Api roll 5: 2014-11-05

discovery/googleapis_beta/genomics__v1beta.json

 {
     "auth": {
         "oauth2": {
             "scopes": {
                 "https://www.googleapis.com/auth/bigquery": {
                     "description": "View and manage your data in Google BigQuery"
                 },
                 "https://www.googleapis.com/auth/devstorage.read_write": {
                     "description": "Manage your data in Google Cloud Storage"
                 },
                 "https://www.googleapis.com/auth/genomics": {
                     "description": "View and manage Genomics data"
                 },
                 "https://www.googleapis.com/auth/genomics.readonly": {
                     "description": "View Genomics data"
                 }
             }
         }
     },
     "basePath": "/genomics/v1beta/",
     "baseUrl": "https://www.googleapis.com/genomics/v1beta/",
     "batchPath": "batch",
     "description": "Provides access to Genomics data.",
     "discoveryVersion": "v1",
     "documentationLink": "https://developers.google.com/genomics/v1beta/reference",
-    "etag": "\"l66ggWbucbkBw9Lpos72oziyefE/QFkFkv2LMi0ob1p4dyYfQYJIVYc\"",
+    "etag": "\"l66ggWbucbkBw9Lpos72oziyefE/xe5Z99J2tlpBm9VuKqX5fLUBm4I\"",
     "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",
     "kind": "discovery#restDescription",
     "name": "genomics",
     "ownerDomain": "google.com",
     "ownerName": "Google",
     "parameters": {
@@ skipping 36 matching lines @@
             "type": "string"
         },
         "userIp": {
             "description": "IP address of the site where the request originates. Use this if you want to enforce per-user limits.",
             "location": "query",
             "type": "string"
         }
     },
     "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": {
-                        "$ref": "Beacon"
-                    }
-                }
-            }
-        },
         "callsets": {
             "methods": {
                 "create": {
                     "description": "Creates a new call set.",
                     "httpMethod": "POST",
                     "id": "genomics.callsets.create",
                     "path": "callsets",
                     "request": {
                         "$ref": "CallSet"
                     },
                     "response": {
                         "$ref": "CallSet"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics"
                     ]
                 },
                 "delete": {
                     "description": "Deletes a call set.",
                     "httpMethod": "DELETE",
                     "id": "genomics.callsets.delete",
                     "parameterOrder": [
                         "callSetId"
                     ],
                     "parameters": {
                         "callSetId": {
-                            "description": "The ID of the callset to be deleted.",
+                            "description": "The ID of the call set to be deleted.",
                             "location": "path",
                             "required": true,
                             "type": "string"
                         }
                     },
                     "path": "callsets/{callSetId}",
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics"
                     ]
                 },
                 "get": {
                     "description": "Gets a call set by ID.",
                     "httpMethod": "GET",
                     "id": "genomics.callsets.get",
                     "parameterOrder": [
                         "callSetId"
                     ],
                     "parameters": {
                         "callSetId": {
-                            "description": "The ID of the callset.",
+                            "description": "The ID of the call set.",
                             "location": "path",
                             "required": true,
                             "type": "string"
                         }
                     },
                     "path": "callsets/{callSetId}",
                     "response": {
                         "$ref": "CallSet"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics",
                         "https://www.googleapis.com/auth/genomics.readonly"
                     ]
                 },
                 "patch": {
                     "description": "Updates a call set. This method supports patch semantics.",
                     "httpMethod": "PATCH",
                     "id": "genomics.callsets.patch",
                     "parameterOrder": [
                         "callSetId"
                     ],
                     "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"
                         }
                     },
                     "path": "callsets/{callSetId}",
                     "request": {
                         "$ref": "CallSet"
                     },
                     "response": {
                         "$ref": "CallSet"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics"
                     ]
                 },
                 "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",
                     "request": {
                         "$ref": "SearchCallSetsRequest"
                     },
                     "response": {
                         "$ref": "SearchCallSetsResponse"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics",
                         "https://www.googleapis.com/auth/genomics.readonly"
                     ]
                 },
                 "update": {
                     "description": "Updates a call set.",
                     "httpMethod": "PUT",
                     "id": "genomics.callsets.update",
                     "parameterOrder": [
                         "callSetId"
                     ],
                     "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"
                         }
                     },
                     "path": "callsets/{callSetId}",
                     "request": {
                         "$ref": "CallSet"
                     },
                     "response": {
@@ skipping 568 matching lines @@
                     "path": "variants/{variantId}",
                     "response": {
                         "$ref": "Variant"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics",
                         "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.",
+                    "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 variant set.",
                     "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",
                     "request": {
                         "$ref": "SearchVariantsRequest"
                     },
                     "response": {
                         "$ref": "SearchVariantsResponse"
                     },
                     "scopes": [
@@ skipping 89 matching lines @@
                             "required": true,
                             "type": "string"
                         }
                     },
                     "path": "variantsets/{variantSetId}/mergeVariants",
                     "request": {
                         "$ref": "MergeVariantsRequest"
                     }
                 },
                 "patch": {
-                    "description": "Updates a variant set's metadata. All other modifications are silently ignored. Returns the modified variant set. This method supports patch semantics.",
+                    "description": "Updates a variant set's metadata. All other modifications are silently ignored. This method supports patch semantics.",
                     "httpMethod": "PATCH",
                     "id": "genomics.variantsets.patch",
                     "parameterOrder": [
                         "variantSetId"
                     ],
                     "parameters": {
                         "variantSetId": {
                             "description": "The ID of the variant to be updated.",
                             "location": "path",
                             "required": true,
                             "type": "string"
                         }
                     },
                     "path": "variantsets/{variantSetId}",
                     "request": {
                         "$ref": "VariantSet"
                     },
                     "response": {
                         "$ref": "VariantSet"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics"
                     ]
                 },
                 "search": {
-                    "description": "Returns a list of all variant sets matching search criteria.",
+                    "description": "Returns a list of all variant sets matching search criteria.\n\nImplements GlobalAllianceApi.searchVariantSets.",
                     "httpMethod": "POST",
                     "id": "genomics.variantsets.search",
                     "path": "variantsets/search",
                     "request": {
                         "$ref": "SearchVariantSetsRequest"
                     },
                     "response": {
                         "$ref": "SearchVariantSetsResponse"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics",
                         "https://www.googleapis.com/auth/genomics.readonly"
                     ]
                 },
                 "update": {
-                    "description": "Updates a variant set's metadata. All other modifications are silently ignored. Returns the modified variant set.",
+                    "description": "Updates a variant set's metadata. All other modifications are silently ignored.",
                     "httpMethod": "PUT",
                     "id": "genomics.variantsets.update",
                     "parameterOrder": [
                         "variantSetId"
                     ],
                     "parameters": {
                         "variantSetId": {
                             "description": "The ID of the variant to be updated.",
                             "location": "path",
                             "required": true,
                             "type": "string"
                         }
                     },
                     "path": "variantsets/{variantSetId}",
                     "request": {
                         "$ref": "VariantSet"
                     },
                     "response": {
                         "$ref": "VariantSet"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics"
                     ]
                 }
             }
         }
     },
-    "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",
-            "properties": {
-                "exists": {
-                    "description": "True if the allele exists on any variant call, false otherwise.",
-                    "type": "boolean"
-                }
-            },
-            "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.",
+            "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": {
                     "description": "The name of the call set this variant call belongs to.",
                     "type": "string"
                 },
@@ skipping 25 matching lines @@
                     "type": "object"
                 },
                 "phaseset": {
                     "description": "If this field is present, this variant call's genotype ordering implies the phase of the bases and is consistent with any other variant calls in the same reference sequence which have the same phaseset value. When importing data from VCF, if the genotype data was phased but no phase set was specified this field will be set to *.",
                     "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": {
                     "description": "The date this call set was created in milliseconds from the epoch.",
                     "format": "int64",
                     "type": "string"
                 },
                 "id": {
                     "description": "The Google generated ID of the call set, immutable.",
                     "type": "string"
                 },
                 "info": {
                     "additionalProperties": {
                         "description": "A string which maps to an array of values.",
                         "items": {
                             "type": "string"
                         },
                         "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": {
                     "description": "The sample ID this call set corresponds to.",
                     "type": "string"
                 },
                 "variantSetIds": {
                     "description": "The IDs of the variant sets this call set belongs to.",
                     "items": {
                         "type": "string"
@@ skipping 41 matching lines @@
                     "type": "string"
                 }
             },
             "type": "object"
         },
         "ExperimentalCreateJobRequest": {
             "description": "The job creation request.",
             "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": {
                     "description": "Specifies where to copy the results of certain pipelines. This should be in the form of gs://bucket/path.",
                     "type": "string"
                 },
                 "pairedSourceUris": {
                     "description": "A list of Google Cloud Storage URIs of paired end .fastq files to operate upon. If specified, this represents the second file of each paired .fastq file. The first file of each pair should be specified in sourceUris.",
                     "items": {
                         "type": "string"
@@ skipping 360 matching lines @@
                 "source": {
                     "description": "The data source of the request, for example, a Google Cloud Storage object path or Readset ID.",
                     "items": {
                         "type": "string"
                     },
                     "type": "array"
                 },
                 "type": {
                     "description": "The original request type.",
                     "enum": [
+                        "alignReadsets",
+                        "callReadsets",
                         "experimentalCreateJob",
                         "exportReadsets",
                         "exportVariants",
                         "importReadsets",
                         "importVariants",
                         "unknownType"
                     ],
                     "enumDescriptions": [
                         "",
                         "",
                         "",
                         "",
                         "",
+                        "",
+                        "",
                         ""
                     ],
                     "type": "string"
                 }
             },
             "type": "object"
         },
         "ListCoverageBucketsResponse": {
             "id": "ListCoverageBucketsResponse",
             "properties": {
@@ skipping 663 matching lines @@
                     "description": "The list of matching Variants.",
                     "items": {
                         "$ref": "Variant"
                     },
                     "type": "array"
                 }
             },
             "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": {
                     "description": "The bases that appear instead of the reference bases.",
                     "items": {
                         "type": "string"
                     },
                     "type": "array"
                 },
                 "calls": {
@@ skipping 61 matching lines @@
                     "type": "string"
                 },
                 "variantSetId": {
                     "description": "The ID of the variant set this variant belongs to.",
                     "type": "string"
                 }
             },
             "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": {
                     "description": "The dataset to which this variant set belongs. Immutable.",
                     "type": "string"
                 },
                 "id": {
                     "description": "The Google-generated ID of the variant set. Immutable.",
                     "type": "string"
                 },
@@ skipping 12 matching lines @@
                     "type": "array"
                 }
             },
             "type": "object"
         }
     },
     "servicePath": "genomics/v1beta/",
     "title": "Genomics API",
     "version": "v1beta"
 }