Api roll 3: 2014-10-08

generated/googleapis_beta/lib/genomics/v1beta.dart

 library googleapis_beta.genomics.v1beta;
 
 import "dart:core" as core;
 import "dart:collection" as collection;
 import "dart:async" as async;
 import "dart:convert" as convert;
 
 import "package:crypto/crypto.dart" as crypto;
 import 'package:http/http.dart' as http;
 import '../src/common_internal.dart' as common_internal;
@@ skipping 1493 matching lines @@
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new Variant.fromJson(data));
   }
 
   /**
    * 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.
+   * 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.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
    * Completes with a [ImportVariantsResponse].
    *
    * Completes with a [common.ApiRequestError] if the API endpoint returned an
    * error.
    *
@@ skipping 216 matching lines @@
    * Request parameters:
    *
    * [variantSetId] - The destination variant set.
    *
    * Completes with a [common.ApiRequestError] if the API endpoint returned an
    * error.
    *
    * If the used [http.Client] completes with an error when making a REST call,
    * this method  will complete with the same error.
    */
-  async.Future mergeVariants(Variant request, core.String variantSetId) {
+  async.Future mergeVariants(MergeVariantsRequest request, core.String variantSetId) {
     var _url = null;
     var _queryParams = new core.Map();
     var _uploadMedia = null;
     var _uploadOptions = null;
     var _downloadOptions = common.DownloadOptions.Metadata;
     var _body = null;
 
     if (request != null) {
       _body = convert.JSON.encode((request).toJson());
     }
@@ skipping 1254 matching lines @@
       _json["datasets"] = datasets.map((value) => (value).toJson()).toList();
     }
     if (nextPageToken != null) {
       _json["nextPageToken"] = nextPageToken;
     }
     return _json;
   }
 }
 
 
+/** Not documented yet. */
+class MergeVariantsRequest {
+  /** The variants to be merged with existing variants. */
+  core.List<Variant> variants;
+
+
+  MergeVariantsRequest();
+
+  MergeVariantsRequest.fromJson(core.Map _json) {
+    if (_json.containsKey("variants")) {
+      variants = _json["variants"].map((value) => new Variant.fromJson(value)).toList();
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (variants != null) {
+      _json["variants"] = variants.map((value) => (value).toJson()).toList();
+    }
+    return _json;
+  }
+}
+
+
 /**
  * Metadata describes a single piece of variant call metadata. These data
  * include a top level key and either a single value string (value) or a list of
  * key-value pairs (info.) Value and info are mutually exclusive.
  */
 class Metadata {
   /** A textual description of this metadata. */
   core.String description;
 
   /**
@@ skipping 1158 matching lines @@
     }
     return _json;
   }
 }
 
 
 /** The variant search request. */
 class SearchVariantsRequest {
   /**
    * Only return variant calls which belong to call sets with these ids. Leaving
-   * this blank returns all variant calls.
+   * this blank returns all variant calls. If a variant has no calls belonging
+   * to any of these call sets, it won't be returned at all. Currently, variants
+   * with no calls from any call set will never be returned.
    */
   core.List<core.String> callSetIds;
 
   /**
    * Required. The end of the window (0-based, exclusive) for which overlapping
    * variants should be returned.
    */
   core.String end;
 
   /**
@@ skipping 339 matching lines @@
       _json["metadata"] = metadata.map((value) => (value).toJson()).toList();
     }
     if (referenceBounds != null) {
       _json["referenceBounds"] = referenceBounds.map((value) => (value).toJson()).toList();
     }
     return _json;
   }
 }