate (reference sequence & position). Reads with equivalent genomic coordinates are returned in a deterministic order.",
|
| + "align": {
|
| + "description": "Aligns read data from existing read group sets or files from Google Cloud Storage. See the alignment and variant calling documentation for more details.",
|
| "httpMethod": "POST",
|
| - "id": "genomics.reads.search",
|
| - "path": "reads/search",
|
| + "id": "genomics.readgroupsets.align",
|
| + "path": "readgroupsets/align",
|
| "request": {
|
| - "$ref": "SearchReadsRequest"
|
| + "$ref": "AlignReadGroupSetsRequest"
|
| },
|
| "response": {
|
| - "$ref": "SearchReadsResponse"
|
| + "$ref": "AlignReadGroupSetsResponse"
|
| },
|
| "scopes": [
|
| - "https://www.googleapis.com/auth/genomics",
|
| - "https://www.googleapis.com/auth/genomics.readonly"
|
| + "https://www.googleapis.com/auth/genomics"
|
| ]
|
| - }
|
| - }
|
| - },
|
| - "readsets": {
|
| - "methods": {
|
| + },
|
| + "call": {
|
| + "description": "Calls variants on read data from existing read group sets or files from Google Cloud Storage. See the alignment and variant calling documentation for more details.",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.readgroupsets.call",
|
| + "path": "readgroupsets/call",
|
| + "request": {
|
| + "$ref": "CallReadGroupSetsRequest"
|
| + },
|
| + "response": {
|
| + "$ref": "CallReadGroupSetsResponse"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/genomics"
|
| + ]
|
| + },
|
| "delete": {
|
| - "description": "Deletes a readset.",
|
| + "description": "Deletes a read group set.",
|
| "httpMethod": "DELETE",
|
| - "id": "genomics.readsets.delete",
|
| + "id": "genomics.readgroupsets.delete",
|
| "parameterOrder": [
|
| - "readsetId"
|
| + "readGroupSetId"
|
| ],
|
| "parameters": {
|
| - "readsetId": {
|
| - "description": "The ID of the readset to be deleted. The caller must have WRITE permissions to the dataset associated with this readset.",
|
| + "readGroupSetId": {
|
| + "description": "The ID of the read group set to be deleted. The caller must have WRITE permissions to the dataset associated with this read group set.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "readsets/{readsetId}",
|
| + "path": "readgroupsets/{readGroupSetId}",
|
| "scopes": [
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| },
|
| "export": {
|
| - "description": "Exports readsets to a BAM file in Google Cloud Storage. Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. In particular, comments in the input file header will not be preserved, and some custom tags will be converted to strings.",
|
| + "description": "Exports read group sets to a BAM file in Google Cloud Storage.\n\nNote that currently there may be some differences between exported BAM files and the original BAM file at the time of import. In particular, comments in the input file header will not be preserved, and some custom tags will be converted to strings.",
|
| "httpMethod": "POST",
|
| - "id": "genomics.readsets.export",
|
| - "path": "readsets/export",
|
| + "id": "genomics.readgroupsets.export",
|
| + "path": "readgroupsets/export",
|
| "request": {
|
| - "$ref": "ExportReadsetsRequest"
|
| + "$ref": "ExportReadGroupSetsRequest"
|
| },
|
| "response": {
|
| - "$ref": "ExportReadsetsResponse"
|
| + "$ref": "ExportReadGroupSetsResponse"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/devstorage.read_write",
|
| @@ -569,23 +539,23 @@
|
| ]
|
| },
|
| "get": {
|
| - "description": "Gets a readset by ID.",
|
| + "description": "Gets a read group set by ID.",
|
| "httpMethod": "GET",
|
| - "id": "genomics.readsets.get",
|
| + "id": "genomics.readgroupsets.get",
|
| "parameterOrder": [
|
| - "readsetId"
|
| + "readGroupSetId"
|
| ],
|
| "parameters": {
|
| - "readsetId": {
|
| - "description": "The ID of the readset.",
|
| + "readGroupSetId": {
|
| + "description": "The ID of the read group set.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "readsets/{readsetId}",
|
| + "path": "readgroupsets/{readGroupSetId}",
|
| "response": {
|
| - "$ref": "Readset"
|
| + "$ref": "ReadGroupSet"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/genomics",
|
| @@ -593,15 +563,15 @@
|
| ]
|
| },
|
| "import": {
|
| - "description": "Creates readsets by asynchronously importing the provided information. Note that currently comments in the input file header are not imported and some custom tags will be converted to strings, rather than preserving tag types. The caller must have WRITE permissions to the dataset.",
|
| + "description": "Creates read group sets by asynchronously importing the provided information.\n\nNote that currently comments in the input file header are not imported and some custom tags will be converted to strings, rather than preserving tag types. The caller must have WRITE permissions to the dataset.",
|
| "httpMethod": "POST",
|
| - "id": "genomics.readsets.import",
|
| - "path": "readsets/import",
|
| + "id": "genomics.readgroupsets.import",
|
| + "path": "readgroupsets/import",
|
| "request": {
|
| - "$ref": "ImportReadsetsRequest"
|
| + "$ref": "ImportReadGroupSetsRequest"
|
| },
|
| "response": {
|
| - "$ref": "ImportReadsetsResponse"
|
| + "$ref": "ImportReadGroupSetsResponse"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/devstorage.read_write",
|
| @@ -609,41 +579,41 @@
|
| ]
|
| },
|
| "patch": {
|
| - "description": "Updates a readset. This method supports patch semantics.",
|
| + "description": "Updates a read group set. This method supports patch semantics.",
|
| "httpMethod": "PATCH",
|
| - "id": "genomics.readsets.patch",
|
| + "id": "genomics.readgroupsets.patch",
|
| "parameterOrder": [
|
| - "readsetId"
|
| + "readGroupSetId"
|
| ],
|
| "parameters": {
|
| - "readsetId": {
|
| - "description": "The ID of the readset to be updated. The caller must have WRITE permissions to the dataset associated with this readset.",
|
| + "readGroupSetId": {
|
| + "description": "The ID of the read group set to be updated. The caller must have WRITE permissions to the dataset associated with this read group set.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "readsets/{readsetId}",
|
| + "path": "readgroupsets/{readGroupSetId}",
|
| "request": {
|
| - "$ref": "Readset"
|
| + "$ref": "ReadGroupSet"
|
| },
|
| "response": {
|
| - "$ref": "Readset"
|
| + "$ref": "ReadGroupSet"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| },
|
| "search": {
|
| - "description": "Gets a list of readsets matching the criteria.",
|
| + "description": "Searches for read group sets matching the criteria.\n\nImplements GlobalAllianceApi.searchReadGroupSets.",
|
| "httpMethod": "POST",
|
| - "id": "genomics.readsets.search",
|
| - "path": "readsets/search",
|
| + "id": "genomics.readgroupsets.search",
|
| + "path": "readgroupsets/search",
|
| "request": {
|
| - "$ref": "SearchReadsetsRequest"
|
| + "$ref": "SearchReadGroupSetsRequest"
|
| },
|
| "response": {
|
| - "$ref": "SearchReadsetsResponse"
|
| + "$ref": "SearchReadGroupSetsResponse"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/genomics",
|
| @@ -651,26 +621,26 @@
|
| ]
|
| },
|
| "update": {
|
| - "description": "Updates a readset.",
|
| + "description": "Updates a read group set.",
|
| "httpMethod": "PUT",
|
| - "id": "genomics.readsets.update",
|
| + "id": "genomics.readgroupsets.update",
|
| "parameterOrder": [
|
| - "readsetId"
|
| + "readGroupSetId"
|
| ],
|
| "parameters": {
|
| - "readsetId": {
|
| - "description": "The ID of the readset to be updated. The caller must have WRITE permissions to the dataset associated with this readset.",
|
| + "readGroupSetId": {
|
| + "description": "The ID of the read group set to be updated. The caller must have WRITE permissions to the dataset associated with this read group set.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| }
|
| },
|
| - "path": "readsets/{readsetId}",
|
| + "path": "readgroupsets/{readGroupSetId}",
|
| "request": {
|
| - "$ref": "Readset"
|
| + "$ref": "ReadGroupSet"
|
| },
|
| "response": {
|
| - "$ref": "Readset"
|
| + "$ref": "ReadGroupSet"
|
| },
|
| "scopes": [
|
| "https://www.googleapis.com/auth/genomics"
|
| @@ -681,56 +651,56 @@
|
| "coveragebuckets": {
|
| "methods": {
|
| "list": {
|
| - "description": "Lists fixed width coverage buckets for a readset, each of which correspond to a range of a reference sequence. Each bucket summarizes coverage information across its corresponding genomic range. Coverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at various bucket widths, enabling various coverage \"zoom levels\". The caller must have READ permissions for the target readset.",
|
| + "description": "Lists fixed width coverage buckets for a read group set, each of which correspond to a range of a reference sequence. Each bucket summarizes coverage information across its corresponding genomic range.\n\nCoverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several precomputed bucket widths, enabling retrieval of various coverage 'zoom levels'. The caller must have READ permissions for the target read group set.",
|
| "httpMethod": "GET",
|
| - "id": "genomics.readsets.coveragebuckets.list",
|
| + "id": "genomics.readgroupsets.coveragebuckets.list",
|
| "parameterOrder": [
|
| - "readsetId"
|
| + "readGroupSetId"
|
| ],
|
| "parameters": {
|
| - "maxResults": {
|
| + "pageSize": {
|
| "default": "1024",
|
| "description": "The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 2048.",
|
| - "format": "uint64",
|
| + "format": "int32",
|
| "location": "query",
|
| - "type": "string"
|
| + "type": "integer"
|
| },
|
| "pageToken": {
|
| "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
|
| "location": "query",
|
| "type": "string"
|
| },
|
| - "range.sequenceEnd": {
|
| - "description": "The end position of the range on the reference, 1-based exclusive. If specified, sequenceName must also be specified.",
|
| - "format": "uint64",
|
| + "range.end": {
|
| + "description": "The end position of the range on the reference, 0-based exclusive. If specified, referenceName must also be specified.",
|
| + "format": "int64",
|
| "location": "query",
|
| "type": "string"
|
| },
|
| - "range.sequenceName": {
|
| + "range.referenceName": {
|
| "description": "The reference sequence name, for example chr1, 1, or chrX.",
|
| "location": "query",
|
| "type": "string"
|
| },
|
| - "range.sequenceStart": {
|
| - "description": "The start position of the range on the reference, 1-based inclusive. If specified, sequenceName must also be specified.",
|
| - "format": "uint64",
|
| + "range.start": {
|
| + "description": "The start position of the range on the reference, 0-based inclusive. If specified, referenceName must also be specified.",
|
| + "format": "int64",
|
| "location": "query",
|
| "type": "string"
|
| },
|
| - "readsetId": {
|
| - "description": "Required. The ID of the readset over which coverage is requested.",
|
| + "readGroupSetId": {
|
| + "description": "Required. The ID of the read group set over which coverage is requested.",
|
| "location": "path",
|
| "required": true,
|
| "type": "string"
|
| },
|
| "targetBucketWidth": {
|
| "description": "The desired width of each reported coverage bucket in base pairs. This will be rounded down to the nearest precomputed bucket width; the value of which is returned as bucketWidth in the response. Defaults to infinity (each bucket spans an entire reference sequence) or the length of the target range, if specified. The smallest precomputed bucketWidth is currently 2048 base pairs; this is subject to change.",
|
| - "format": "uint64",
|
| + "format": "int64",
|
| "location": "query",
|
| "type": "string"
|
| }
|
| },
|
| - "path": "readsets/{readsetId}/coveragebuckets",
|
| + "path": "readgroupsets/{readGroupSetId}/coveragebuckets",
|
| "response": {
|
| "$ref": "ListCoverageBucketsResponse"
|
| },
|
| @@ -743,6 +713,168 @@
|
| }
|
| }
|
| },
|
| + "reads": {
|
| + "methods": {
|
| + "search": {
|
| + "description": "Gets a list of reads for one or more read group sets. Reads search operates over a genomic coordinate space of reference sequence & position defined over the reference sequences to which the requested read group sets are aligned.\n\nIf a target positional range is specified, search returns all reads whose alignment to the reference genome overlap the range. A query which specifies only read group set IDs yields all reads in those read group sets, including unmapped reads.\n\nAll reads returned (including reads on subsequent pages) are ordered by genomic coordinate (reference sequence & position). Reads with equivalent genomic coordinates are returned in a deterministic order.\n\nImplements GlobalAllianceApi.searchReads.",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.reads.search",
|
| + "path": "reads/search",
|
| + "request": {
|
| + "$ref": "SearchReadsRequest"
|
| + },
|
| + "response": {
|
| + "$ref": "SearchReadsResponse"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| + ]
|
| + }
|
| + }
|
| + },
|
| + "references": {
|
| + "methods": {
|
| + "get": {
|
| + "description": "Gets a reference.\n\nImplements GlobalAllianceApi.getReference.",
|
| + "httpMethod": "GET",
|
| + "id": "genomics.references.get",
|
| + "parameterOrder": [
|
| + "referenceId"
|
| + ],
|
| + "parameters": {
|
| + "referenceId": {
|
| + "description": "The ID of the reference.",
|
| + "location": "path",
|
| + "required": true,
|
| + "type": "string"
|
| + }
|
| + },
|
| + "path": "references/{referenceId}",
|
| + "response": {
|
| + "$ref": "Reference"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| + ]
|
| + },
|
| + "search": {
|
| + "description": "Searches for references which match the given criteria.\n\nImplements GlobalAllianceApi.searchReferences.",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.references.search",
|
| + "path": "references/search",
|
| + "request": {
|
| + "$ref": "SearchReferencesRequest"
|
| + },
|
| + "response": {
|
| + "$ref": "SearchReferencesResponse"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| + ]
|
| + }
|
| + },
|
| + "resources": {
|
| + "bases": {
|
| + "methods": {
|
| + "list": {
|
| + "description": "Lists the bases in a reference, optionally restricted to a range.\n\nImplements GlobalAllianceApi.getReferenceBases.",
|
| + "httpMethod": "GET",
|
| + "id": "genomics.references.bases.list",
|
| + "parameterOrder": [
|
| + "referenceId"
|
| + ],
|
| + "parameters": {
|
| + "end": {
|
| + "description": "The end position (0-based, exclusive) of this query. Defaults to the length of this reference.",
|
| + "format": "int64",
|
| + "location": "query",
|
| + "type": "string"
|
| + },
|
| + "pageSize": {
|
| + "default": "200000",
|
| + "description": "Specifies the maximum number of bases to return in a single page.",
|
| + "format": "int32",
|
| + "location": "query",
|
| + "type": "integer"
|
| + },
|
| + "pageToken": {
|
| + "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
|
| + "location": "query",
|
| + "type": "string"
|
| + },
|
| + "referenceId": {
|
| + "description": "The ID of the reference.",
|
| + "location": "path",
|
| + "required": true,
|
| + "type": "string"
|
| + },
|
| + "start": {
|
| + "description": "The start position (0-based) of this query. Defaults to 0.",
|
| + "format": "int64",
|
| + "location": "query",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "path": "references/{referenceId}/bases",
|
| + "response": {
|
| + "$ref": "ListBasesResponse"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| + ]
|
| + }
|
| + }
|
| + }
|
| + }
|
| + },
|
| + "referencesets": {
|
| + "methods": {
|
| + "get": {
|
| + "description": "Gets a reference set.\n\nImplements GlobalAllianceApi.getReferenceSet.",
|
| + "httpMethod": "GET",
|
| + "id": "genomics.referencesets.get",
|
| + "parameterOrder": [
|
| + "referenceSetId"
|
| + ],
|
| + "parameters": {
|
| + "referenceSetId": {
|
| + "description": "The ID of the reference set.",
|
| + "location": "path",
|
| + "required": true,
|
| + "type": "string"
|
| + }
|
| + },
|
| + "path": "referencesets/{referenceSetId}",
|
| + "response": {
|
| + "$ref": "ReferenceSet"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| + ]
|
| + },
|
| + "search": {
|
| + "description": "Searches for reference sets which match the given criteria.\n\nImplements GlobalAllianceApi.searchReferenceSets.",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.referencesets.search",
|
| + "path": "referencesets/search",
|
| + "request": {
|
| + "$ref": "SearchReferenceSetsRequest"
|
| + },
|
| + "response": {
|
| + "$ref": "SearchReferenceSetsResponse"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/genomics",
|
| + "https://www.googleapis.com/auth/genomics.readonly"
|
| + ]
|
| + }
|
| + }
|
| + },
|
| "variants": {
|
| "methods": {
|
| "create": {
|
| @@ -780,22 +912,6 @@
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| },
|
| - "export": {
|
| - "description": "Exports variant data to an external destination.",
|
| - "httpMethod": "POST",
|
| - "id": "genomics.variants.export",
|
| - "path": "variants/export",
|
| - "request": {
|
| - "$ref": "ExportVariantsRequest"
|
| - },
|
| - "response": {
|
| - "$ref": "ExportVariantsResponse"
|
| - },
|
| - "scopes": [
|
| - "https://www.googleapis.com/auth/bigquery",
|
| - "https://www.googleapis.com/auth/genomics"
|
| - ]
|
| - },
|
| "get": {
|
| "description": "Gets a variant by ID.",
|
| "httpMethod": "GET",
|
| @@ -820,24 +936,8 @@
|
| "https://www.googleapis.com/auth/genomics.readonly"
|
| ]
|
| },
|
| - "import": {
|
| - "description": "Creates variant data by asynchronously importing the provided information. The variants for import will be merged with any existing data and each other according to the behavior of mergeVariants. In particular, this means for merged VCF variants that have conflicting INFO fields, some data will be arbitrarily discarded. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a VariantSet.",
|
| - "httpMethod": "POST",
|
| - "id": "genomics.variants.import",
|
| - "path": "variants/import",
|
| - "request": {
|
| - "$ref": "ImportVariantsRequest"
|
| - },
|
| - "response": {
|
| - "$ref": "ImportVariantsResponse"
|
| - },
|
| - "scopes": [
|
| - "https://www.googleapis.com/auth/devstorage.read_write",
|
| - "https://www.googleapis.com/auth/genomics"
|
| - ]
|
| - },
|
| "search": {
|
| - "description": "Gets a list of variants matching the criteria.",
|
| + "description": "Gets a list of variants matching the criteria.\n\nImplements GlobalAllianceApi.searchVariants.",
|
| "httpMethod": "POST",
|
| "id": "genomics.variants.search",
|
| "path": "variants/search",
|
| @@ -902,6 +1002,33 @@
|
| "https://www.googleapis.com/auth/genomics"
|
| ]
|
| },
|
| + "export": {
|
| + "description": "Exports variant set data to an external destination.",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.variantsets.export",
|
| + "parameterOrder": [
|
| + "variantSetId"
|
| + ],
|
| + "parameters": {
|
| + "variantSetId": {
|
| + "description": "Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ access to this variant set.",
|
| + "location": "path",
|
| + "required": true,
|
| + "type": "string"
|
| + }
|
| + },
|
| + "path": "variantsets/{variantSetId}/export",
|
| + "request": {
|
| + "$ref": "ExportVariantSetRequest"
|
| + },
|
| + "response": {
|
| + "$ref": "ExportVariantSetResponse"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/bigquery",
|
| + "https://www.googleapis.com/auth/genomics"
|
| + ]
|
| + },
|
| "get": {
|
| "description": "Gets a variant set by ID.",
|
| "httpMethod": "GET",
|
| @@ -926,6 +1053,33 @@
|
| "https://www.googleapis.com/auth/genomics.readonly"
|
| ]
|
| },
|
| + "importVariants": {
|
| + "description": "Creates variant data by asynchronously importing the provided information.\n\nThe variants for import will be merged with any existing data and each other according to the behavior of mergeVariants. In particular, this means for merged VCF variants that have conflicting INFO fields, some data will be arbitrarily discarded. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set.",
|
| + "httpMethod": "POST",
|
| + "id": "genomics.variantsets.importVariants",
|
| + "parameterOrder": [
|
| + "variantSetId"
|
| + ],
|
| + "parameters": {
|
| + "variantSetId": {
|
| + "description": "Required. The variant set to which variant data should be imported.",
|
| + "location": "path",
|
| + "required": true,
|
| + "type": "string"
|
| + }
|
| + },
|
| + "path": "variantsets/{variantSetId}/importVariants",
|
| + "request": {
|
| + "$ref": "ImportVariantsRequest"
|
| + },
|
| + "response": {
|
| + "$ref": "ImportVariantsResponse"
|
| + },
|
| + "scopes": [
|
| + "https://www.googleapis.com/auth/devstorage.read_write",
|
| + "https://www.googleapis.com/auth/genomics"
|
| + ]
|
| + },
|
| "mergeVariants": {
|
| "description": "Merges the given variants with existing variants. Each variant will be merged with an existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created.\n\nWhen variants are merged, the call information from the new variant is added to the existing variant, and other fields (such as key/value pairs) are discarded.",
|
| "httpMethod": "POST",
|
| @@ -947,7 +1101,7 @@
|
| }
|
| },
|
| "patch": {
|
| - "description": "Updates a variant set's metadata. All other modifications are silently ignored. Returns the modified variant set. This method supports patch semantics.",
|
| + "description": "Updates a variant set's metadata. All other modifications are silently ignored. This method supports patch semantics.",
|
| "httpMethod": "PATCH",
|
| "id": "genomics.variantsets.patch",
|
| "parameterOrder": [
|
| @@ -973,7 +1127,7 @@
|
| ]
|
| },
|
| "search": {
|
| - "description": "Returns a list of all variant sets matching search criteria.",
|
| + "description": "Returns a list of all variant sets matching search criteria.\n\nImplements GlobalAllianceApi.searchVariantSets.",
|
| "httpMethod": "POST",
|
| "id": "genomics.variantsets.search",
|
| "path": "variantsets/search",
|
| @@ -989,7 +1143,7 @@
|
| ]
|
| },
|
| "update": {
|
| - "description": "Updates a variant set's metadata. All other modifications are silently ignored. Returns the modified variant set.",
|
| + "description": "Updates a variant set's metadata. All other modifications are silently ignored.",
|
| "httpMethod": "PUT",
|
| "id": "genomics.variantsets.update",
|
| "parameterOrder": [
|
| @@ -1017,26 +1171,59 @@
|
| }
|
| }
|
| },
|
| - "revision": "20141015",
|
| + "revision": "20141028",
|
| "rootUrl": "https://www.googleapis.com/",
|
| "schemas": {
|
| - "Beacon": {
|
| - "description": "A beacon represents whether any variant call in a variant set has a specific allele at a particular position.",
|
| - "id": "Beacon",
|
| + "AlignReadGroupSetsRequest": {
|
| + "description": "The read group set align request.",
|
| + "id": "AlignReadGroupSetsRequest",
|
| "properties": {
|
| - "exists": {
|
| - "description": "True if the allele exists on any variant call, false otherwise.",
|
| - "type": "boolean"
|
| + "bamSourceUris": {
|
| + "description": "The BAM source files for alignment. Exactly one of readGroupSetIds, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided. The caller must have READ permissions for these files.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "datasetId": {
|
| + "description": "Required. The ID of the dataset the newly aligned read group sets will belong to. The caller must have WRITE permissions to this dataset.",
|
| + "type": "string"
|
| + },
|
| + "interleavedFastqSource": {
|
| + "$ref": "InterleavedFastqSource",
|
| + "description": "The interleaved FASTQ source files for alignment, where both members of each pair of reads are found on consecutive records within the same FASTQ file. Exactly one of readGroupSetIds, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided."
|
| + },
|
| + "pairedFastqSource": {
|
| + "$ref": "PairedFastqSource",
|
| + "description": "The paired end FASTQ source files for alignment, where each member of a pair of reads are found in separate files. Exactly one of readGroupSetIds, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided."
|
| + },
|
| + "readGroupSetIds": {
|
| + "description": "The IDs of the read group sets which will be aligned. New read group sets will be generated to hold the aligned data, the originals will not be modified. The caller must have READ permissions for these read group sets. Exactly one of readGroupSetIds, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| }
|
| },
|
| "type": "object"
|
| },
|
| - "Call": {
|
| - "description": "A Call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a Call might assign a probability of 0.32 to the occurrence of a SNP named rs1234 in a call set with the name NA12345.",
|
| - "id": "Call",
|
| + "AlignReadGroupSetsResponse": {
|
| + "description": "The read group set align response.",
|
| + "id": "AlignReadGroupSetsResponse",
|
| "properties": {
|
| - "callSetId": {
|
| - "description": "The ID of the call set this variant call belongs to.",
|
| + "jobId": {
|
| + "description": "A job ID that can be used to get status information.",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "Call": {
|
| + "description": "A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named rs1234 in a call set with the name NA12345.",
|
| + "id": "Call",
|
| + "properties": {
|
| + "callSetId": {
|
| + "description": "The ID of the call set this variant call belongs to.",
|
| "type": "string"
|
| },
|
| "callSetName": {
|
| @@ -1077,8 +1264,44 @@
|
| },
|
| "type": "object"
|
| },
|
| + "CallReadGroupSetsRequest": {
|
| + "description": "The read group set call request.",
|
| + "id": "CallReadGroupSetsRequest",
|
| + "properties": {
|
| + "datasetId": {
|
| + "description": "Required. The ID of the dataset the called variants will belong to. The caller must have WRITE permissions to this dataset.",
|
| + "type": "string"
|
| + },
|
| + "readGroupSetIds": {
|
| + "description": "The IDs of the read group sets which will be called. The caller must have READ permissions for these read group sets. One of readGroupSetIds or sourceUris must be provided.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "sourceUris": {
|
| + "description": "A list of URIs pointing at BAM files in Google Cloud Storage which will be called. FASTQ files are not allowed. The caller must have READ permissions for these files. One of readGroupSetIds or sourceUris must be provided.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "CallReadGroupSetsResponse": {
|
| + "description": "The read group set call response.",
|
| + "id": "CallReadGroupSetsResponse",
|
| + "properties": {
|
| + "jobId": {
|
| + "description": "A job ID that can be used to get status information.",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| "CallSet": {
|
| - "description": "A CallSet is a collection of variant calls. It belongs to a variant set.",
|
| + "description": "A call set is a collection of variant calls, typically for one sample. It belongs to a variant set.",
|
| "id": "CallSet",
|
| "properties": {
|
| "created": {
|
| @@ -1098,11 +1321,11 @@
|
| },
|
| "type": "array"
|
| },
|
| - "description": "A map of additional callset information.",
|
| + "description": "A map of additional call set information.",
|
| "type": "object"
|
| },
|
| "name": {
|
| - "description": "The callset name.",
|
| + "description": "The call set name.",
|
| "type": "string"
|
| },
|
| "sampleId": {
|
| @@ -1119,6 +1342,47 @@
|
| },
|
| "type": "object"
|
| },
|
| + "CigarUnit": {
|
| + "description": "A single CIGAR operation.",
|
| + "id": "CigarUnit",
|
| + "properties": {
|
| + "operation": {
|
| + "enum": [
|
| + "ALIGNMENT_MATCH",
|
| + "CLIP_HARD",
|
| + "CLIP_SOFT",
|
| + "DELETE",
|
| + "INSERT",
|
| + "PAD",
|
| + "SEQUENCE_MATCH",
|
| + "SEQUENCE_MISMATCH",
|
| + "SKIP"
|
| + ],
|
| + "enumDescriptions": [
|
| + "",
|
| + "",
|
| + "",
|
| + "",
|
| + "",
|
| + "",
|
| + "",
|
| + "",
|
| + ""
|
| + ],
|
| + "type": "string"
|
| + },
|
| + "operationLength": {
|
| + "description": "The number of bases that the operation runs for. Required.",
|
| + "format": "int64",
|
| + "type": "string"
|
| + },
|
| + "referenceSequence": {
|
| + "description": "referenceSequence is only used at mismatches (SEQUENCE_MISMATCH) and deletions (DELETE). Filling this field replaces SAM's MD tag. If the relevant information is not available, this field is unset.",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| "CoverageBucket": {
|
| "description": "A bucket over which read coverage has been precomputed. A bucket corresponds to a specific range of the reference sequence.",
|
| "id": "CoverageBucket",
|
| @@ -1129,7 +1393,7 @@
|
| "type": "number"
|
| },
|
| "range": {
|
| - "$ref": "GenomicRange",
|
| + "$ref": "Range",
|
| "description": "The genomic coordinate range spanned by this bucket."
|
| }
|
| },
|
| @@ -1151,7 +1415,7 @@
|
| "description": "The dataset name.",
|
| "type": "string"
|
| },
|
| - "projectId": {
|
| + "projectNumber": {
|
| "description": "The Google Developers Console project number that this dataset belongs to.",
|
| "format": "int64",
|
| "type": "string"
|
| @@ -1164,11 +1428,11 @@
|
| "id": "ExperimentalCreateJobRequest",
|
| "properties": {
|
| "align": {
|
| - "description": "Specifies whether or not to run the alignment pipeline. At least one of align or callVariants must be provided.",
|
| + "description": "Specifies whether or not to run the alignment pipeline. Either align or callVariants must be set.",
|
| "type": "boolean"
|
| },
|
| "callVariants": {
|
| - "description": "Specifies whether or not to run the variant calling pipeline. If specified, alignment will be performed first and the aligned BAMs will passed as input to the variant caller. At least one of align or callVariants must be provided.",
|
| + "description": "Specifies whether or not to run the variant calling pipeline. Either align or callVariants must be set.",
|
| "type": "boolean"
|
| },
|
| "gcsOutputPath": {
|
| @@ -1182,7 +1446,7 @@
|
| },
|
| "type": "array"
|
| },
|
| - "projectId": {
|
| + "projectNumber": {
|
| "description": "Required. The Google Cloud Project ID with which to associate the request.",
|
| "format": "int64",
|
| "type": "string"
|
| @@ -1208,21 +1472,21 @@
|
| },
|
| "type": "object"
|
| },
|
| - "ExportReadsetsRequest": {
|
| - "description": "The readset export request.",
|
| - "id": "ExportReadsetsRequest",
|
| + "ExportReadGroupSetsRequest": {
|
| + "description": "The read group set export request.",
|
| + "id": "ExportReadGroupSetsRequest",
|
| "properties": {
|
| "exportUri": {
|
| "description": "A Google Cloud Storage URI where the exported BAM file will be created. The currently authenticated user must have write access to the new file location. An error will be returned if the URI already contains data.",
|
| "type": "string"
|
| },
|
| - "projectId": {
|
| + "projectNumber": {
|
| "description": "The Google Developers Console project number that owns this export.",
|
| "format": "int64",
|
| "type": "string"
|
| },
|
| - "readsetIds": {
|
| - "description": "The IDs of the readsets to export.",
|
| + "readGroupSetIds": {
|
| + "description": "The IDs of the read group sets to export.",
|
| "items": {
|
| "type": "string"
|
| },
|
| @@ -1238,9 +1502,9 @@
|
| },
|
| "type": "object"
|
| },
|
| - "ExportReadsetsResponse": {
|
| - "description": "The readset export response.",
|
| - "id": "ExportReadsetsResponse",
|
| + "ExportReadGroupSetsResponse": {
|
| + "description": "The read group set export response.",
|
| + "id": "ExportReadGroupSetsResponse",
|
| "properties": {
|
| "jobId": {
|
| "description": "A job ID that can be used to get status information.",
|
| @@ -1249,9 +1513,9 @@
|
| },
|
| "type": "object"
|
| },
|
| - "ExportVariantsRequest": {
|
| + "ExportVariantSetRequest": {
|
| "description": "The variant data export request.",
|
| - "id": "ExportVariantsRequest",
|
| + "id": "ExportVariantSetRequest",
|
| "properties": {
|
| "bigqueryDataset": {
|
| "description": "The BigQuery dataset to export data to. Note that this is distinct from the Genomics concept of \"dataset\".",
|
| @@ -1271,28 +1535,24 @@
|
| "format": {
|
| "description": "The format for the exported data.",
|
| "enum": [
|
| - "bigquery"
|
| + "BIGQUERY"
|
| ],
|
| "enumDescriptions": [
|
| ""
|
| ],
|
| "type": "string"
|
| },
|
| - "projectId": {
|
| + "projectNumber": {
|
| "description": "The Google Cloud project number that owns the destination BigQuery dataset. The caller must have WRITE access to this project. This project will also own the resulting export job.",
|
| "format": "int64",
|
| "type": "string"
|
| - },
|
| - "variantSetId": {
|
| - "description": "Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ access to this variant set.",
|
| - "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| },
|
| - "ExportVariantsResponse": {
|
| + "ExportVariantSetResponse": {
|
| "description": "The variant data export response.",
|
| - "id": "ExportVariantsResponse",
|
| + "id": "ExportVariantSetResponse",
|
| "properties": {
|
| "jobId": {
|
| "description": "A job ID that can be used to get status information.",
|
| @@ -1301,97 +1561,42 @@
|
| },
|
| "type": "object"
|
| },
|
| - "GenomicRange": {
|
| - "description": "An inclusive, exclusive genomic coordinate range over a reference sequence.",
|
| - "id": "GenomicRange",
|
| + "FastqMetadata": {
|
| + "id": "FastqMetadata",
|
| "properties": {
|
| - "sequenceEnd": {
|
| - "description": "The end position of the range on the reference, 1-based exclusive. If specified, sequenceName must also be specified.",
|
| - "format": "uint64",
|
| + "libraryName": {
|
| + "description": "Optionally specifies the library name for alignment from FASTQ.",
|
| "type": "string"
|
| },
|
| - "sequenceName": {
|
| - "description": "The reference sequence name, for example chr1, 1, or chrX.",
|
| + "platformName": {
|
| + "description": "Optionally specifies the platform name for alignment from FASTQ. For example: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, PACBIO.",
|
| "type": "string"
|
| },
|
| - "sequenceStart": {
|
| - "description": "The start position of the range on the reference, 1-based inclusive. If specified, sequenceName must also be specified.",
|
| - "format": "uint64",
|
| - "type": "string"
|
| - }
|
| - },
|
| - "type": "object"
|
| - },
|
| - "Header": {
|
| - "id": "Header",
|
| - "properties": {
|
| - "sortingOrder": {
|
| - "description": "(SO) Sorting order of alignments.",
|
| - "type": "string"
|
| - },
|
| - "version": {
|
| - "description": "(VN) BAM format version.",
|
| + "platformUnit": {
|
| + "description": "Optionally specifies the platform unit for alignment from FASTQ. For example: flowcell-barcode.lane for Illumina or slide for SOLID.",
|
| "type": "string"
|
| - }
|
| - },
|
| - "type": "object"
|
| - },
|
| - "HeaderSection": {
|
| - "description": "The header section of the BAM/SAM file.",
|
| - "id": "HeaderSection",
|
| - "properties": {
|
| - "comments": {
|
| - "description": "(@CO) One-line text comments.",
|
| - "items": {
|
| - "type": "string"
|
| - },
|
| - "type": "array"
|
| },
|
| - "fileUri": {
|
| - "description": "[Deprecated] This field is deprecated and will no longer be populated. Please use filename instead.",
|
| + "readGroupName": {
|
| + "description": "Optionally specifies the read group name for alignment from FASTQ.",
|
| "type": "string"
|
| },
|
| - "filename": {
|
| - "description": "The name of the file from which this data was imported.",
|
| + "sampleName": {
|
| + "description": "Optionally specifies the sample name for alignment from FASTQ.",
|
| "type": "string"
|
| - },
|
| - "headers": {
|
| - "description": "(@HD) The header line.",
|
| - "items": {
|
| - "$ref": "Header"
|
| - },
|
| - "type": "array"
|
| - },
|
| - "programs": {
|
| - "description": "(@PG) Programs.",
|
| - "items": {
|
| - "$ref": "Program"
|
| - },
|
| - "type": "array"
|
| - },
|
| - "readGroups": {
|
| - "description": "(@RG) Read group.",
|
| - "items": {
|
| - "$ref": "ReadGroup"
|
| - },
|
| - "type": "array"
|
| - },
|
| - "refSequences": {
|
| - "description": "(@SQ) Reference sequence dictionary.",
|
| - "items": {
|
| - "$ref": "ReferenceSequence"
|
| - },
|
| - "type": "array"
|
| }
|
| },
|
| "type": "object"
|
| },
|
| - "ImportReadsetsRequest": {
|
| - "description": "The readset import request.",
|
| - "id": "ImportReadsetsRequest",
|
| + "ImportReadGroupSetsRequest": {
|
| + "description": "The read group set import request.",
|
| + "id": "ImportReadGroupSetsRequest",
|
| "properties": {
|
| "datasetId": {
|
| - "description": "Required. The ID of the dataset these readsets will belong to. The caller must have WRITE permissions to this dataset.",
|
| + "description": "Required. The ID of the dataset these read group sets will belong to. The caller must have WRITE permissions to this dataset.",
|
| + "type": "string"
|
| + },
|
| + "referenceSetId": {
|
| + "description": "The reference set to which the imported read group sets are aligned to, if any. The reference names of this reference set must be a superset of those found in the imported file headers. If no reference set id is provided, a best effort is made to associate with a matching reference set.",
|
| "type": "string"
|
| },
|
| "sourceUris": {
|
| @@ -1404,9 +1609,9 @@
|
| },
|
| "type": "object"
|
| },
|
| - "ImportReadsetsResponse": {
|
| - "description": "The readset import response.",
|
| - "id": "ImportReadsetsResponse",
|
| + "ImportReadGroupSetsResponse": {
|
| + "description": "The read group set import response.",
|
| + "id": "ImportReadGroupSetsResponse",
|
| "properties": {
|
| "jobId": {
|
| "description": "A job ID that can be used to get status information.",
|
| @@ -1422,8 +1627,8 @@
|
| "format": {
|
| "description": "The format of the variant data being imported.",
|
| "enum": [
|
| - "completeGenomics",
|
| - "vcf"
|
| + "COMPLETE_GENOMICS",
|
| + "VCF"
|
| ],
|
| "enumDescriptions": [
|
| "",
|
| @@ -1437,10 +1642,6 @@
|
| "type": "string"
|
| },
|
| "type": "array"
|
| - },
|
| - "variantSetId": {
|
| - "description": "Required. The variant set to which variant data should be imported.",
|
| - "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| @@ -1456,6 +1657,24 @@
|
| },
|
| "type": "object"
|
| },
|
| + "InterleavedFastqSource": {
|
| + "description": "Describes an interleaved FASTQ file source for alignment.",
|
| + "id": "InterleavedFastqSource",
|
| + "properties": {
|
| + "metadata": {
|
| + "$ref": "FastqMetadata",
|
| + "description": "Optionally specifies the metadata to be associated with the final aligned read group set."
|
| + },
|
| + "sourceUris": {
|
| + "description": "A list of URIs pointing at interleaved FASTQ files in Google Cloud Storage which will be aligned. The caller must have READ permissions for these files.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| "Job": {
|
| "description": "A Job represents an ongoing process that can be monitored for status information.",
|
| "id": "Job",
|
| @@ -1465,7 +1684,7 @@
|
| "format": "int64",
|
| "type": "string"
|
| },
|
| - "description": {
|
| + "detailedStatus": {
|
| "description": "A more detailed description of this job's current status.",
|
| "type": "string"
|
| },
|
| @@ -1487,7 +1706,7 @@
|
| },
|
| "type": "array"
|
| },
|
| - "projectId": {
|
| + "projectNumber": {
|
| "description": "The Google Developers Console project number to which this job belongs.",
|
| "format": "int64",
|
| "type": "string"
|
| @@ -1499,13 +1718,13 @@
|
| "status": {
|
| "description": "The status of this job.",
|
| "enum": [
|
| - "canceled",
|
| - "failure",
|
| - "new",
|
| - "pending",
|
| - "running",
|
| - "success",
|
| - "unknownStatus"
|
| + "CANCELED",
|
| + "FAILURE",
|
| + "NEW",
|
| + "PENDING",
|
| + "RUNNING",
|
| + "SUCCESS",
|
| + "UNKNOWN_STATUS"
|
| ],
|
| "enumDescriptions": [
|
| "",
|
| @@ -1549,12 +1768,14 @@
|
| "type": {
|
| "description": "The original request type.",
|
| "enum": [
|
| - "experimentalCreateJob",
|
| - "exportReadsets",
|
| - "exportVariants",
|
| - "importReadsets",
|
| - "importVariants",
|
| - "unknownType"
|
| + "ALIGN_READSETS",
|
| + "CALL_READSETS",
|
| + "EXPERIMENTAL_CREATE_JOB",
|
| + "EXPORT_READSETS",
|
| + "EXPORT_VARIANTS",
|
| + "IMPORT_READSETS",
|
| + "IMPORT_VARIANTS",
|
| + "UNKNOWN_TYPE"
|
| ],
|
| "enumDescriptions": [
|
| "",
|
| @@ -1562,6 +1783,8 @@
|
| "",
|
| "",
|
| "",
|
| + "",
|
| + "",
|
| ""
|
| ],
|
| "type": "string"
|
| @@ -1569,12 +1792,54 @@
|
| },
|
| "type": "object"
|
| },
|
| + "LinearAlignment": {
|
| + "description": "A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference.",
|
| + "id": "LinearAlignment",
|
| + "properties": {
|
| + "cigar": {
|
| + "description": "Represents the local alignment of this sequence (alignment matches, indels, etc) against the reference.",
|
| + "items": {
|
| + "$ref": "CigarUnit"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "mappingQuality": {
|
| + "description": "The mapping quality of this alignment. Represents how likely the read maps to this position as opposed to other locations.",
|
| + "format": "int32",
|
| + "type": "integer"
|
| + },
|
| + "position": {
|
| + "$ref": "Position",
|
| + "description": "The position of this alignment."
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "ListBasesResponse": {
|
| + "id": "ListBasesResponse",
|
| + "properties": {
|
| + "nextPageToken": {
|
| + "description": "The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.",
|
| + "type": "string"
|
| + },
|
| + "offset": {
|
| + "description": "The offset position (0-based) of the given sequence from the start of this Reference. This value will differ for each page in a paginated request.",
|
| + "format": "int64",
|
| + "type": "string"
|
| + },
|
| + "sequence": {
|
| + "description": "A substring of the bases that make up this reference.",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| "ListCoverageBucketsResponse": {
|
| "id": "ListCoverageBucketsResponse",
|
| "properties": {
|
| "bucketWidth": {
|
| "description": "The length of each coverage bucket in base pairs. Note that buckets at the end of a reference sequence may be shorter. This value is omitted if the bucket width is infinity (the default behaviour, with no range or targetBucketWidth).",
|
| - "format": "uint64",
|
| + "format": "int64",
|
| "type": "string"
|
| },
|
| "coverageBuckets": {
|
| @@ -1656,12 +1921,12 @@
|
| "type": {
|
| "description": "The type of data. Possible types include: Integer, Float, Flag, Character, and String.",
|
| "enum": [
|
| - "character",
|
| - "flag",
|
| - "float",
|
| - "integer",
|
| - "string",
|
| - "unknownType"
|
| + "CHARACTER",
|
| + "FLAG",
|
| + "FLOAT",
|
| + "INTEGER",
|
| + "STRING",
|
| + "UNKNOWN_TYPE"
|
| ],
|
| "enumDescriptions": [
|
| "",
|
| @@ -1680,93 +1945,182 @@
|
| },
|
| "type": "object"
|
| },
|
| - "Program": {
|
| - "id": "Program",
|
| + "PairedFastqSource": {
|
| + "description": "Describes a paired-end FASTQ file source for alignment.",
|
| + "id": "PairedFastqSource",
|
| "properties": {
|
| - "commandLine": {
|
| - "description": "(CL) Command line.",
|
| + "firstSourceUris": {
|
| + "description": "A list of URIs pointing at paired end FASTQ files in Google Cloud Storage which will be aligned. The first of each paired file should be specified here, in an order that matches the second of each paired file specified in secondSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq], secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ permissions for these files.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "metadata": {
|
| + "$ref": "FastqMetadata",
|
| + "description": "Optionally specifies the metadata to be associated with the final aligned read group set."
|
| + },
|
| + "secondSourceUris": {
|
| + "description": "A list of URIs pointing at paired end FASTQ files in Google Cloud Storage which will be aligned. The second of each paired file should be specified here, in an order that matches the first of each paired file specified in firstSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq], secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ permissions for these files.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "Position": {
|
| + "description": "An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic position as a reference name, a base number on that reference (0-based), and a determination of forward or reverse strand.",
|
| + "id": "Position",
|
| + "properties": {
|
| + "position": {
|
| + "description": "The 0-based offset from the start of the forward strand for that reference.",
|
| + "format": "int64",
|
| "type": "string"
|
| },
|
| - "id": {
|
| - "description": "(ID) Program record identifier.",
|
| + "referenceName": {
|
| + "description": "The name of the reference in whatever reference set is being used.",
|
| "type": "string"
|
| },
|
| - "name": {
|
| - "description": "(PN) Program name.",
|
| + "reverseStrand": {
|
| + "description": "Whether this position is on the reverse strand, as opposed to the forward strand.",
|
| + "type": "boolean"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "Range": {
|
| + "description": "A 0-based half-open genomic coordinate range over a reference sequence.",
|
| + "id": "Range",
|
| + "properties": {
|
| + "end": {
|
| + "description": "The end position of the range on the reference, 0-based exclusive. If specified, referenceName must also be specified.",
|
| + "format": "int64",
|
| "type": "string"
|
| },
|
| - "prevProgramId": {
|
| - "description": "(PP) Previous program ID.",
|
| + "referenceName": {
|
| + "description": "The reference sequence name, for example chr1, 1, or chrX.",
|
| "type": "string"
|
| },
|
| - "version": {
|
| - "description": "(VN) Program version.",
|
| + "start": {
|
| + "description": "The start position of the range on the reference, 0-based inclusive. If specified, referenceName must also be specified.",
|
| + "format": "int64",
|
| "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| },
|
| "Read": {
|
| - "description": "A Read is a group of bases that may or may not have been aligned to a reference. It contains quality information and other metadata.",
|
| + "description": "A read alignment describes a linear alignment of a string of DNA to a reference sequence, in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one read group set.",
|
| "id": "Read",
|
| "properties": {
|
| - "alignedBases": {
|
| - "description": "The originalBases after the cigar field has been applied. Deletions are represented with '-' and insertions are omitted.",
|
| - "type": "string"
|
| + "alignedQuality": {
|
| + "description": "The quality of the read sequence contained in this alignment record. alignedSequence and alignedQuality may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence.",
|
| + "items": {
|
| + "format": "int32",
|
| + "type": "integer"
|
| + },
|
| + "type": "array"
|
| },
|
| - "baseQuality": {
|
| - "description": "Represents the quality of each base in this read. Each character represents one base. To get the quality, take the ASCII value of the character and subtract 33. (QUAL)",
|
| + "alignedSequence": {
|
| + "description": "The bases of the read sequence contained in this alignment record. alignedSequence and alignedQuality may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence.",
|
| "type": "string"
|
| },
|
| - "cigar": {
|
| - "description": "A condensed representation of how this read matches up to the reference. (CIGAR)",
|
| - "type": "string"
|
| + "alignment": {
|
| + "$ref": "LinearAlignment",
|
| + "description": "The linear alignment for this alignment record. This field will be null if the read is unmapped."
|
| + },
|
| + "duplicateFragment": {
|
| + "description": "The fragment is a PCR or optical duplicate (SAM flag 0x400)",
|
| + "type": "boolean"
|
| },
|
| - "flags": {
|
| - "description": "Each bit of this number has a different meaning if enabled. See the full BAM spec for more details. (FLAG)",
|
| + "failedVendorQualityChecks": {
|
| + "description": "SAM flag 0x200",
|
| + "type": "boolean"
|
| + },
|
| + "fragmentLength": {
|
| + "description": "The observed length of the fragment, equivalent to TLEN in SAM.",
|
| "format": "int32",
|
| "type": "integer"
|
| },
|
| + "fragmentName": {
|
| + "description": "The fragment name. Equivalent to QNAME (query template name) in SAM.",
|
| + "type": "string"
|
| + },
|
| "id": {
|
| - "description": "The Google generated ID of the read, immutable.",
|
| + "description": "The unique ID for this read. This is a generated unique ID, not to be confused with fragmentName.",
|
| "type": "string"
|
| },
|
| - "mappingQuality": {
|
| - "description": "A score up to 255 that represents how likely this read's aligned position is to be correct. A higher value is better. (MAPQ)",
|
| - "format": "int32",
|
| - "type": "integer"
|
| + "info": {
|
| + "additionalProperties": {
|
| + "description": "A string which maps to an array of values.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "description": "A map of additional read alignment information.",
|
| + "type": "object"
|
| },
|
| - "matePosition": {
|
| - "description": "The 1-based start position of the paired read. (PNEXT)",
|
| + "nextMatePosition": {
|
| + "$ref": "Position",
|
| + "description": "The mapping of the primary alignment of the (readNumber+1)%numberReads read in the fragment. It replaces mate position and mate strand in SAM."
|
| + },
|
| + "numberReads": {
|
| + "description": "The number of reads in the fragment (extension to SAM flag 0x1).",
|
| "format": "int32",
|
| "type": "integer"
|
| },
|
| - "mateReferenceSequenceName": {
|
| - "description": "The name of the sequence that the paired read is aligned to. This is usually the same as referenceSequenceName. (RNEXT)",
|
| - "type": "string"
|
| + "properPlacement": {
|
| + "description": "The orientation and the distance between reads from the fragment are consistent with the sequencing protocol (extension to SAM flag 0x2)",
|
| + "type": "boolean"
|
| },
|
| - "name": {
|
| - "description": "The name of the read. When imported from a BAM file, this is the query template name. (QNAME)",
|
| + "readGroupId": {
|
| + "description": "The ID of the read group this read belongs to. (Every read must belong to exactly one read group.)",
|
| "type": "string"
|
| },
|
| - "originalBases": {
|
| - "description": "The list of bases that this read represents (such as \"CATCGA\"). (SEQ)",
|
| + "readGroupSetId": {
|
| + "description": "The ID of the read group set this read belongs to. (Every read must belong to exactly one read group set.)",
|
| "type": "string"
|
| },
|
| - "position": {
|
| - "description": "The 1-based start position of the aligned read. If the first base starts at the very beginning of the reference sequence, then the position would be '1'. (POS)",
|
| + "readNumber": {
|
| + "description": "The read number in sequencing. 0-based and less than numberReads. This field replaces SAM flag 0x40 and 0x80.",
|
| "format": "int32",
|
| "type": "integer"
|
| },
|
| - "readsetId": {
|
| - "description": "The ID of the readset this read belongs to.",
|
| + "secondaryAlignment": {
|
| + "description": "Whether this alignment is secondary. Equivalent to SAM flag 0x100. A secondary alignment represents an alternative to the primary alignment for this read. Aligners may return secondary alignments if a read can map ambiguously to multiple coordinates in the genome. By convention, each read has one and only one alignment where both secondaryAlignment and supplementaryAlignment are false.",
|
| + "type": "boolean"
|
| + },
|
| + "supplementaryAlignment": {
|
| + "description": "Whether this alignment is supplementary. Equivalent to SAM flag 0x800. Supplementary alignments are used in the representation of a chimeric alignment. In a chimeric alignment, a read is split into multiple linear alignments that map to different reference contigs. The first linear alignment in the read will be designated as the representative alignment; the remaining linear alignments will be designated as supplementary alignments. These alignments may have different mapping quality scores. In each linear alignment in a chimeric alignment, the read will be hard clipped. The alignedSequence and alignedQuality fields in the alignment record will only represent the bases for its respective linear alignment.",
|
| + "type": "boolean"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "ReadGroup": {
|
| + "description": "A read group is all the data that's processed the same way by the sequencer.",
|
| + "id": "ReadGroup",
|
| + "properties": {
|
| + "datasetId": {
|
| + "description": "The ID of the dataset this read group belongs to.",
|
| "type": "string"
|
| },
|
| - "referenceSequenceName": {
|
| - "description": "The name of the sequence that this read is aligned to. This would be, for example, 'X' for the X Chromosome or '20' for Chromosome 20. (RNAME)",
|
| + "description": {
|
| + "description": "A free-form text description of this read group.",
|
| + "type": "string"
|
| + },
|
| + "experiment": {
|
| + "$ref": "ReadGroupExperiment",
|
| + "description": "The experiment used to generate this read group."
|
| + },
|
| + "id": {
|
| + "description": "The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.",
|
| "type": "string"
|
| },
|
| - "tags": {
|
| + "info": {
|
| "additionalProperties": {
|
| "description": "A string which maps to an array of values.",
|
| "items": {
|
| @@ -1774,93 +2128,153 @@
|
| },
|
| "type": "array"
|
| },
|
| - "description": "A map of additional read information. (TAG)",
|
| + "description": "A map of additional read group information.",
|
| "type": "object"
|
| },
|
| - "templateLength": {
|
| - "description": "Length of the original piece of DNA that produced both this read and the paired read. (TLEN)",
|
| + "name": {
|
| + "description": "The read group name. This corresponds to the @RG ID field in the SAM spec.",
|
| + "type": "string"
|
| + },
|
| + "predictedInsertSize": {
|
| + "description": "The predicted insert size of this read group. The insert size is the length the sequenced DNA fragment from end-to-end, not including the adapters.",
|
| "format": "int32",
|
| "type": "integer"
|
| + },
|
| + "programs": {
|
| + "description": "The programs used to generate this read group. Programs are always identical for all read groups within a read group set. For this reason, only the first read group in a returned set will have this field populated.",
|
| + "items": {
|
| + "$ref": "ReadGroupProgram"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "referenceSetId": {
|
| + "description": "The reference set the reads in this read group are aligned to. Required if there are any read alignments.",
|
| + "type": "string"
|
| + },
|
| + "sampleId": {
|
| + "description": "The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.",
|
| + "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| },
|
| - "ReadGroup": {
|
| - "id": "ReadGroup",
|
| + "ReadGroupExperiment": {
|
| + "id": "ReadGroupExperiment",
|
| "properties": {
|
| - "date": {
|
| - "description": "(DT) Date the run was produced (ISO8601 date or date/time).",
|
| + "instrumentModel": {
|
| + "description": "The instrument model used as part of this experiment. This maps to sequencing technology in BAM.",
|
| "type": "string"
|
| },
|
| - "description": {
|
| - "description": "(DS) Description.",
|
| + "libraryId": {
|
| + "description": "The library used as part of this experiment. Note: This is not an actual ID within this repository, but rather an identifier for a library which may be meaningful to some external system.",
|
| "type": "string"
|
| },
|
| - "flowOrder": {
|
| - "description": "(FO) Flow order. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read.",
|
| + "platformUnit": {
|
| + "description": "The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the",
|
| "type": "string"
|
| },
|
| - "id": {
|
| - "description": "(ID) Read group identifier.",
|
| + "sequencingCenter": {
|
| + "description": "The sequencing center used as part of this experiment.",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "ReadGroupProgram": {
|
| + "id": "ReadGroupProgram",
|
| + "properties": {
|
| + "commandLine": {
|
| + "description": "The command line used to run this program.",
|
| "type": "string"
|
| },
|
| - "keySequence": {
|
| - "description": "(KS) The array of nucleotide bases that correspond to the key sequence of each read.",
|
| + "id": {
|
| + "description": "The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.",
|
| "type": "string"
|
| },
|
| - "library": {
|
| - "description": "(LS) Library.",
|
| + "name": {
|
| + "description": "The name of the program.",
|
| "type": "string"
|
| },
|
| - "platformUnit": {
|
| - "description": "(PU) Platform unit.",
|
| + "prevProgramId": {
|
| + "description": "The ID of the program run before this one.",
|
| "type": "string"
|
| },
|
| - "predictedInsertSize": {
|
| - "description": "(PI) Predicted median insert size.",
|
| - "format": "int32",
|
| - "type": "integer"
|
| + "version": {
|
| + "description": "The version of the program run.",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "ReadGroupSet": {
|
| + "description": "A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way. \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.",
|
| + "id": "ReadGroupSet",
|
| + "properties": {
|
| + "datasetId": {
|
| + "description": "The dataset ID.",
|
| + "type": "string"
|
| },
|
| - "processingProgram": {
|
| - "description": "(PG) Programs used for processing the read group.",
|
| + "filename": {
|
| + "description": "The filename of the original source file for this read group set, if any.",
|
| "type": "string"
|
| },
|
| - "sample": {
|
| - "description": "(SM) Sample.",
|
| + "id": {
|
| + "description": "The read group set ID.",
|
| "type": "string"
|
| },
|
| - "sequencingCenterName": {
|
| - "description": "(CN) Name of sequencing center producing the read.",
|
| + "name": {
|
| + "description": "The read group set name. By default this will be initialized to the sample name of the sequenced data contained in this set.",
|
| "type": "string"
|
| },
|
| - "sequencingTechnology": {
|
| - "description": "(PL) Platform/technology used to produce the reads.",
|
| + "readGroups": {
|
| + "description": "The read groups in this set. There are typically 1-10 read groups in a read group set.",
|
| + "items": {
|
| + "$ref": "ReadGroup"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "referenceSetId": {
|
| + "description": "The reference set the reads in this read group set are aligned to.",
|
| "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| },
|
| - "Readset": {
|
| - "description": "A Readset is a collection of Reads.",
|
| - "id": "Readset",
|
| + "Reference": {
|
| + "description": "A reference is a canonical assembled DNA sequence, intended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, for instance. A reference belongs to one or more reference sets.",
|
| + "id": "Reference",
|
| "properties": {
|
| - "datasetId": {
|
| - "description": "The ID of the dataset this readset belongs to.",
|
| + "id": {
|
| + "description": "The Google generated immutable ID of the reference.",
|
| "type": "string"
|
| },
|
| - "fileData": {
|
| - "description": "File information from the original BAM import. See the BAM format specification for additional information on each field.",
|
| - "items": {
|
| - "$ref": "HeaderSection"
|
| - },
|
| - "type": "array"
|
| + "length": {
|
| + "description": "The length of this reference's sequence.",
|
| + "format": "int64",
|
| + "type": "string"
|
| },
|
| - "id": {
|
| - "description": "The Google generated ID of the readset, immutable.",
|
| + "md5checksum": {
|
| + "description": "MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM). This value is represented in lower case hexadecimal format.",
|
| "type": "string"
|
| },
|
| "name": {
|
| - "description": "The readset name, typically this is the sample name.",
|
| + "description": "The name of this reference, for example 22.",
|
| + "type": "string"
|
| + },
|
| + "ncbiTaxonId": {
|
| + "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not specified by the containing reference set.",
|
| + "format": "int32",
|
| + "type": "integer"
|
| + },
|
| + "sourceAccessions": {
|
| + "description": "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example GCF_000001405.26.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "sourceURI": {
|
| + "description": "The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair.",
|
| "type": "string"
|
| }
|
| },
|
| @@ -1882,32 +2296,47 @@
|
| },
|
| "type": "object"
|
| },
|
| - "ReferenceSequence": {
|
| - "id": "ReferenceSequence",
|
| + "ReferenceSet": {
|
| + "description": "A reference set is a set of references which typically comprise a reference assembly for a species, such as GRCh38 which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references.",
|
| + "id": "ReferenceSet",
|
| "properties": {
|
| "assemblyId": {
|
| - "description": "(AS) Genome assembly identifier.",
|
| + "description": "Public id of this reference set, such as GRCh37.",
|
| "type": "string"
|
| },
|
| - "length": {
|
| - "description": "(LN) Reference sequence length.",
|
| - "format": "int32",
|
| - "type": "integer"
|
| - },
|
| - "md5Checksum": {
|
| - "description": "(M5) MD5 checksum of the sequence in the uppercase, excluding spaces but including pads as *.",
|
| + "description": {
|
| + "description": "Optional free text description of this reference set.",
|
| "type": "string"
|
| },
|
| - "name": {
|
| - "description": "(SN) Reference sequence name.",
|
| + "id": {
|
| + "description": "The Google generated immutable ID of the reference set.",
|
| "type": "string"
|
| },
|
| - "species": {
|
| - "description": "(SP) Species.",
|
| + "md5checksum": {
|
| + "description": "Order-independent MD5 checksum which identifies this reference set. The checksum is computed by sorting all lower case hexidecimal string reference.md5checksum (for all reference in this set) in ascending lexicographic order, concatenating, and taking the MD5 of that value. The resulting value is represented in lower case hexadecimal format.",
|
| "type": "string"
|
| },
|
| - "uri": {
|
| - "description": "(UR) URI of the sequence.",
|
| + "ncbiTaxonId": {
|
| + "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating the species which this assembly is intended to model. Note that contained references may specify a different ncbiTaxonId, as assemblies may contain reference sequences which do not belong to the modeled species, e.g. EBV in a human reference genome.",
|
| + "format": "int32",
|
| + "type": "integer"
|
| + },
|
| + "referenceIds": {
|
| + "description": "The IDs of the reference objects that are part of this set. Reference.md5checksum must be unique within this set.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "sourceAccessions": {
|
| + "description": "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with 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"
|
| }
|
| },
|
| @@ -1972,16 +2401,16 @@
|
| "format": "int64",
|
| "type": "string"
|
| },
|
| - "maxResults": {
|
| + "pageSize": {
|
| "description": "Specifies the number of results to return in a single page. Defaults to 128. The maximum value is 256.",
|
| - "format": "uint64",
|
| - "type": "string"
|
| + "format": "int32",
|
| + "type": "integer"
|
| },
|
| "pageToken": {
|
| "description": "The continuation token which is used to page through large result sets. To get the next page of results, set this parameter to the value of the nextPageToken from the previous response.",
|
| "type": "string"
|
| },
|
| - "projectId": {
|
| + "projectNumber": {
|
| "description": "Required. Only return jobs which belong to this Google Developers",
|
| "format": "int64",
|
| "type": "string"
|
| @@ -1990,13 +2419,13 @@
|
| "description": "Only return jobs which have a matching status.",
|
| "items": {
|
| "enum": [
|
| - "canceled",
|
| - "failure",
|
| - "new",
|
| - "pending",
|
| - "running",
|
| - "success",
|
| - "unknownStatus"
|
| + "CANCELED",
|
| + "FAILURE",
|
| + "NEW",
|
| + "PENDING",
|
| + "RUNNING",
|
| + "SUCCESS",
|
| + "UNKNOWN_STATUS"
|
| ],
|
| "enumDescriptions": [
|
| "",
|
| @@ -2032,38 +2461,90 @@
|
| },
|
| "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 one 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 string.",
|
| + "type": "string"
|
| + },
|
| + "pageSize": {
|
| + "description": "Specifies number of results to return in a single page. If unspecified, it will default to 128. The maximum value is 1024.",
|
| + "format": "int32",
|
| + "type": "integer"
|
| + },
|
| + "pageToken": {
|
| + "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "SearchReadGroupSetsResponse": {
|
| + "description": "The read group set search response.",
|
| + "id": "SearchReadGroupSetsResponse",
|
| + "properties": {
|
| + "nextPageToken": {
|
| + "description": "The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. 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"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| "SearchReadsRequest": {
|
| "description": "The read search request.",
|
| "id": "SearchReadsRequest",
|
| "properties": {
|
| - "maxResults": {
|
| - "description": "Specifies number of results to return in a single page. If unspecified, it will default to 256. The maximum value is 2048.",
|
| - "format": "uint64",
|
| + "end": {
|
| + "description": "The end position of the range on the reference, 0-based exclusive. If specified, referenceName must also be specified.",
|
| + "format": "int64",
|
| "type": "string"
|
| },
|
| + "pageSize": {
|
| + "description": "Specifies number of results to return in a single page. If unspecified, it will default to 256. The maximum value is 2048.",
|
| + "format": "int32",
|
| + "type": "integer"
|
| + },
|
| "pageToken": {
|
| "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
|
| "type": "string"
|
| },
|
| - "readsetIds": {
|
| - "description": "The readsets within which to search for reads. At least one readset ID must be provided. All specified readsets must be aligned against a common set of reference sequences; this defines the genomic coordinates for the query.",
|
| + "readGroupIds": {
|
| + "description": "The IDs of the read groups within which to search for reads. All specified read groups must belong to the same read group sets. Must specify one of readGroupSetIds or readGroupIds.",
|
| "items": {
|
| "type": "string"
|
| },
|
| "type": "array"
|
| },
|
| - "sequenceEnd": {
|
| - "description": "The end position (1-based, inclusive) of the target range. If specified, sequenceName must also be specified. Defaults to the end of the target reference sequence, if any.",
|
| - "format": "uint64",
|
| - "type": "string"
|
| + "readGroupSetIds": {
|
| + "description": "The IDs of the read groups sets within which to search for reads. All specified read group sets must be aligned against a common set of reference sequences; this defines the genomic coordinates for the query. Must specify one of readGroupSetIds or readGroupIds.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| },
|
| - "sequenceName": {
|
| - "description": "Restricts the results to a particular reference sequence such as 1, chr1, or X. The set of valid references sequences depends on the readsets specified. If set to *, only unmapped Reads are returned.",
|
| + "referenceName": {
|
| + "description": "The reference sequence name, for example chr1, 1, or chrX. If set to *, only unmapped reads are returned.",
|
| "type": "string"
|
| },
|
| - "sequenceStart": {
|
| - "description": "The start position (1-based, inclusive) of the target range. If specified, sequenceName must also be specified. Defaults to the start of the target reference sequence, if any.",
|
| - "format": "uint64",
|
| + "start": {
|
| + "description": "The start position of the range on the reference, 0-based inclusive. If specified, referenceName must also be specified.",
|
| + "format": "int64",
|
| "type": "string"
|
| }
|
| },
|
| @@ -2073,59 +2554,111 @@
|
| "description": "The read search response.",
|
| "id": "SearchReadsResponse",
|
| "properties": {
|
| + "alignments": {
|
| + "description": "The list of matching alignments sorted by mapped genomic coordinate, if any, ascending in position within the same reference. Unmapped reads, which have no position, are returned last and are further sorted in ascending lexicographic order by fragment name.",
|
| + "items": {
|
| + "$ref": "Read"
|
| + },
|
| + "type": "array"
|
| + },
|
| "nextPageToken": {
|
| "description": "The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.",
|
| "type": "string"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "SearchReferenceSetsRequest": {
|
| + "id": "SearchReferenceSetsRequest",
|
| + "properties": {
|
| + "accessions": {
|
| + "description": "If present, return references for which the accession matches any of these strings. Best to give a version number, for example GCF_000001405.26. If only the main accession number is given then all records with that main accession will be returned, whichever version. Note that different versions will have different sequences.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| },
|
| - "reads": {
|
| - "description": "The list of matching Reads. The resulting Reads are sorted by position; the smallest positions are returned first. Unmapped reads, which have no position, are returned last and are further sorted alphabetically by name.",
|
| + "md5checksums": {
|
| + "description": "If present, return references for which the md5checksum matches. See ReferenceSet.md5checksum for details.",
|
| "items": {
|
| - "$ref": "Read"
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| + },
|
| + "pageSize": {
|
| + "description": "Specifies the maximum number of results to return in a single page.",
|
| + "format": "int32",
|
| + "type": "integer"
|
| + },
|
| + "pageToken": {
|
| + "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
|
| + "type": "string"
|
| + }
|
| + },
|
| + "type": "object"
|
| + },
|
| + "SearchReferenceSetsResponse": {
|
| + "id": "SearchReferenceSetsResponse",
|
| + "properties": {
|
| + "nextPageToken": {
|
| + "description": "The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. 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"
|
| }
|
| },
|
| "type": "object"
|
| },
|
| - "SearchReadsetsRequest": {
|
| - "description": "The readset search request.",
|
| - "id": "SearchReadsetsRequest",
|
| + "SearchReferencesRequest": {
|
| + "description": "",
|
| + "id": "SearchReferencesRequest",
|
| "properties": {
|
| - "datasetIds": {
|
| - "description": "Restricts this query to readsets within the given datasets. At least one ID must be provided.",
|
| + "accessions": {
|
| + "description": "If present, return references for which the accession matches this string. Best to give a version number, for example GCF_000001405.26. If only the main accession number is given then all records with that main accession will be returned, whichever version. Note that different versions will have different sequences.",
|
| "items": {
|
| "type": "string"
|
| },
|
| "type": "array"
|
| },
|
| - "maxResults": {
|
| - "description": "Specifies number of results to return in a single page. If unspecified, it will default to 128. The maximum value is 1024.",
|
| - "format": "uint64",
|
| - "type": "string"
|
| + "md5checksums": {
|
| + "description": "If present, return references for which the md5checksum matches. See Reference.md5checksum for construction details.",
|
| + "items": {
|
| + "type": "string"
|
| + },
|
| + "type": "array"
|
| },
|
| - "name": {
|
| - "description": "Only return readsets for which a substring of the name matches this string.",
|
| - "type": "string"
|
| + "pageSize": {
|
| + "description": "Specifies the maximum number of results to return in a single page.",
|
| + "format": "int32",
|
| + "type": "integer"
|
| },
|
| "pageToken": {
|
| "description": "The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",
|
| "type": "string"
|
| + },
|
| + "referenceSetId": {
|
| + "description": "If present, return only references which belong to this reference set.",
|
| + "type": "string"
|
| }
|
| },
|
| "type": "object"
|
| },
|
| - "SearchReadsetsResponse": {
|
| - "description": "The readset search response.",
|
| - "id": "SearchReadsetsResponse",
|
| + "SearchReferencesResponse": {
|
| + "id": "SearchReferencesResponse",
|
| "properties": {
|
| "nextPageToken": {
|
| "description": "The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.",
|
| "type": "string"
|
| },
|
| - "readsets": {
|
| - "description": "The list of matching Readsets.",
|
| + "references": {
|
| + "description": "The matching references.",
|
| "items": {
|
| - "$ref": "Readset"
|
| + "$ref": "Reference"
|
| },
|
| "type": "array"
|
| }
|
| @@ -2245,7 +2778,7 @@
|
| "type": "object"
|
| },
|
| "Variant": {
|
| - "description": "A Variant represents a change in DNA sequence relative to some reference. For example, a Variant could represent a SNP or an insertion. Variants belong to a variant set.",
|
| + "description": "A variant represents a change in DNA sequence relative to a reference sequence. For example, a variant could represent a SNP or an insertion. Variants belong to a variant set. Each of the calls on a variant represent a determination of genotype with respect to that variant. For example, a call might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related calls typically from one sample.",
|
| "id": "Variant",
|
| "properties": {
|
| "alternateBases": {
|
| @@ -2327,7 +2860,7 @@
|
| "type": "object"
|
| },
|
| "VariantSet": {
|
| - "description": "A VariantSet represents a collection of Variants and their summary statistics.",
|
| + "description": "A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.",
|
| "id": "VariantSet",
|
| "properties": {
|
| "datasetId": {
|
| @@ -2356,7 +2889,7 @@
|
| "type": "object"
|
| }
|
| },
|
| - "servicePath": "genomics/v1beta/",
|
| + "servicePath": "genomics/v1beta2/",
|
| "title": "Genomics API",
|
| - "version": "v1beta"
|
| + "version": "v1beta2"
|
| }
|
|
|
Chromium Code Reviews
Issue 698403003:
Api roll 5: 2014-11-05 (Closed)
Base URL: git@github.com:dart-lang/googleapis.git@master