Api roll 2: 2014-09-29

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": "\"uUWyYHXmEn-ab7WLvo8qNz2S8ws/Z3uHhhm6ncEawcl8acPHr16tDuw\"",
+    "etag": "\"uUWyYHXmEn-ab7WLvo8qNz2S8ws/JbtSbt7h4k1-H-5yVc1lnMxsqb4\"",
     "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 777 matching lines @@
                     "path": "variants/{variantId}",
                     "response": {
                         "$ref": "Variant"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics",
                         "https://www.googleapis.com/auth/genomics.readonly"
                     ]
                 },
                 "import": {
-                    "description": "Creates variant data by asynchronously importing the provided information.",
+                    "description": "Creates variant data by asynchronously importing the provided information. If the destination variant set already contains data, new variants will be merged according to the behavior of mergeVariants.",
                     "httpMethod": "POST",
                     "id": "genomics.variants.import",
                     "path": "variants/import",
                     "request": {
                         "$ref": "ImportVariantsRequest"
                     },
                     "response": {
                         "$ref": "ImportVariantsResponse"
                     },
                     "scopes": [
@@ skipping 84 matching lines @@
                     },
                     "path": "variantsets/{variantSetId}",
                     "response": {
                         "$ref": "VariantSet"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics",
                         "https://www.googleapis.com/auth/genomics.readonly"
                     ]
                 },
+                "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",
+                    "id": "genomics.variantsets.mergeVariants",
+                    "parameterOrder": [
+                        "variantSetId"
+                    ],
+                    "parameters": {
+                        "variantSetId": {
+                            "description": "The destination variant set.",
+                            "location": "path",
+                            "required": true,
+                            "type": "string"
+                        }
+                    },
+                    "path": "variantsets/{variantSetId}/mergeVariants",
+                    "request": {
+                        "$ref": "Variant"
+                    }
+                },
                 "search": {
                     "description": "Returns a list of all variant sets matching search criteria.",
                     "httpMethod": "POST",
                     "id": "genomics.variantsets.search",
                     "path": "variantsets/search",
                     "request": {
                         "$ref": "SearchVariantSetsRequest"
                     },
                     "response": {
                         "$ref": "SearchVariantSetsResponse"
                     },
                     "scopes": [
                         "https://www.googleapis.com/auth/genomics",
                         "https://www.googleapis.com/auth/genomics.readonly"
                     ]
                 }
             }
         }
     },
-    "revision": "20140917",
+    "revision": "20140924",
     "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"
                 }
@@ skipping 122 matching lines @@
                 },
                 "projectId": {
                     "description": "The Google Developers Console project number that this dataset belongs to.",
                     "format": "int64",
                     "type": "string"
                 }
             },
             "type": "object"
         },
         "ExperimentalCreateJobRequest": {
-            "description": "The job creation request.",
+            "description": "The job creation request. Next ID: 12",
             "id": "ExperimentalCreateJobRequest",
             "properties": {
                 "align": {
                     "description": "Specifies whether or not to run the alignment pipeline. At least one of align or callVariants must be provided.",
                     "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.",
                     "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"
                 },
+                "libraryName": {
+                    "description": "For alignment from FASTQ files, this specifies the library name.",
+                    "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"
                     },
                     "type": "array"
                 },
+                "platformName": {
+                    "description": "For alignment from FASTQ files, this specifies the platform name.",
+                    "type": "string"
+                },
+                "platformUnit": {
+                    "description": "For alignment from FASTQ files, this specifies the platform unit.",
+                    "type": "string"
+                },
                 "projectId": {
                     "description": "Required. The Google Cloud Project ID with which to associate the request.",
                     "format": "int64",
                     "type": "string"
                 },
+                "readGroupId": {
+                    "description": "For alignment from FASTQ files, this specifies the read group ID.",
+                    "type": "string"
+                },
+                "sampleName": {
+                    "description": "For alignment from FASTQ files, this specifies the sample name.",
+                    "type": "string"
+                },
                 "sourceUris": {
                     "description": "A list of Google Cloud Storage URIs of data files to operate upon. These can be .bam, interleaved .fastq, or paired .fastq. If specifying paired .fastq files, the first of each pair of files should be listed here, and the second of each pair should be listed in pairedSourceUris.",
                     "items": {
                         "type": "string"
                     },
                     "type": "array"
                 }
             },
             "type": "object"
         },
@@ skipping 10 matching lines @@
         },
         "ExportReadsetsRequest": {
             "description": "The readset export request.",
             "id": "ExportReadsetsRequest",
             "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": {
-                    "description": "The Google Developers Console project number that owns this export. This is the project that will be billed.",
+                    "description": "The Google Developers Console project number that owns this export.",
                     "format": "int64",
                     "type": "string"
                 },
                 "readsetIds": {
                     "description": "The IDs of the readsets to export.",
                     "items": {
                         "type": "string"
                     },
                     "type": "array"
                 },
@@ skipping 16 matching lines @@
                     "type": "string"
                 }
             },
             "type": "object"
         },
         "ExportVariantsRequest": {
             "description": "The variant data export request.",
             "id": "ExportVariantsRequest",
             "properties": {
                 "bigqueryDataset": {
-                    "description": "The BigQuery dataset to export data to. Note that this is distinct from the Genomics concept of \"dataset\". The caller must have WRITE access to this BigQuery dataset.",
+                    "description": "The BigQuery dataset to export data to. Note that this is distinct from the Genomics concept of \"dataset\".",
                     "type": "string"
                 },
                 "bigqueryTable": {
-                    "description": "The BigQuery table to export data to. The caller must have WRITE access to this BigQuery table.",
+                    "description": "The BigQuery table to export data to. If the table doesn't exist, it will be created. If it already exists, it will be overwritten.",
                     "type": "string"
                 },
                 "callSetIds": {
                     "description": "If provided, only variant call information from the specified call sets will be exported. By default all variant calls are exported.",
                     "items": {
                         "type": "string"
                     },
                     "type": "array"
                 },
                 "format": {
                     "description": "The format for the exported data.",
                     "enum": [
                         "bigquery"
                     ],
                     "enumDescriptions": [
                         ""
                     ],
                     "type": "string"
                 },
                 "projectId": {
-                    "description": "The Google Cloud project number that owns this export. This is the project that will be billed.",
+                    "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"
         },
@@ skipping 959 matching lines @@
                 "created": {
                     "description": "The date this variant was created, in milliseconds from the epoch.",
                     "format": "int64",
                     "type": "string"
                 },
                 "end": {
                     "description": "The end position (0-based) of this variant. This corresponds to the first base after the last base in the reference allele. So, the length of the reference allele is (end - start). This is useful for variants that don't explicitly give alternate bases, for example large deletions.",
                     "format": "int64",
                     "type": "string"
                 },
+                "filter": {
+                    "description": "A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters.",
+                    "items": {
+                        "type": "string"
+                    },
+                    "type": "array"
+                },
                 "id": {
                     "description": "The Google generated ID of the variant, 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 variant information.",
                     "type": "object"
                 },
                 "names": {
                     "description": "Names for the variant, for example a RefSNP ID.",
                     "items": {
                         "type": "string"
                     },
                     "type": "array"
                 },
+                "quality": {
+                    "description": "A measure of how likely this variant is to be real. A higher value is better.",
+                    "format": "double",
+                    "type": "number"
+                },
                 "referenceBases": {
                     "description": "The reference bases for this variant. They start at the given position.",
                     "type": "string"
                 },
                 "referenceName": {
                     "description": "The reference on which this variant occurs. (such as chr20 or X)",
                     "type": "string"
                 },
                 "start": {
                     "description": "The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.",
@@ skipping 34 matching lines @@
                     "type": "array"
                 }
             },
             "type": "object"
         }
     },
     "servicePath": "genomics/v1beta/",
     "title": "Genomics API",
     "version": "v1beta"
 }