Api roll 5: 2014-11-05

generated/googleapis_beta/lib/genomics/v1beta2.dart

-library googleapis_beta.genomics.v1beta;
+library googleapis_beta.genomics.v1beta2;
 
 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;
 import '../common/common.dart' as common;
@@ skipping 11 matching lines @@
 
   /** View and manage Genomics data */
   static const GenomicsScope = "https://www.googleapis.com/auth/genomics";
 
   /** View Genomics data */
   static const GenomicsReadonlyScope = "https://www.googleapis.com/auth/genomics.readonly";
 
 
   final common_internal.ApiRequester _requester;
 
-  BeaconsResourceApi get beacons => new BeaconsResourceApi(_requester);
   CallsetsResourceApi get callsets => new CallsetsResourceApi(_requester);
   DatasetsResourceApi get datasets => new DatasetsResourceApi(_requester);
   ExperimentalResourceApi get experimental => new ExperimentalResourceApi(_requester);
   JobsResourceApi get jobs => new JobsResourceApi(_requester);
+  ReadgroupsetsResourceApi get readgroupsets => new ReadgroupsetsResourceApi(_requester);
   ReadsResourceApi get reads => new ReadsResourceApi(_requester);
-  ReadsetsResourceApi get readsets => new ReadsetsResourceApi(_requester);
+  ReferencesResourceApi get references => new ReferencesResourceApi(_requester);
+  ReferencesetsResourceApi get referencesets => new ReferencesetsResourceApi(_requester);
   VariantsResourceApi get variants => new VariantsResourceApi(_requester);
   VariantsetsResourceApi get variantsets => new VariantsetsResourceApi(_requester);
 
   GenomicsApi(http.Client client) : 
-      _requester = new common_internal.ApiRequester(client, "https://www.googleapis.com/", "genomics/v1beta/");
+      _requester = new common_internal.ApiRequester(client, "https://www.googleapis.com/", "genomics/v1beta2/");
 }
 
 
-/** Not documented yet. */
-class BeaconsResourceApi {
-  final common_internal.ApiRequester _requester;
-
-  BeaconsResourceApi(common_internal.ApiRequester client) : 
-      _requester = client;
-
-  /**
-   * This is an experimental API that provides a Global Alliance for Genomics
-   * and Health Beacon. It may change at any time.
-   *
-   * Request parameters:
-   *
-   * [variantSetId] - The ID of the variant set to query over. It must be
-   * public. Private variant sets will return an unauthorized exception.
-   *
-   * [allele] - Required. The allele to look for ('A', 'C', 'G' or 'T').
-   *
-   * [position] - Required. The 0-based position to query.
-   *
-   * [referenceName] - Required. The reference to query over.
-   *
-   * Completes with a [Beacon].
-   *
-   * 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<Beacon> get(core.String variantSetId, {core.String allele, core.String position, core.String referenceName}) {
-    var _url = null;
-    var _queryParams = new core.Map();
-    var _uploadMedia = null;
-    var _uploadOptions = null;
-    var _downloadOptions = common.DownloadOptions.Metadata;
-    var _body = null;
-
-    if (variantSetId == null) {
-      throw new core.ArgumentError("Parameter variantSetId is required.");
-    }
-    if (allele != null) {
-      _queryParams["allele"] = [allele];
-    }
-    if (position != null) {
-      _queryParams["position"] = [position];
-    }
-    if (referenceName != null) {
-      _queryParams["referenceName"] = [referenceName];
-    }
-
-
-    _url = 'beacons/' + common_internal.Escaper.ecapeVariable('$variantSetId');
-
-    var _response = _requester.request(_url,
-                                       "GET",
-                                       body: _body,
-                                       queryParams: _queryParams,
-                                       uploadOptions: _uploadOptions,
-                                       uploadMedia: _uploadMedia,
-                                       downloadOptions: _downloadOptions);
-    return _response.then((data) => new Beacon.fromJson(data));
-  }
-
-}
-
-
 /** Not documented yet. */
 class CallsetsResourceApi {
   final common_internal.ApiRequester _requester;
 
   CallsetsResourceApi(common_internal.ApiRequester client) : 
       _requester = client;
 
   /**
    * Creates a new call set.
    *
@@ skipping 32 matching lines @@
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new CallSet.fromJson(data));
   }
 
   /**
    * Deletes a call set.
    *
    * Request parameters:
    *
-   * [callSetId] - The ID of the callset to be deleted.
+   * [callSetId] - The ID of the call set to be deleted.
    *
    * 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 delete(core.String callSetId) {
     var _url = null;
     var _queryParams = new core.Map();
@@ skipping 18 matching lines @@
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => null);
   }
 
   /**
    * Gets a call set by ID.
    *
    * Request parameters:
    *
-   * [callSetId] - The ID of the callset.
+   * [callSetId] - The ID of the call set.
    *
    * Completes with a [CallSet].
    *
    * 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<CallSet> get(core.String callSetId) {
@@ skipping 21 matching lines @@
     return _response.then((data) => new CallSet.fromJson(data));
   }
 
   /**
    * Updates a call set. This method supports patch semantics.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * [callSetId] - The ID of the callset to be updated.
+   * [callSetId] - The ID of the call set to be updated.
    *
    * Completes with a [CallSet].
    *
    * 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<CallSet> patch(CallSet request, core.String callSetId) {
@@ skipping 20 matching lines @@
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new CallSet.fromJson(data));
   }
 
   /**
    * Gets a list of call sets matching the criteria.
    *
+   * Implements GlobalAllianceApi.searchCallSets.
+   *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
    * Completes with a [SearchCallSetsResponse].
    *
    * 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,
@@ skipping 24 matching lines @@
     return _response.then((data) => new SearchCallSetsResponse.fromJson(data));
   }
 
   /**
    * Updates a call set.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * [callSetId] - The ID of the callset to be updated.
+   * [callSetId] - The ID of the call set to be updated.
    *
    * Completes with a [CallSet].
    *
    * 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<CallSet> update(CallSet request, core.String callSetId) {
@@ skipping 151 matching lines @@
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new Dataset.fromJson(data));
   }
 
   /**
    * Lists all datasets.
    *
    * Request parameters:
    *
-   * [maxResults] - The maximum number of results returned by this request.
+   * [pageSize] - The maximum number of results returned by this request.
    *
    * [pageToken] - 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.
    *
-   * [projectId] - 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.
+   * [projectNumber] - 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.
    *
    * Completes with a [ListDatasetsResponse].
    *
    * 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<ListDatasetsResponse> list({core.String maxResults, core.String pageToken, core.String projectId}) {
+  async.Future<ListDatasetsResponse> list({core.int pageSize, core.String pageToken, core.String projectNumber}) {
     var _url = null;
     var _queryParams = new core.Map();
     var _uploadMedia = null;
     var _uploadOptions = null;
     var _downloadOptions = common.DownloadOptions.Metadata;
     var _body = null;
 
-    if (maxResults != null) {
-      _queryParams["maxResults"] = [maxResults];
+    if (pageSize != null) {
+      _queryParams["pageSize"] = ["${pageSize}"];
     }
     if (pageToken != null) {
       _queryParams["pageToken"] = [pageToken];
     }
-    if (projectId != null) {
-      _queryParams["projectId"] = [projectId];
+    if (projectNumber != null) {
+      _queryParams["projectNumber"] = [projectNumber];
     }
 
 
     _url = 'datasets';
 
     var _response = _requester.request(_url,
                                        "GET",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
@@ skipping 322 matching lines @@
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new SearchJobsResponse.fromJson(data));
   }
 
 }
 
 
 /** Not documented yet. */
-class ReadsResourceApi {
+class ReadgroupsetsResourceApi {
   final common_internal.ApiRequester _requester;
 
-  ReadsResourceApi(common_internal.ApiRequester client) : 
+  ReadgroupsetsCoveragebucketsResourceApi get coveragebuckets => new ReadgroupsetsCoveragebucketsResourceApi(_requester);
+
+  ReadgroupsetsResourceApi(common_internal.ApiRequester client) : 
       _requester = client;
 
   /**
-   * 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.
+   * Aligns read data from existing read group sets or files from Google Cloud
+   * Storage. See the  alignment and variant calling documentation for more
+   * details.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * Completes with a [SearchReadsResponse].
+   * Completes with a [AlignReadGroupSetsResponse].
    *
    * 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<SearchReadsResponse> search(SearchReadsRequest request) {
+  async.Future<AlignReadGroupSetsResponse> align(AlignReadGroupSetsRequest request) {
     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());
     }
 
 
-    _url = 'reads/search';
+    _url = 'readgroupsets/align';
 
     var _response = _requester.request(_url,
                                        "POST",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new SearchReadsResponse.fromJson(data));
+    return _response.then((data) => new AlignReadGroupSetsResponse.fromJson(data));
   }
 
-}
-
-
-/** Not documented yet. */
-class ReadsetsResourceApi {
-  final common_internal.ApiRequester _requester;
-
-  ReadsetsCoveragebucketsResourceApi get coveragebuckets => new ReadsetsCoveragebucketsResourceApi(_requester);
-
-  ReadsetsResourceApi(common_internal.ApiRequester client) : 
-      _requester = client;
-
   /**
-   * Deletes a readset.
+   * 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.
+   *
+   * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * [readsetId] - The ID of the readset to be deleted. The caller must have
-   * WRITE permissions to the dataset associated with this readset.
+   * Completes with a [CallReadGroupSetsResponse].
    *
    * 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<CallReadGroupSetsResponse> call(CallReadGroupSetsRequest request) {
+    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());
+    }
+
+
+    _url = 'readgroupsets/call';
+
+    var _response = _requester.request(_url,
+                                       "POST",
+                                       body: _body,
+                                       queryParams: _queryParams,
+                                       uploadOptions: _uploadOptions,
+                                       uploadMedia: _uploadMedia,
+                                       downloadOptions: _downloadOptions);
+    return _response.then((data) => new CallReadGroupSetsResponse.fromJson(data));
+  }
+
+  /**
+   * Deletes a read group set.
+   *
+   * Request parameters:
+   *
+   * [readGroupSetId] - 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.
+   *
+   * 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 delete(core.String readsetId) {
+  async.Future delete(core.String readGroupSetId) {
     var _url = null;
     var _queryParams = new core.Map();
     var _uploadMedia = null;
     var _uploadOptions = null;
     var _downloadOptions = common.DownloadOptions.Metadata;
     var _body = null;
 
-    if (readsetId == null) {
-      throw new core.ArgumentError("Parameter readsetId is required.");
+    if (readGroupSetId == null) {
+      throw new core.ArgumentError("Parameter readGroupSetId is required.");
     }
 
     _downloadOptions = null;
 
-    _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
+    _url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
 
     var _response = _requester.request(_url,
                                        "DELETE",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => null);
   }
 
   /**
-   * 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.
+   * Exports read group sets 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.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * Completes with a [ExportReadsetsResponse].
+   * Completes with a [ExportReadGroupSetsResponse].
    *
    * 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<ExportReadsetsResponse> export(ExportReadsetsRequest request) {
+  async.Future<ExportReadGroupSetsResponse> export(ExportReadGroupSetsRequest request) {
     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());
     }
 
 
-    _url = 'readsets/export';
+    _url = 'readgroupsets/export';
 
     var _response = _requester.request(_url,
                                        "POST",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new ExportReadsetsResponse.fromJson(data));
+    return _response.then((data) => new ExportReadGroupSetsResponse.fromJson(data));
   }
 
   /**
-   * Gets a readset by ID.
+   * Gets a read group set by ID.
    *
    * Request parameters:
    *
-   * [readsetId] - The ID of the readset.
+   * [readGroupSetId] - The ID of the read group set.
    *
-   * Completes with a [Readset].
+   * Completes with a [ReadGroupSet].
    *
    * 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<Readset> get(core.String readsetId) {
+  async.Future<ReadGroupSet> get(core.String readGroupSetId) {
     var _url = null;
     var _queryParams = new core.Map();
     var _uploadMedia = null;
     var _uploadOptions = null;
     var _downloadOptions = common.DownloadOptions.Metadata;
     var _body = null;
 
-    if (readsetId == null) {
-      throw new core.ArgumentError("Parameter readsetId is required.");
+    if (readGroupSetId == null) {
+      throw new core.ArgumentError("Parameter readGroupSetId is required.");
     }
 
 
-    _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
+    _url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
 
     var _response = _requester.request(_url,
                                        "GET",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new Readset.fromJson(data));
+    return _response.then((data) => new ReadGroupSet.fromJson(data));
   }
 
   /**
-   * 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.
+   * Creates read group sets 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.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * Completes with a [ImportReadsetsResponse].
+   * Completes with a [ImportReadGroupSetsResponse].
    *
    * 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<ImportReadsetsResponse> import(ImportReadsetsRequest request) {
+  async.Future<ImportReadGroupSetsResponse> import(ImportReadGroupSetsRequest request) {
     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());
     }
 
 
-    _url = 'readsets/import';
+    _url = 'readgroupsets/import';
 
     var _response = _requester.request(_url,
                                        "POST",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new ImportReadsetsResponse.fromJson(data));
+    return _response.then((data) => new ImportReadGroupSetsResponse.fromJson(data));
   }
 
   /**
-   * Updates a readset. This method supports patch semantics.
+   * Updates a read group set. This method supports patch semantics.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * [readsetId] - The ID of the readset to be updated. The caller must have
-   * WRITE permissions to the dataset associated with this readset.
+   * [readGroupSetId] - 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.
    *
-   * Completes with a [Readset].
+   * Completes with a [ReadGroupSet].
    *
    * 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<Readset> patch(Readset request, core.String readsetId) {
+  async.Future<ReadGroupSet> patch(ReadGroupSet request, core.String readGroupSetId) {
     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());
     }
-    if (readsetId == null) {
-      throw new core.ArgumentError("Parameter readsetId is required.");
+    if (readGroupSetId == null) {
+      throw new core.ArgumentError("Parameter readGroupSetId is required.");
     }
 
 
-    _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
+    _url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
 
     var _response = _requester.request(_url,
                                        "PATCH",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new Readset.fromJson(data));
+    return _response.then((data) => new ReadGroupSet.fromJson(data));
   }
 
   /**
-   * Gets a list of readsets matching the criteria.
+   * Searches for read group sets matching the criteria.
+   *
+   * Implements GlobalAllianceApi.searchReadGroupSets.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * Completes with a [SearchReadsetsResponse].
+   * Completes with a [SearchReadGroupSetsResponse].
    *
    * 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<SearchReadsetsResponse> search(SearchReadsetsRequest request) {
+  async.Future<SearchReadGroupSetsResponse> search(SearchReadGroupSetsRequest request) {
     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());
     }
 
 
-    _url = 'readsets/search';
+    _url = 'readgroupsets/search';
 
     var _response = _requester.request(_url,
                                        "POST",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new SearchReadsetsResponse.fromJson(data));
+    return _response.then((data) => new SearchReadGroupSetsResponse.fromJson(data));
   }
 
   /**
-   * Updates a readset.
+   * Updates a read group set.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * [readsetId] - The ID of the readset to be updated. The caller must have
-   * WRITE permissions to the dataset associated with this readset.
+   * [readGroupSetId] - 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.
    *
-   * Completes with a [Readset].
+   * Completes with a [ReadGroupSet].
    *
    * 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<Readset> update(Readset request, core.String readsetId) {
+  async.Future<ReadGroupSet> update(ReadGroupSet request, core.String readGroupSetId) {
     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());
     }
-    if (readsetId == null) {
-      throw new core.ArgumentError("Parameter readsetId is required.");
+    if (readGroupSetId == null) {
+      throw new core.ArgumentError("Parameter readGroupSetId is required.");
     }
 
 
-    _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
+    _url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
 
     var _response = _requester.request(_url,
                                        "PUT",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new Readset.fromJson(data));
+    return _response.then((data) => new ReadGroupSet.fromJson(data));
   }
 
 }
 
 
 /** Not documented yet. */
-class ReadsetsCoveragebucketsResourceApi {
+class ReadgroupsetsCoveragebucketsResourceApi {
   final common_internal.ApiRequester _requester;
 
-  ReadsetsCoveragebucketsResourceApi(common_internal.ApiRequester client) : 
+  ReadgroupsetsCoveragebucketsResourceApi(common_internal.ApiRequester client) : 
       _requester = client;
 
   /**
-   * 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.
+   * 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.
+   *
+   * Coverage 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.
    *
    * Request parameters:
    *
-   * [readsetId] - Required. The ID of the readset over which coverage is
-   * requested.
+   * [readGroupSetId] - Required. The ID of the read group set over which
+   * coverage is requested.
    *
-   * [maxResults] - The maximum number of results to return in a single page. If
+   * [pageSize] - The maximum number of results to return in a single page. If
    * unspecified, defaults to 1024. The maximum value is 2048.
    *
    * [pageToken] - 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.
    *
-   * [range_sequenceEnd] - The end position of the range on the reference,
-   * 1-based exclusive. If specified, sequenceName must also be specified.
+   * [range_end] - The end position of the range on the reference, 0-based
+   * exclusive. If specified, referenceName must also be specified.
    *
-   * [range_sequenceName] - The reference sequence name, for example chr1, 1, or
-   * chrX.
+   * [range_referenceName] - The reference sequence name, for example chr1, 1,
+   * or chrX.
    *
-   * [range_sequenceStart] - The start position of the range on the reference,
-   * 1-based inclusive. If specified, sequenceName must also be specified.
+   * [range_start] - The start position of the range on the reference, 0-based
+   * inclusive. If specified, referenceName must also be specified.
    *
    * [targetBucketWidth] - 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.
    *
    * Completes with a [ListCoverageBucketsResponse].
    *
    * 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<ListCoverageBucketsResponse> list(core.String readsetId, {core.String maxResults, core.String pageToken, core.String range_sequenceEnd, core.String range_sequenceName, core.String range_sequenceStart, core.String targetBucketWidth}) {
+  async.Future<ListCoverageBucketsResponse> list(core.String readGroupSetId, {core.int pageSize, core.String pageToken, core.String range_end, core.String range_referenceName, core.String range_start, core.String targetBucketWidth}) {
     var _url = null;
     var _queryParams = new core.Map();
     var _uploadMedia = null;
     var _uploadOptions = null;
     var _downloadOptions = common.DownloadOptions.Metadata;
     var _body = null;
 
-    if (readsetId == null) {
-      throw new core.ArgumentError("Parameter readsetId is required.");
+    if (readGroupSetId == null) {
+      throw new core.ArgumentError("Parameter readGroupSetId is required.");
     }
-    if (maxResults != null) {
-      _queryParams["maxResults"] = [maxResults];
+    if (pageSize != null) {
+      _queryParams["pageSize"] = ["${pageSize}"];
     }
     if (pageToken != null) {
       _queryParams["pageToken"] = [pageToken];
     }
-    if (range_sequenceEnd != null) {
-      _queryParams["range.sequenceEnd"] = [range_sequenceEnd];
+    if (range_end != null) {
+      _queryParams["range.end"] = [range_end];
     }
-    if (range_sequenceName != null) {
-      _queryParams["range.sequenceName"] = [range_sequenceName];
+    if (range_referenceName != null) {
+      _queryParams["range.referenceName"] = [range_referenceName];
     }
-    if (range_sequenceStart != null) {
-      _queryParams["range.sequenceStart"] = [range_sequenceStart];
+    if (range_start != null) {
+      _queryParams["range.start"] = [range_start];
     }
     if (targetBucketWidth != null) {
       _queryParams["targetBucketWidth"] = [targetBucketWidth];
     }
 
 
-    _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId') + '/coveragebuckets';
+    _url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId') + '/coveragebuckets';
 
     var _response = _requester.request(_url,
                                        "GET",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new ListCoverageBucketsResponse.fromJson(data));
   }
 
 }
 
 
 /** Not documented yet. */
-class VariantsResourceApi {
+class ReadsResourceApi {
   final common_internal.ApiRequester _requester;
 
-  VariantsResourceApi(common_internal.ApiRequester client) : 
+  ReadsResourceApi(common_internal.ApiRequester client) : 
       _requester = client;
 
   /**
-   * Creates a new variant.
+   * 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.
+   *
+   * 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 read group set IDs yields all reads in those read group
+   * sets, 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.
+   *
+   * Implements GlobalAllianceApi.searchReads.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * Completes with a [Variant].
+   * Completes with a [SearchReadsResponse].
    *
    * 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<Variant> create(Variant request) {
+  async.Future<SearchReadsResponse> search(SearchReadsRequest request) {
     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());
     }
 
 
-    _url = 'variants';
+    _url = 'reads/search';
 
     var _response = _requester.request(_url,
                                        "POST",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new Variant.fromJson(data));
+    return _response.then((data) => new SearchReadsResponse.fromJson(data));
   }
 
+}
+
+
+/** Not documented yet. */
+class ReferencesResourceApi {
+  final common_internal.ApiRequester _requester;
+
+  ReferencesBasesResourceApi get bases => new ReferencesBasesResourceApi(_requester);
+
+  ReferencesResourceApi(common_internal.ApiRequester client) : 
+      _requester = client;
+
   /**
-   * Deletes a variant.
+   * Gets a reference.
+   *
+   * Implements GlobalAllianceApi.getReference.
    *
    * Request parameters:
    *
-   * [variantId] - The ID of the variant to be deleted.
+   * [referenceId] - The ID of the reference.
+   *
+   * Completes with a [Reference].
    *
    * 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 delete(core.String variantId) {
+  async.Future<Reference> get(core.String referenceId) {
     var _url = null;
     var _queryParams = new core.Map();
     var _uploadMedia = null;
     var _uploadOptions = null;
     var _downloadOptions = common.DownloadOptions.Metadata;
     var _body = null;
 
-    if (variantId == null) {
-      throw new core.ArgumentError("Parameter variantId is required.");
+    if (referenceId == null) {
+      throw new core.ArgumentError("Parameter referenceId is required.");
     }
 
-    _downloadOptions = null;
 
-    _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
+    _url = 'references/' + common_internal.Escaper.ecapeVariable('$referenceId');
 
     var _response = _requester.request(_url,
-                                       "DELETE",
+                                       "GET",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => null);
+    return _response.then((data) => new Reference.fromJson(data));
   }
 
   /**
-   * Exports variant data to an external destination.
+   * Searches for references which match the given criteria.
+   *
+   * Implements GlobalAllianceApi.searchReferences.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * Completes with a [ExportVariantsResponse].
+   * Completes with a [SearchReferencesResponse].
    *
    * 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<ExportVariantsResponse> export(ExportVariantsRequest request) {
+  async.Future<SearchReferencesResponse> search(SearchReferencesRequest request) {
     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());
     }
 
 
-    _url = 'variants/export';
+    _url = 'references/search';
 
     var _response = _requester.request(_url,
                                        "POST",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new ExportVariantsResponse.fromJson(data));
+    return _response.then((data) => new SearchReferencesResponse.fromJson(data));
   }
 
+}
+
+
+/** Not documented yet. */
+class ReferencesBasesResourceApi {
+  final common_internal.ApiRequester _requester;
+
+  ReferencesBasesResourceApi(common_internal.ApiRequester client) : 
+      _requester = client;
+
   /**
-   * Gets a variant by ID.
+   * Lists the bases in a reference, optionally restricted to a range.
+   *
+   * Implements GlobalAllianceApi.getReferenceBases.
    *
    * Request parameters:
    *
-   * [variantId] - The ID of the variant.
+   * [referenceId] - The ID of the reference.
    *
-   * Completes with a [Variant].
+   * [end] - The end position (0-based, exclusive) of this query. Defaults to
+   * the length of this reference.
+   *
+   * [pageSize] - Specifies the maximum number of bases to return in a single
+   * page.
+   *
+   * [pageToken] - 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.
+   *
+   * [start] - The start position (0-based) of this query. Defaults to 0.
+   *
+   * Completes with a [ListBasesResponse].
    *
    * 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<Variant> get(core.String variantId) {
+  async.Future<ListBasesResponse> list(core.String referenceId, {core.String end, core.int pageSize, core.String pageToken, core.String start}) {
     var _url = null;
     var _queryParams = new core.Map();
     var _uploadMedia = null;
     var _uploadOptions = null;
     var _downloadOptions = common.DownloadOptions.Metadata;
     var _body = null;
 
-    if (variantId == null) {
-      throw new core.ArgumentError("Parameter variantId is required.");
+    if (referenceId == null) {
+      throw new core.ArgumentError("Parameter referenceId is required.");
+    }
+    if (end != null) {
+      _queryParams["end"] = [end];
+    }
+    if (pageSize != null) {
+      _queryParams["pageSize"] = ["${pageSize}"];
+    }
+    if (pageToken != null) {
+      _queryParams["pageToken"] = [pageToken];
+    }
+    if (start != null) {
+      _queryParams["start"] = [start];
     }
 
 
-    _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
+    _url = 'references/' + common_internal.Escaper.ecapeVariable('$referenceId') + '/bases';
 
     var _response = _requester.request(_url,
                                        "GET",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new Variant.fromJson(data));
+    return _response.then((data) => new ListBasesResponse.fromJson(data));
   }
 
+}
+
+
+/** Not documented yet. */
+class ReferencesetsResourceApi {
+  final common_internal.ApiRequester _requester;
+
+  ReferencesetsResourceApi(common_internal.ApiRequester client) : 
+      _requester = client;
+
   /**
-   * 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.
+   * Gets a reference set.
    *
-   * [request] - The metadata request object.
+   * Implements GlobalAllianceApi.getReferenceSet.
    *
    * Request parameters:
    *
-   * Completes with a [ImportVariantsResponse].
+   * [referenceSetId] - The ID of the reference set.
+   *
+   * Completes with a [ReferenceSet].
    *
    * 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<ImportVariantsResponse> import(ImportVariantsRequest request) {
+  async.Future<ReferenceSet> get(core.String referenceSetId) {
     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());
+    if (referenceSetId == null) {
+      throw new core.ArgumentError("Parameter referenceSetId is required.");
     }
 
 
-    _url = 'variants/import';
+    _url = 'referencesets/' + common_internal.Escaper.ecapeVariable('$referenceSetId');
 
     var _response = _requester.request(_url,
-                                       "POST",
+                                       "GET",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new ImportVariantsResponse.fromJson(data));
+    return _response.then((data) => new ReferenceSet.fromJson(data));
   }
 
   /**
-   * Gets a list of variants matching the criteria.
+   * Searches for reference sets which match the given criteria.
+   *
+   * Implements GlobalAllianceApi.searchReferenceSets.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * Completes with a [SearchVariantsResponse].
+   * Completes with a [SearchReferenceSetsResponse].
    *
    * 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<SearchVariantsResponse> search(SearchVariantsRequest request) {
+  async.Future<SearchReferenceSetsResponse> search(SearchReferenceSetsRequest request) {
     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());
     }
 
 
-    _url = 'variants/search';
+    _url = 'referencesets/search';
 
     var _response = _requester.request(_url,
                                        "POST",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
-    return _response.then((data) => new SearchVariantsResponse.fromJson(data));
+    return _response.then((data) => new SearchReferenceSetsResponse.fromJson(data));
   }
 
+}
+
+
+/** Not documented yet. */
+class VariantsResourceApi {
+  final common_internal.ApiRequester _requester;
+
+  VariantsResourceApi(common_internal.ApiRequester client) : 
+      _requester = client;
+
   /**
-   * Updates a variant's names and info fields. All other modifications are
-   * silently ignored. Returns the modified variant without its calls.
+   * Creates a new variant.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
-   * [variantId] - The ID of the variant to be updated.
-   *
    * Completes with a [Variant].
    *
    * 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<Variant> update(Variant request, core.String variantId) {
+  async.Future<Variant> create(Variant request) {
     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());
     }
-    if (variantId == null) {
-      throw new core.ArgumentError("Parameter variantId is required.");
-    }
 
 
-    _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
+    _url = 'variants';
 
     var _response = _requester.request(_url,
-                                       "PUT",
+                                       "POST",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new Variant.fromJson(data));
   }
 
-}
-
-
-/** Not documented yet. */
-class VariantsetsResourceApi {
-  final common_internal.ApiRequester _requester;
-
-  VariantsetsResourceApi(common_internal.ApiRequester client) : 
-      _requester = client;
-
   /**
-   * Deletes the contents of a variant set. The variant set object is not
-   * deleted.
+   * Deletes a variant.
    *
    * Request parameters:
    *
-   * [variantSetId] - The ID of the variant set to be deleted.
+   * [variantId] - The ID of the variant to be deleted.
    *
    * 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 delete(core.String variantSetId) {
+  async.Future delete(core.String variantId) {
     var _url = null;
     var _queryParams = new core.Map();
     var _uploadMedia = null;
     var _uploadOptions = null;
     var _downloadOptions = common.DownloadOptions.Metadata;
     var _body = null;
 
-    if (variantSetId == null) {
-      throw new core.ArgumentError("Parameter variantSetId is required.");
+    if (variantId == null) {
+      throw new core.ArgumentError("Parameter variantId is required.");
     }
 
     _downloadOptions = null;
 
-    _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
+    _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
 
     var _response = _requester.request(_url,
                                        "DELETE",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => null);
   }
 
   /**
-   * Gets a variant set by ID.
+   * Gets a variant by ID.
    *
    * Request parameters:
    *
-   * [variantSetId] - Required. The ID of the variant set.
+   * [variantId] - The ID of the variant.
    *
-   * Completes with a [VariantSet].
+   * Completes with a [Variant].
    *
    * 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<VariantSet> get(core.String variantSetId) {
+  async.Future<Variant> get(core.String variantId) {
     var _url = null;
     var _queryParams = new core.Map();
     var _uploadMedia = null;
     var _uploadOptions = null;
     var _downloadOptions = common.DownloadOptions.Metadata;
     var _body = null;
 
+    if (variantId == null) {
+      throw new core.ArgumentError("Parameter variantId is required.");
+    }
+
+
+    _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
+
+    var _response = _requester.request(_url,
+                                       "GET",
+                                       body: _body,
+                                       queryParams: _queryParams,
+                                       uploadOptions: _uploadOptions,
+                                       uploadMedia: _uploadMedia,
+                                       downloadOptions: _downloadOptions);
+    return _response.then((data) => new Variant.fromJson(data));
+  }
+
+  /**
+   * Gets a list of variants matching the criteria.
+   *
+   * Implements GlobalAllianceApi.searchVariants.
+   *
+   * [request] - The metadata request object.
+   *
+   * Request parameters:
+   *
+   * Completes with a [SearchVariantsResponse].
+   *
+   * 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<SearchVariantsResponse> search(SearchVariantsRequest request) {
+    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());
+    }
+
+
+    _url = 'variants/search';
+
+    var _response = _requester.request(_url,
+                                       "POST",
+                                       body: _body,
+                                       queryParams: _queryParams,
+                                       uploadOptions: _uploadOptions,
+                                       uploadMedia: _uploadMedia,
+                                       downloadOptions: _downloadOptions);
+    return _response.then((data) => new SearchVariantsResponse.fromJson(data));
+  }
+
+  /**
+   * Updates a variant's names and info fields. All other modifications are
+   * silently ignored. Returns the modified variant without its calls.
+   *
+   * [request] - The metadata request object.
+   *
+   * Request parameters:
+   *
+   * [variantId] - The ID of the variant to be updated.
+   *
+   * Completes with a [Variant].
+   *
+   * 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<Variant> update(Variant request, core.String variantId) {
+    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());
+    }
+    if (variantId == null) {
+      throw new core.ArgumentError("Parameter variantId is required.");
+    }
+
+
+    _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
+
+    var _response = _requester.request(_url,
+                                       "PUT",
+                                       body: _body,
+                                       queryParams: _queryParams,
+                                       uploadOptions: _uploadOptions,
+                                       uploadMedia: _uploadMedia,
+                                       downloadOptions: _downloadOptions);
+    return _response.then((data) => new Variant.fromJson(data));
+  }
+
+}
+
+
+/** Not documented yet. */
+class VariantsetsResourceApi {
+  final common_internal.ApiRequester _requester;
+
+  VariantsetsResourceApi(common_internal.ApiRequester client) : 
+      _requester = client;
+
+  /**
+   * Deletes the contents of a variant set. The variant set object is not
+   * deleted.
+   *
+   * Request parameters:
+   *
+   * [variantSetId] - The ID of the variant set to be deleted.
+   *
+   * 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 delete(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 (variantSetId == null) {
       throw new core.ArgumentError("Parameter variantSetId is required.");
     }
 
+    _downloadOptions = null;
+
+    _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
+
+    var _response = _requester.request(_url,
+                                       "DELETE",
+                                       body: _body,
+                                       queryParams: _queryParams,
+                                       uploadOptions: _uploadOptions,
+                                       uploadMedia: _uploadMedia,
+                                       downloadOptions: _downloadOptions);
+    return _response.then((data) => null);
+  }
+
+  /**
+   * Exports variant set data to an external destination.
+   *
+   * [request] - The metadata request object.
+   *
+   * Request parameters:
+   *
+   * [variantSetId] - Required. The ID of the variant set that contains variant
+   * data which should be exported. The caller must have READ access to this
+   * variant set.
+   *
+   * Completes with a [ExportVariantSetResponse].
+   *
+   * Completes with a [common.ApiRequestError] if the API endpoint returned an
+   * error.
+   *
+   * If the used [http.Client] completes with an error when making a REST call,
+   * this method  will complete with the same error.
+   */
+  async.Future<ExportVariantSetResponse> export(ExportVariantSetRequest request, core.String variantSetId) {
+    var _url = null;
+    var _queryParams = new core.Map();
+    var _uploadMedia = null;
+    var _uploadOptions = null;
+    var _downloadOptions = common.DownloadOptions.Metadata;
+    var _body = null;
+
+    if (request != null) {
+      _body = convert.JSON.encode((request).toJson());
+    }
+    if (variantSetId == null) {
+      throw new core.ArgumentError("Parameter variantSetId is required.");
+    }
+
+
+    _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId') + '/export';
+
+    var _response = _requester.request(_url,
+                                       "POST",
+                                       body: _body,
+                                       queryParams: _queryParams,
+                                       uploadOptions: _uploadOptions,
+                                       uploadMedia: _uploadMedia,
+                                       downloadOptions: _downloadOptions);
+    return _response.then((data) => new ExportVariantSetResponse.fromJson(data));
+  }
+
+  /**
+   * Gets a variant set by ID.
+   *
+   * Request parameters:
+   *
+   * [variantSetId] - Required. The ID of the variant set.
+   *
+   * Completes with a [VariantSet].
+   *
+   * 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<VariantSet> get(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 (variantSetId == null) {
+      throw new core.ArgumentError("Parameter variantSetId is required.");
+    }
+
 
     _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
 
     var _response = _requester.request(_url,
                                        "GET",
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new VariantSet.fromJson(data));
   }
 
   /**
+   * 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.
+   *
+   * [request] - The metadata request object.
+   *
+   * Request parameters:
+   *
+   * [variantSetId] - Required. The variant set to which variant data should be
+   * imported.
+   *
+   * Completes with a [ImportVariantsResponse].
+   *
+   * 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<ImportVariantsResponse> importVariants(ImportVariantsRequest 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());
+    }
+    if (variantSetId == null) {
+      throw new core.ArgumentError("Parameter variantSetId is required.");
+    }
+
+
+    _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId') + '/importVariants';
+
+    var _response = _requester.request(_url,
+                                       "POST",
+                                       body: _body,
+                                       queryParams: _queryParams,
+                                       uploadOptions: _uploadOptions,
+                                       uploadMedia: _uploadMedia,
+                                       downloadOptions: _downloadOptions);
+    return _response.then((data) => new ImportVariantsResponse.fromJson(data));
+  }
+
+  /**
    * 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.
    *
    * When 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.
    *
    * [request] - The metadata request object.
@@ skipping 32 matching lines @@
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => null);
   }
 
   /**
    * Updates a variant set's metadata. All other modifications are silently
-   * ignored. Returns the modified variant set. This method supports patch
-   * semantics.
+   * ignored. This method supports patch semantics.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
    * [variantSetId] - The ID of the variant to be updated.
    *
    * Completes with a [VariantSet].
    *
    * Completes with a [common.ApiRequestError] if the API endpoint returned an
@@ skipping 26 matching lines @@
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new VariantSet.fromJson(data));
   }
 
   /**
    * Returns a list of all variant sets matching search criteria.
    *
+   * Implements GlobalAllianceApi.searchVariantSets.
+   *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
    * Completes with a [SearchVariantSetsResponse].
    *
    * 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,
@@ skipping 19 matching lines @@
                                        body: _body,
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new SearchVariantSetsResponse.fromJson(data));
   }
 
   /**
    * Updates a variant set's metadata. All other modifications are silently
-   * ignored. Returns the modified variant set.
+   * ignored.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
    * [variantSetId] - The ID of the variant to be updated.
    *
    * Completes with a [VariantSet].
    *
    * Completes with a [common.ApiRequestError] if the API endpoint returned an
@@ skipping 27 matching lines @@
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new VariantSet.fromJson(data));
   }
 
 }
 
 
 
-/**
- * A beacon represents whether any variant call in a variant set has a specific
- * allele at a particular position.
- */
-class Beacon {
-  /** True if the allele exists on any variant call, false otherwise. */
-  core.bool exists;
+/** The read group set align request. */
+class AlignReadGroupSetsRequest {
+  /**
+   * 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.
+   */
+  core.List<core.String> bamSourceUris;
+
+  /**
+   * Required. The ID of the dataset the newly aligned read group sets will
+   * belong to. The caller must have WRITE permissions to this dataset.
+   */
+  core.String datasetId;
+
+  /**
+   * 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.
+   */
+  InterleavedFastqSource interleavedFastqSource;
+
+  /**
+   * 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.
+   */
+  PairedFastqSource pairedFastqSource;
+
+  /**
+   * 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.
+   */
+  core.List<core.String> readGroupSetIds;
 
 
-  Beacon();
+  AlignReadGroupSetsRequest();
 
-  Beacon.fromJson(core.Map _json) {
-    if (_json.containsKey("exists")) {
-      exists = _json["exists"];
+  AlignReadGroupSetsRequest.fromJson(core.Map _json) {
+    if (_json.containsKey("bamSourceUris")) {
+      bamSourceUris = _json["bamSourceUris"];
+    }
+    if (_json.containsKey("datasetId")) {
+      datasetId = _json["datasetId"];
+    }
+    if (_json.containsKey("interleavedFastqSource")) {
+      interleavedFastqSource = new InterleavedFastqSource.fromJson(_json["interleavedFastqSource"]);
+    }
+    if (_json.containsKey("pairedFastqSource")) {
+      pairedFastqSource = new PairedFastqSource.fromJson(_json["pairedFastqSource"]);
+    }
+    if (_json.containsKey("readGroupSetIds")) {
+      readGroupSetIds = _json["readGroupSetIds"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
-    if (exists != null) {
-      _json["exists"] = exists;
+    if (bamSourceUris != null) {
+      _json["bamSourceUris"] = bamSourceUris;
+    }
+    if (datasetId != null) {
+      _json["datasetId"] = datasetId;
+    }
+    if (interleavedFastqSource != null) {
+      _json["interleavedFastqSource"] = (interleavedFastqSource).toJson();
+    }
+    if (pairedFastqSource != null) {
+      _json["pairedFastqSource"] = (pairedFastqSource).toJson();
+    }
+    if (readGroupSetIds != null) {
+      _json["readGroupSetIds"] = readGroupSetIds;
     }
     return _json;
   }
+}
+
+
+/** The read group set align response. */
+class AlignReadGroupSetsResponse {
+  /** A job ID that can be used to get status information. */
+  core.String jobId;
+
+
+  AlignReadGroupSetsResponse();
+
+  AlignReadGroupSetsResponse.fromJson(core.Map _json) {
+    if (_json.containsKey("jobId")) {
+      jobId = _json["jobId"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (jobId != null) {
+      _json["jobId"] = jobId;
+    }
+    return _json;
+  }
 }
 
 
 /**
- * A Call represents the determination of genotype with respect to a particular
+ * 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
+ * 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.
  */
 class Call {
   /** The ID of the call set this variant call belongs to. */
   core.String callSetId;
 
   /** The name of the call set this variant call belongs to. */
   core.String callSetName;
 
   /**
@@ skipping 69 matching lines @@
       _json["info"] = info;
     }
     if (phaseset != null) {
       _json["phaseset"] = phaseset;
     }
     return _json;
   }
 }
 
 
-/** A CallSet is a collection of variant calls. It belongs to a variant set. */
+/** The read group set call request. */
+class CallReadGroupSetsRequest {
+  /**
+   * Required. The ID of the dataset the called variants will belong to. The
+   * caller must have WRITE permissions to this dataset.
+   */
+  core.String datasetId;
+
+  /**
+   * 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.
+   */
+  core.List<core.String> readGroupSetIds;
+
+  /**
+   * 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.
+   */
+  core.List<core.String> sourceUris;
+
+
+  CallReadGroupSetsRequest();
+
+  CallReadGroupSetsRequest.fromJson(core.Map _json) {
+    if (_json.containsKey("datasetId")) {
+      datasetId = _json["datasetId"];
+    }
+    if (_json.containsKey("readGroupSetIds")) {
+      readGroupSetIds = _json["readGroupSetIds"];
+    }
+    if (_json.containsKey("sourceUris")) {
+      sourceUris = _json["sourceUris"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (datasetId != null) {
+      _json["datasetId"] = datasetId;
+    }
+    if (readGroupSetIds != null) {
+      _json["readGroupSetIds"] = readGroupSetIds;
+    }
+    if (sourceUris != null) {
+      _json["sourceUris"] = sourceUris;
+    }
+    return _json;
+  }
+}
+
+
+/** The read group set call response. */
+class CallReadGroupSetsResponse {
+  /** A job ID that can be used to get status information. */
+  core.String jobId;
+
+
+  CallReadGroupSetsResponse();
+
+  CallReadGroupSetsResponse.fromJson(core.Map _json) {
+    if (_json.containsKey("jobId")) {
+      jobId = _json["jobId"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (jobId != null) {
+      _json["jobId"] = jobId;
+    }
+    return _json;
+  }
+}
+
+
+/**
+ * A call set is a collection of variant calls, typically for one sample. It
+ * belongs to a variant set.
+ */
 class CallSet {
   /** The date this call set was created in milliseconds from the epoch. */
   core.String created;
 
   /** The Google generated ID of the call set, immutable. */
   core.String id;
 
-  /** A map of additional callset information. */
+  /** A map of additional call set information. */
   core.Map<core.String, core.List<core.String>> info;
 
-  /** The callset name. */
+  /** The call set name. */
   core.String name;
 
   /** The sample ID this call set corresponds to. */
   core.String sampleId;
 
   /** The IDs of the variant sets this call set belongs to. */
   core.List<core.String> variantSetIds;
 
 
   CallSet();
@@ skipping 37 matching lines @@
       _json["sampleId"] = sampleId;
     }
     if (variantSetIds != null) {
       _json["variantSetIds"] = variantSetIds;
     }
     return _json;
   }
 }
 
 
+/** A single CIGAR operation. */
+class CigarUnit {
+  /**
+   * Not documented yet.
+   * Possible string values are:
+   * - "ALIGNMENT_MATCH"
+   * - "CLIP_HARD"
+   * - "CLIP_SOFT"
+   * - "DELETE"
+   * - "INSERT"
+   * - "PAD"
+   * - "SEQUENCE_MATCH"
+   * - "SEQUENCE_MISMATCH"
+   * - "SKIP"
+   */
+  core.String operation;
+
+  /** The number of bases that the operation runs for. Required. */
+  core.String operationLength;
+
+  /**
+   * 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.
+   */
+  core.String referenceSequence;
+
+
+  CigarUnit();
+
+  CigarUnit.fromJson(core.Map _json) {
+    if (_json.containsKey("operation")) {
+      operation = _json["operation"];
+    }
+    if (_json.containsKey("operationLength")) {
+      operationLength = _json["operationLength"];
+    }
+    if (_json.containsKey("referenceSequence")) {
+      referenceSequence = _json["referenceSequence"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (operation != null) {
+      _json["operation"] = operation;
+    }
+    if (operationLength != null) {
+      _json["operationLength"] = operationLength;
+    }
+    if (referenceSequence != null) {
+      _json["referenceSequence"] = referenceSequence;
+    }
+    return _json;
+  }
+}
+
+
 /**
  * A bucket over which read coverage has been precomputed. A bucket corresponds
  * to a specific range of the reference sequence.
  */
 class CoverageBucket {
   /**
    * The average number of reads which are aligned to each individual reference
    * base in this bucket.
    */
   core.double meanCoverage;
 
   /** The genomic coordinate range spanned by this bucket. */
-  GenomicRange range;
+  Range range;
 
 
   CoverageBucket();
 
   CoverageBucket.fromJson(core.Map _json) {
     if (_json.containsKey("meanCoverage")) {
       meanCoverage = _json["meanCoverage"];
     }
     if (_json.containsKey("range")) {
-      range = new GenomicRange.fromJson(_json["range"]);
+      range = new Range.fromJson(_json["range"]);
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (meanCoverage != null) {
       _json["meanCoverage"] = meanCoverage;
     }
     if (range != null) {
       _json["range"] = (range).toJson();
@@ skipping 13 matching lines @@
    * is not public, it inherits viewing permissions from its project.
    */
   core.bool isPublic;
 
   /** The dataset name. */
   core.String name;
 
   /**
    * The Google Developers Console project number that this dataset belongs to.
    */
-  core.String projectId;
+  core.String projectNumber;
 
 
   Dataset();
 
   Dataset.fromJson(core.Map _json) {
     if (_json.containsKey("id")) {
       id = _json["id"];
     }
     if (_json.containsKey("isPublic")) {
       isPublic = _json["isPublic"];
     }
     if (_json.containsKey("name")) {
       name = _json["name"];
     }
-    if (_json.containsKey("projectId")) {
-      projectId = _json["projectId"];
+    if (_json.containsKey("projectNumber")) {
+      projectNumber = _json["projectNumber"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (id != null) {
       _json["id"] = id;
     }
     if (isPublic != null) {
       _json["isPublic"] = isPublic;
     }
     if (name != null) {
       _json["name"] = name;
     }
-    if (projectId != null) {
-      _json["projectId"] = projectId;
+    if (projectNumber != null) {
+      _json["projectNumber"] = projectNumber;
     }
     return _json;
   }
 }
 
 
 /** The job creation request. */
 class ExperimentalCreateJobRequest {
   /**
-   * Specifies whether or not to run the alignment pipeline. At least one of
-   * align or callVariants must be provided.
+   * Specifies whether or not to run the alignment pipeline. Either align or
+   * callVariants must be set.
    */
   core.bool align;
 
   /**
-   * 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.
+   * Specifies whether or not to run the variant calling pipeline. Either align
+   * or callVariants must be set.
    */
   core.bool callVariants;
 
   /**
    * Specifies where to copy the results of certain pipelines. This should be in
    * the form of gs://bucket/path.
    */
   core.String gcsOutputPath;
 
   /**
    * 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.
    */
   core.List<core.String> pairedSourceUris;
 
   /**
    * Required. The Google Cloud Project ID with which to associate the request.
    */
-  core.String projectId;
+  core.String projectNumber;
 
   /**
    * 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.
    */
   core.List<core.String> sourceUris;
 
 
   ExperimentalCreateJobRequest();
 
   ExperimentalCreateJobRequest.fromJson(core.Map _json) {
     if (_json.containsKey("align")) {
       align = _json["align"];
     }
     if (_json.containsKey("callVariants")) {
       callVariants = _json["callVariants"];
     }
     if (_json.containsKey("gcsOutputPath")) {
       gcsOutputPath = _json["gcsOutputPath"];
     }
     if (_json.containsKey("pairedSourceUris")) {
       pairedSourceUris = _json["pairedSourceUris"];
     }
-    if (_json.containsKey("projectId")) {
-      projectId = _json["projectId"];
+    if (_json.containsKey("projectNumber")) {
+      projectNumber = _json["projectNumber"];
     }
     if (_json.containsKey("sourceUris")) {
       sourceUris = _json["sourceUris"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (align != null) {
       _json["align"] = align;
     }
     if (callVariants != null) {
       _json["callVariants"] = callVariants;
     }
     if (gcsOutputPath != null) {
       _json["gcsOutputPath"] = gcsOutputPath;
     }
     if (pairedSourceUris != null) {
       _json["pairedSourceUris"] = pairedSourceUris;
     }
-    if (projectId != null) {
-      _json["projectId"] = projectId;
+    if (projectNumber != null) {
+      _json["projectNumber"] = projectNumber;
     }
     if (sourceUris != null) {
       _json["sourceUris"] = sourceUris;
     }
     return _json;
   }
 }
 
 
 /** The job creation response. */
@@ skipping 13 matching lines @@
   core.Map toJson() {
     var _json = new core.Map();
     if (jobId != null) {
       _json["jobId"] = jobId;
     }
     return _json;
   }
 }
 
 
-/** The readset export request. */
-class ExportReadsetsRequest {
+/** The read group set export request. */
+class ExportReadGroupSetsRequest {
   /**
    * 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.
    */
   core.String exportUri;
 
   /** The Google Developers Console project number that owns this export. */
-  core.String projectId;
+  core.String projectNumber;
 
-  /** The IDs of the readsets to export. */
-  core.List<core.String> readsetIds;
+  /** The IDs of the read group sets to export. */
+  core.List<core.String> readGroupSetIds;
 
   /**
    * The reference names to export. If this is not specified, all reference
    * sequences, including unmapped reads, are exported. Use * to export only
    * unmapped reads.
    */
   core.List<core.String> referenceNames;
 
 
-  ExportReadsetsRequest();
+  ExportReadGroupSetsRequest();
 
-  ExportReadsetsRequest.fromJson(core.Map _json) {
+  ExportReadGroupSetsRequest.fromJson(core.Map _json) {
     if (_json.containsKey("exportUri")) {
       exportUri = _json["exportUri"];
     }
-    if (_json.containsKey("projectId")) {
-      projectId = _json["projectId"];
+    if (_json.containsKey("projectNumber")) {
+      projectNumber = _json["projectNumber"];
     }
-    if (_json.containsKey("readsetIds")) {
-      readsetIds = _json["readsetIds"];
+    if (_json.containsKey("readGroupSetIds")) {
+      readGroupSetIds = _json["readGroupSetIds"];
     }
     if (_json.containsKey("referenceNames")) {
       referenceNames = _json["referenceNames"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (exportUri != null) {
       _json["exportUri"] = exportUri;
     }
-    if (projectId != null) {
-      _json["projectId"] = projectId;
+    if (projectNumber != null) {
+      _json["projectNumber"] = projectNumber;
     }
-    if (readsetIds != null) {
-      _json["readsetIds"] = readsetIds;
+    if (readGroupSetIds != null) {
+      _json["readGroupSetIds"] = readGroupSetIds;
     }
     if (referenceNames != null) {
       _json["referenceNames"] = referenceNames;
     }
     return _json;
   }
 }
 
 
-/** The readset export response. */
-class ExportReadsetsResponse {
+/** The read group set export response. */
+class ExportReadGroupSetsResponse {
   /** A job ID that can be used to get status information. */
   core.String jobId;
 
 
-  ExportReadsetsResponse();
+  ExportReadGroupSetsResponse();
 
-  ExportReadsetsResponse.fromJson(core.Map _json) {
+  ExportReadGroupSetsResponse.fromJson(core.Map _json) {
     if (_json.containsKey("jobId")) {
       jobId = _json["jobId"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (jobId != null) {
       _json["jobId"] = jobId;
     }
     return _json;
   }
 }
 
 
 /** The variant data export request. */
-class ExportVariantsRequest {
+class ExportVariantSetRequest {
   /**
    * The BigQuery dataset to export data to. Note that this is distinct from the
    * Genomics concept of "dataset".
    */
   core.String bigqueryDataset;
 
   /**
    * 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.
    */
   core.String bigqueryTable;
 
   /**
    * If provided, only variant call information from the specified call sets
    * will be exported. By default all variant calls are exported.
    */
   core.List<core.String> callSetIds;
 
   /**
    * The format for the exported data.
    * Possible string values are:
-   * - "bigquery"
+   * - "BIGQUERY"
    */
   core.String format;
 
   /**
    * 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.
    */
-  core.String projectId;
-
-  /**
-   * 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.
-   */
-  core.String variantSetId;
+  core.String projectNumber;
 
 
-  ExportVariantsRequest();
+  ExportVariantSetRequest();
 
-  ExportVariantsRequest.fromJson(core.Map _json) {
+  ExportVariantSetRequest.fromJson(core.Map _json) {
     if (_json.containsKey("bigqueryDataset")) {
       bigqueryDataset = _json["bigqueryDataset"];
     }
     if (_json.containsKey("bigqueryTable")) {
       bigqueryTable = _json["bigqueryTable"];
     }
     if (_json.containsKey("callSetIds")) {
       callSetIds = _json["callSetIds"];
     }
     if (_json.containsKey("format")) {
       format = _json["format"];
     }
-    if (_json.containsKey("projectId")) {
-      projectId = _json["projectId"];
-    }
-    if (_json.containsKey("variantSetId")) {
-      variantSetId = _json["variantSetId"];
+    if (_json.containsKey("projectNumber")) {
+      projectNumber = _json["projectNumber"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (bigqueryDataset != null) {
       _json["bigqueryDataset"] = bigqueryDataset;
     }
     if (bigqueryTable != null) {
       _json["bigqueryTable"] = bigqueryTable;
     }
     if (callSetIds != null) {
       _json["callSetIds"] = callSetIds;
     }
     if (format != null) {
       _json["format"] = format;
     }
-    if (projectId != null) {
-      _json["projectId"] = projectId;
-    }
-    if (variantSetId != null) {
-      _json["variantSetId"] = variantSetId;
+    if (projectNumber != null) {
+      _json["projectNumber"] = projectNumber;
     }
     return _json;
   }
 }
 
 
 /** The variant data export response. */
-class ExportVariantsResponse {
+class ExportVariantSetResponse {
   /** A job ID that can be used to get status information. */
   core.String jobId;
 
 
-  ExportVariantsResponse();
+  ExportVariantSetResponse();
 
-  ExportVariantsResponse.fromJson(core.Map _json) {
+  ExportVariantSetResponse.fromJson(core.Map _json) {
     if (_json.containsKey("jobId")) {
       jobId = _json["jobId"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (jobId != null) {
       _json["jobId"] = jobId;
     }
     return _json;
   }
 }
 
 
-/**
- * An inclusive, exclusive genomic coordinate range over a reference sequence.
- */
-class GenomicRange {
-  /**
-   * The end position of the range on the reference, 1-based exclusive. If
-   * specified, sequenceName must also be specified.
-   */
-  core.String sequenceEnd;
-
-  /** The reference sequence name, for example chr1, 1, or chrX. */
-  core.String sequenceName;
+/** Not documented yet. */
+class FastqMetadata {
+  /** Optionally specifies the library name for alignment from FASTQ. */
+  core.String libraryName;
 
   /**
-   * The start position of the range on the reference, 1-based inclusive. If
-   * specified, sequenceName must also be specified.
+   * Optionally specifies the platform name for alignment from FASTQ. For
+   * example: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, PACBIO.
    */
-  core.String sequenceStart;
+  core.String platformName;
+
+  /**
+   * Optionally specifies the platform unit for alignment from FASTQ. For
+   * example: flowcell-barcode.lane for Illumina or slide for SOLID.
+   */
+  core.String platformUnit;
+
+  /** Optionally specifies the read group name for alignment from FASTQ. */
+  core.String readGroupName;
+
+  /** Optionally specifies the sample name for alignment from FASTQ. */
+  core.String sampleName;
 
 
-  GenomicRange();
+  FastqMetadata();
 
-  GenomicRange.fromJson(core.Map _json) {
-    if (_json.containsKey("sequenceEnd")) {
-      sequenceEnd = _json["sequenceEnd"];
+  FastqMetadata.fromJson(core.Map _json) {
+    if (_json.containsKey("libraryName")) {
+      libraryName = _json["libraryName"];
     }
-    if (_json.containsKey("sequenceName")) {
-      sequenceName = _json["sequenceName"];
+    if (_json.containsKey("platformName")) {
+      platformName = _json["platformName"];
     }
-    if (_json.containsKey("sequenceStart")) {
-      sequenceStart = _json["sequenceStart"];
+    if (_json.containsKey("platformUnit")) {
+      platformUnit = _json["platformUnit"];
+    }
+    if (_json.containsKey("readGroupName")) {
+      readGroupName = _json["readGroupName"];
+    }
+    if (_json.containsKey("sampleName")) {
+      sampleName = _json["sampleName"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
-    if (sequenceEnd != null) {
-      _json["sequenceEnd"] = sequenceEnd;
+    if (libraryName != null) {
+      _json["libraryName"] = libraryName;
     }
-    if (sequenceName != null) {
-      _json["sequenceName"] = sequenceName;
+    if (platformName != null) {
+      _json["platformName"] = platformName;
     }
-    if (sequenceStart != null) {
-      _json["sequenceStart"] = sequenceStart;
+    if (platformUnit != null) {
+      _json["platformUnit"] = platformUnit;
+    }
+    if (readGroupName != null) {
+      _json["readGroupName"] = readGroupName;
+    }
+    if (sampleName != null) {
+      _json["sampleName"] = sampleName;
     }
     return _json;
   }
 }
 
 
-/** Not documented yet. */
-class Header {
-  /** (SO) Sorting order of alignments. */
-  core.String sortingOrder;
-
-  /** (VN) BAM format version. */
-  core.String version;
-
-
-  Header();
-
-  Header.fromJson(core.Map _json) {
-    if (_json.containsKey("sortingOrder")) {
-      sortingOrder = _json["sortingOrder"];
-    }
-    if (_json.containsKey("version")) {
-      version = _json["version"];
-    }
-  }
-
-  core.Map toJson() {
-    var _json = new core.Map();
-    if (sortingOrder != null) {
-      _json["sortingOrder"] = sortingOrder;
-    }
-    if (version != null) {
-      _json["version"] = version;
-    }
-    return _json;
-  }
-}
-
-
-/** The header section of the BAM/SAM file. */
-class HeaderSection {
-  /** (@CO) One-line text comments. */
-  core.List<core.String> comments;
+/** The read group set import request. */
+class ImportReadGroupSetsRequest {
+  /**
+   * Required. The ID of the dataset these read group sets will belong to. The
+   * caller must have WRITE permissions to this dataset.
+   */
+  core.String datasetId;
 
   /**
-   * [Deprecated] This field is deprecated and will no longer be populated.
-   * Please use filename instead.
+   * 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.
    */
-  core.String fileUri;
-
-  /** The name of the file from which this data was imported. */
-  core.String filename;
-
-  /** (@HD) The header line. */
-  core.List<Header> headers;
-
-  /** (@PG) Programs. */
-  core.List<Program> programs;
-
-  /** (@RG) Read group. */
-  core.List<ReadGroup> readGroups;
-
-  /** (@SQ) Reference sequence dictionary. */
-  core.List<ReferenceSequence> refSequences;
-
-
-  HeaderSection();
-
-  HeaderSection.fromJson(core.Map _json) {
-    if (_json.containsKey("comments")) {
-      comments = _json["comments"];
-    }
-    if (_json.containsKey("fileUri")) {
-      fileUri = _json["fileUri"];
-    }
-    if (_json.containsKey("filename")) {
-      filename = _json["filename"];
-    }
-    if (_json.containsKey("headers")) {
-      headers = _json["headers"].map((value) => new Header.fromJson(value)).toList();
-    }
-    if (_json.containsKey("programs")) {
-      programs = _json["programs"].map((value) => new Program.fromJson(value)).toList();
-    }
-    if (_json.containsKey("readGroups")) {
-      readGroups = _json["readGroups"].map((value) => new ReadGroup.fromJson(value)).toList();
-    }
-    if (_json.containsKey("refSequences")) {
-      refSequences = _json["refSequences"].map((value) => new ReferenceSequence.fromJson(value)).toList();
-    }
-  }
-
-  core.Map toJson() {
-    var _json = new core.Map();
-    if (comments != null) {
-      _json["comments"] = comments;
-    }
-    if (fileUri != null) {
-      _json["fileUri"] = fileUri;
-    }
-    if (filename != null) {
-      _json["filename"] = filename;
-    }
-    if (headers != null) {
-      _json["headers"] = headers.map((value) => (value).toJson()).toList();
-    }
-    if (programs != null) {
-      _json["programs"] = programs.map((value) => (value).toJson()).toList();
-    }
-    if (readGroups != null) {
-      _json["readGroups"] = readGroups.map((value) => (value).toJson()).toList();
-    }
-    if (refSequences != null) {
-      _json["refSequences"] = refSequences.map((value) => (value).toJson()).toList();
-    }
-    return _json;
-  }
-}
-
-
-/** The readset import request. */
-class ImportReadsetsRequest {
-  /**
-   * Required. The ID of the dataset these readsets will belong to. The caller
-   * must have WRITE permissions to this dataset.
-   */
-  core.String datasetId;
+  core.String referenceSetId;
 
   /** A list of URIs pointing at BAM files in Google Cloud Storage. */
   core.List<core.String> sourceUris;
 
 
-  ImportReadsetsRequest();
+  ImportReadGroupSetsRequest();
 
-  ImportReadsetsRequest.fromJson(core.Map _json) {
+  ImportReadGroupSetsRequest.fromJson(core.Map _json) {
     if (_json.containsKey("datasetId")) {
       datasetId = _json["datasetId"];
     }
+    if (_json.containsKey("referenceSetId")) {
+      referenceSetId = _json["referenceSetId"];
+    }
     if (_json.containsKey("sourceUris")) {
       sourceUris = _json["sourceUris"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (datasetId != null) {
       _json["datasetId"] = datasetId;
     }
+    if (referenceSetId != null) {
+      _json["referenceSetId"] = referenceSetId;
+    }
     if (sourceUris != null) {
       _json["sourceUris"] = sourceUris;
     }
     return _json;
   }
 }
 
 
-/** The readset import response. */
-class ImportReadsetsResponse {
+/** The read group set import response. */
+class ImportReadGroupSetsResponse {
   /** A job ID that can be used to get status information. */
   core.String jobId;
 
 
-  ImportReadsetsResponse();
+  ImportReadGroupSetsResponse();
 
-  ImportReadsetsResponse.fromJson(core.Map _json) {
+  ImportReadGroupSetsResponse.fromJson(core.Map _json) {
     if (_json.containsKey("jobId")) {
       jobId = _json["jobId"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (jobId != null) {
       _json["jobId"] = jobId;
     }
     return _json;
   }
 }
 
 
 /** The variant data import request. */
 class ImportVariantsRequest {
   /**
    * The format of the variant data being imported.
    * Possible string values are:
-   * - "completeGenomics"
-   * - "vcf"
+   * - "COMPLETE_GENOMICS"
+   * - "VCF"
    */
   core.String format;
 
   /**
    * A list of URIs pointing at VCF files in Google Cloud Storage. See the VCF
    * Specification for more details on the input format.
    */
   core.List<core.String> sourceUris;
 
-  /** Required. The variant set to which variant data should be imported. */
-  core.String variantSetId;
-
 
   ImportVariantsRequest();
 
   ImportVariantsRequest.fromJson(core.Map _json) {
     if (_json.containsKey("format")) {
       format = _json["format"];
     }
     if (_json.containsKey("sourceUris")) {
       sourceUris = _json["sourceUris"];
     }
-    if (_json.containsKey("variantSetId")) {
-      variantSetId = _json["variantSetId"];
-    }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (format != null) {
       _json["format"] = format;
     }
     if (sourceUris != null) {
       _json["sourceUris"] = sourceUris;
     }
-    if (variantSetId != null) {
-      _json["variantSetId"] = variantSetId;
-    }
     return _json;
   }
 }
 
 
 /** The variant data import response. */
 class ImportVariantsResponse {
   /** A job ID that can be used to get status information. */
   core.String jobId;
 
 
   ImportVariantsResponse();
 
   ImportVariantsResponse.fromJson(core.Map _json) {
     if (_json.containsKey("jobId")) {
       jobId = _json["jobId"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (jobId != null) {
       _json["jobId"] = jobId;
     }
     return _json;
   }
 }
 
 
+/** Describes an interleaved FASTQ file source for alignment. */
+class InterleavedFastqSource {
+  /**
+   * Optionally specifies the metadata to be associated with the final aligned
+   * read group set.
+   */
+  FastqMetadata metadata;
+
+  /**
+   * 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.
+   */
+  core.List<core.String> sourceUris;
+
+
+  InterleavedFastqSource();
+
+  InterleavedFastqSource.fromJson(core.Map _json) {
+    if (_json.containsKey("metadata")) {
+      metadata = new FastqMetadata.fromJson(_json["metadata"]);
+    }
+    if (_json.containsKey("sourceUris")) {
+      sourceUris = _json["sourceUris"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (metadata != null) {
+      _json["metadata"] = (metadata).toJson();
+    }
+    if (sourceUris != null) {
+      _json["sourceUris"] = sourceUris;
+    }
+    return _json;
+  }
+}
+
+
 /**
  * A Job represents an ongoing process that can be monitored for status
  * information.
  */
 class Job {
   /** The date this job was created, in milliseconds from the epoch. */
   core.String created;
 
   /** A more detailed description of this job's current status. */
-  core.String description;
+  core.String detailedStatus;
 
   /** Any errors that occurred during processing. */
   core.List<core.String> errors;
 
   /** The job ID. */
   core.String id;
 
   /**
    * If this Job represents an import, this field will contain the IDs of the
    * objects that were successfully imported.
    */
   core.List<core.String> importedIds;
 
   /**
    * The Google Developers Console project number to which this job belongs.
    */
-  core.String projectId;
+  core.String projectNumber;
 
   /** A summarized representation of the original service request. */
   JobRequest request;
 
   /**
    * The status of this job.
    * Possible string values are:
-   * - "canceled"
-   * - "failure"
-   * - "new"
-   * - "pending"
-   * - "running"
-   * - "success"
-   * - "unknownStatus"
+   * - "CANCELED"
+   * - "FAILURE"
+   * - "NEW"
+   * - "PENDING"
+   * - "RUNNING"
+   * - "SUCCESS"
+   * - "UNKNOWN_STATUS"
    */
   core.String status;
 
   /** Any warnings that occurred during processing. */
   core.List<core.String> warnings;
 
 
   Job();
 
   Job.fromJson(core.Map _json) {
     if (_json.containsKey("created")) {
       created = _json["created"];
     }
-    if (_json.containsKey("description")) {
-      description = _json["description"];
+    if (_json.containsKey("detailedStatus")) {
+      detailedStatus = _json["detailedStatus"];
     }
     if (_json.containsKey("errors")) {
       errors = _json["errors"];
     }
     if (_json.containsKey("id")) {
       id = _json["id"];
     }
     if (_json.containsKey("importedIds")) {
       importedIds = _json["importedIds"];
     }
-    if (_json.containsKey("projectId")) {
-      projectId = _json["projectId"];
+    if (_json.containsKey("projectNumber")) {
+      projectNumber = _json["projectNumber"];
     }
     if (_json.containsKey("request")) {
       request = new JobRequest.fromJson(_json["request"]);
     }
     if (_json.containsKey("status")) {
       status = _json["status"];
     }
     if (_json.containsKey("warnings")) {
       warnings = _json["warnings"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (created != null) {
       _json["created"] = created;
     }
-    if (description != null) {
-      _json["description"] = description;
+    if (detailedStatus != null) {
+      _json["detailedStatus"] = detailedStatus;
     }
     if (errors != null) {
       _json["errors"] = errors;
     }
     if (id != null) {
       _json["id"] = id;
     }
     if (importedIds != null) {
       _json["importedIds"] = importedIds;
     }
-    if (projectId != null) {
-      _json["projectId"] = projectId;
+    if (projectNumber != null) {
+      _json["projectNumber"] = projectNumber;
     }
     if (request != null) {
       _json["request"] = (request).toJson();
     }
     if (status != null) {
       _json["status"] = status;
     }
     if (warnings != null) {
       _json["warnings"] = warnings;
     }
@@ skipping 12 matching lines @@
 
   /**
    * The data source of the request, for example, a Google Cloud Storage object
    * path or Readset ID.
    */
   core.List<core.String> source;
 
   /**
    * The original request type.
    * Possible string values are:
-   * - "experimentalCreateJob"
-   * - "exportReadsets"
-   * - "exportVariants"
-   * - "importReadsets"
-   * - "importVariants"
-   * - "unknownType"
+   * - "ALIGN_READSETS"
+   * - "CALL_READSETS"
+   * - "EXPERIMENTAL_CREATE_JOB"
+   * - "EXPORT_READSETS"
+   * - "EXPORT_VARIANTS"
+   * - "IMPORT_READSETS"
+   * - "IMPORT_VARIANTS"
+   * - "UNKNOWN_TYPE"
    */
   core.String type;
 
 
   JobRequest();
 
   JobRequest.fromJson(core.Map _json) {
     if (_json.containsKey("destination")) {
       destination = _json["destination"];
     }
@@ skipping 14 matching lines @@
       _json["source"] = source;
     }
     if (type != null) {
       _json["type"] = type;
     }
     return _json;
   }
 }
 
 
+/**
+ * A linear alignment can be represented by one CIGAR string. Describes the
+ * mapped position and local alignment of the read to the reference.
+ */
+class LinearAlignment {
+  /**
+   * Represents the local alignment of this sequence (alignment matches, indels,
+   * etc) against the reference.
+   */
+  core.List<CigarUnit> cigar;
+
+  /**
+   * The mapping quality of this alignment. Represents how likely the read maps
+   * to this position as opposed to other locations.
+   */
+  core.int mappingQuality;
+
+  /** The position of this alignment. */
+  Position position;
+
+
+  LinearAlignment();
+
+  LinearAlignment.fromJson(core.Map _json) {
+    if (_json.containsKey("cigar")) {
+      cigar = _json["cigar"].map((value) => new CigarUnit.fromJson(value)).toList();
+    }
+    if (_json.containsKey("mappingQuality")) {
+      mappingQuality = _json["mappingQuality"];
+    }
+    if (_json.containsKey("position")) {
+      position = new Position.fromJson(_json["position"]);
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (cigar != null) {
+      _json["cigar"] = cigar.map((value) => (value).toJson()).toList();
+    }
+    if (mappingQuality != null) {
+      _json["mappingQuality"] = mappingQuality;
+    }
+    if (position != null) {
+      _json["position"] = (position).toJson();
+    }
+    return _json;
+  }
+}
+
+
+/** Not documented yet. */
+class ListBasesResponse {
+  /**
+   * 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.
+   */
+  core.String nextPageToken;
+
+  /**
+   * 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.
+   */
+  core.String offset;
+
+  /** A substring of the bases that make up this reference. */
+  core.String sequence;
+
+
+  ListBasesResponse();
+
+  ListBasesResponse.fromJson(core.Map _json) {
+    if (_json.containsKey("nextPageToken")) {
+      nextPageToken = _json["nextPageToken"];
+    }
+    if (_json.containsKey("offset")) {
+      offset = _json["offset"];
+    }
+    if (_json.containsKey("sequence")) {
+      sequence = _json["sequence"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (nextPageToken != null) {
+      _json["nextPageToken"] = nextPageToken;
+    }
+    if (offset != null) {
+      _json["offset"] = offset;
+    }
+    if (sequence != null) {
+      _json["sequence"] = sequence;
+    }
+    return _json;
+  }
+}
+
+
 /** Not documented yet. */
 class ListCoverageBucketsResponse {
   /**
    * 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).
    */
   core.String bucketWidth;
 
@@ skipping 129 matching lines @@
   /**
    * The number of values that can be included in a field described by this
    * metadata.
    */
   core.String number;
 
   /**
    * The type of data. Possible types include: Integer, Float, Flag, Character,
    * and String.
    * Possible string values are:
-   * - "character"
-   * - "flag"
-   * - "float"
-   * - "integer"
-   * - "string"
-   * - "unknownType"
+   * - "CHARACTER"
+   * - "FLAG"
+   * - "FLOAT"
+   * - "INTEGER"
+   * - "STRING"
+   * - "UNKNOWN_TYPE"
    */
   core.String type;
 
   /** The value field for simple metadata */
   core.String value;
 
 
   Metadata();
 
   Metadata.fromJson(core.Map _json) {
@@ skipping 41 matching lines @@
       _json["type"] = type;
     }
     if (value != null) {
       _json["value"] = value;
     }
     return _json;
   }
 }
 
 
-/** Not documented yet. */
-class Program {
-  /** (CL) Command line. */
-  core.String commandLine;
+/** Describes a paired-end FASTQ file source for alignment. */
+class PairedFastqSource {
+  /**
+   * 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.
+   */
+  core.List<core.String> firstSourceUris;
 
-  /** (ID) Program record identifier. */
-  core.String id;
+  /**
+   * Optionally specifies the metadata to be associated with the final aligned
+   * read group set.
+   */
+  FastqMetadata metadata;
 
-  /** (PN) Program name. */
-  core.String name;
-
-  /** (PP) Previous program ID. */
-  core.String prevProgramId;
-
-  /** (VN) Program version. */
-  core.String version;
+  /**
+   * 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.
+   */
+  core.List<core.String> secondSourceUris;
 
 
-  Program();
+  PairedFastqSource();
 
-  Program.fromJson(core.Map _json) {
-    if (_json.containsKey("commandLine")) {
-      commandLine = _json["commandLine"];
+  PairedFastqSource.fromJson(core.Map _json) {
+    if (_json.containsKey("firstSourceUris")) {
+      firstSourceUris = _json["firstSourceUris"];
     }
-    if (_json.containsKey("id")) {
-      id = _json["id"];
+    if (_json.containsKey("metadata")) {
+      metadata = new FastqMetadata.fromJson(_json["metadata"]);
     }
-    if (_json.containsKey("name")) {
-      name = _json["name"];
-    }
-    if (_json.containsKey("prevProgramId")) {
-      prevProgramId = _json["prevProgramId"];
-    }
-    if (_json.containsKey("version")) {
-      version = _json["version"];
+    if (_json.containsKey("secondSourceUris")) {
+      secondSourceUris = _json["secondSourceUris"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
-    if (commandLine != null) {
-      _json["commandLine"] = commandLine;
+    if (firstSourceUris != null) {
+      _json["firstSourceUris"] = firstSourceUris;
     }
-    if (id != null) {
-      _json["id"] = id;
+    if (metadata != null) {
+      _json["metadata"] = (metadata).toJson();
     }
-    if (name != null) {
-      _json["name"] = name;
-    }
-    if (prevProgramId != null) {
-      _json["prevProgramId"] = prevProgramId;
-    }
-    if (version != null) {
-      _json["version"] = version;
+    if (secondSourceUris != null) {
+      _json["secondSourceUris"] = secondSourceUris;
     }
     return _json;
   }
+}
+
+
+/**
+ * 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.
+ */
+class Position {
+  /**
+   * The 0-based offset from the start of the forward strand for that reference.
+   */
+  core.String position;
+
+  /** The name of the reference in whatever reference set is being used. */
+  core.String referenceName;
+
+  /**
+   * Whether this position is on the reverse strand, as opposed to the forward
+   * strand.
+   */
+  core.bool reverseStrand;
+
+
+  Position();
+
+  Position.fromJson(core.Map _json) {
+    if (_json.containsKey("position")) {
+      position = _json["position"];
+    }
+    if (_json.containsKey("referenceName")) {
+      referenceName = _json["referenceName"];
+    }
+    if (_json.containsKey("reverseStrand")) {
+      reverseStrand = _json["reverseStrand"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (position != null) {
+      _json["position"] = position;
+    }
+    if (referenceName != null) {
+      _json["referenceName"] = referenceName;
+    }
+    if (reverseStrand != null) {
+      _json["reverseStrand"] = reverseStrand;
+    }
+    return _json;
+  }
+}
+
+
+/** A 0-based half-open genomic coordinate range over a reference sequence. */
+class Range {
+  /**
+   * The end position of the range on the reference, 0-based exclusive. If
+   * specified, referenceName must also be specified.
+   */
+  core.String end;
+
+  /** The reference sequence name, for example chr1, 1, or chrX. */
+  core.String referenceName;
+
+  /**
+   * The start position of the range on the reference, 0-based inclusive. If
+   * specified, referenceName must also be specified.
+   */
+  core.String start;
+
+
+  Range();
+
+  Range.fromJson(core.Map _json) {
+    if (_json.containsKey("end")) {
+      end = _json["end"];
+    }
+    if (_json.containsKey("referenceName")) {
+      referenceName = _json["referenceName"];
+    }
+    if (_json.containsKey("start")) {
+      start = _json["start"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (end != null) {
+      _json["end"] = end;
+    }
+    if (referenceName != null) {
+      _json["referenceName"] = referenceName;
+    }
+    if (start != null) {
+      _json["start"] = start;
+    }
+    return _json;
+  }
 }
 
 
 /**
- * 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.
+ * 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.
  */
 class Read {
   /**
-   * The originalBases after the cigar field has been applied. Deletions are
-   * represented with '-' and insertions are omitted.
-   */
-  core.String alignedBases;
-
-  /**
-   * 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)
-   */
-  core.String baseQuality;
-
-  /**
-   * A condensed representation of how this read matches up to the reference.
-   * (CIGAR)
-   */
-  core.String cigar;
-
-  /**
-   * Each bit of this number has a different meaning if enabled. See the full
-   * BAM spec for more details. (FLAG)
-   */
-  core.int flags;
-
-  /** The Google generated ID of the read, immutable. */
+   * 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.
+   */
+  core.List<core.int> alignedQuality;
+
+  /**
+   * 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.
+   */
+  core.String alignedSequence;
+
+  /**
+   * The linear alignment for this alignment record. This field will be null if
+   * the read is unmapped.
+   */
+  LinearAlignment alignment;
+
+  /** The fragment is a PCR or optical duplicate (SAM flag 0x400) */
+  core.bool duplicateFragment;
+
+  /** SAM flag 0x200 */
+  core.bool failedVendorQualityChecks;
+
+  /** The observed length of the fragment, equivalent to TLEN in SAM. */
+  core.int fragmentLength;
+
+  /** The fragment name. Equivalent to QNAME (query template name) in SAM. */
+  core.String fragmentName;
+
+  /**
+   * The unique ID for this read. This is a generated unique ID, not to be
+   * confused with fragmentName.
+   */
   core.String id;
 
-  /**
-   * A score up to 255 that represents how likely this read's aligned position
-   * is to be correct. A higher value is better. (MAPQ)
-   */
-  core.int mappingQuality;
-
-  /** The 1-based start position of the paired read. (PNEXT) */
-  core.int matePosition;
-
-  /**
-   * The name of the sequence that the paired read is aligned to. This is
-   * usually the same as referenceSequenceName. (RNEXT)
-   */
-  core.String mateReferenceSequenceName;
-
-  /**
-   * The name of the read. When imported from a BAM file, this is the query
-   * template name. (QNAME)
-   */
-  core.String name;
-
-  /** The list of bases that this read represents (such as "CATCGA"). (SEQ) */
-  core.String originalBases;
-
-  /**
-   * 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)
-   */
-  core.int position;
-
-  /** The ID of the readset this read belongs to. */
-  core.String readsetId;
-
-  /**
-   * 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)
-   */
-  core.String referenceSequenceName;
-
-  /** A map of additional read information. (TAG) */
-  core.Map<core.String, core.List<core.String>> tags;
-
-  /**
-   * Length of the original piece of DNA that produced both this read and the
-   * paired read. (TLEN)
-   */
-  core.int templateLength;
+  /** A map of additional read alignment information. */
+  core.Map<core.String, core.List<core.String>> info;
+
+  /**
+   * The mapping of the primary alignment of the (readNumber+1)%numberReads read
+   * in the fragment. It replaces mate position and mate strand in SAM.
+   */
+  Position nextMatePosition;
+
+  /** The number of reads in the fragment (extension to SAM flag 0x1). */
+  core.int numberReads;
+
+  /**
+   * The orientation and the distance between reads from the fragment are
+   * consistent with the sequencing protocol (extension to SAM flag 0x2)
+   */
+  core.bool properPlacement;
+
+  /**
+   * The ID of the read group this read belongs to. (Every read must belong to
+   * exactly one read group.)
+   */
+  core.String readGroupId;
+
+  /**
+   * The ID of the read group set this read belongs to. (Every read must belong
+   * to exactly one read group set.)
+   */
+  core.String readGroupSetId;
+
+  /**
+   * The read number in sequencing. 0-based and less than numberReads. This
+   * field replaces SAM flag 0x40 and 0x80.
+   */
+  core.int readNumber;
+
+  /**
+   * 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.
+   */
+  core.bool secondaryAlignment;
+
+  /**
+   * 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.
+   */
+  core.bool supplementaryAlignment;
 
 
   Read();
 
   Read.fromJson(core.Map _json) {
-    if (_json.containsKey("alignedBases")) {
-      alignedBases = _json["alignedBases"];
-    }
-    if (_json.containsKey("baseQuality")) {
-      baseQuality = _json["baseQuality"];
-    }
-    if (_json.containsKey("cigar")) {
-      cigar = _json["cigar"];
-    }
-    if (_json.containsKey("flags")) {
-      flags = _json["flags"];
+    if (_json.containsKey("alignedQuality")) {
+      alignedQuality = _json["alignedQuality"];
+    }
+    if (_json.containsKey("alignedSequence")) {
+      alignedSequence = _json["alignedSequence"];
+    }
+    if (_json.containsKey("alignment")) {
+      alignment = new LinearAlignment.fromJson(_json["alignment"]);
+    }
+    if (_json.containsKey("duplicateFragment")) {
+      duplicateFragment = _json["duplicateFragment"];
+    }
+    if (_json.containsKey("failedVendorQualityChecks")) {
+      failedVendorQualityChecks = _json["failedVendorQualityChecks"];
+    }
+    if (_json.containsKey("fragmentLength")) {
+      fragmentLength = _json["fragmentLength"];
+    }
+    if (_json.containsKey("fragmentName")) {
+      fragmentName = _json["fragmentName"];
     }
     if (_json.containsKey("id")) {
       id = _json["id"];
     }
-    if (_json.containsKey("mappingQuality")) {
-      mappingQuality = _json["mappingQuality"];
-    }
-    if (_json.containsKey("matePosition")) {
-      matePosition = _json["matePosition"];
-    }
-    if (_json.containsKey("mateReferenceSequenceName")) {
-      mateReferenceSequenceName = _json["mateReferenceSequenceName"];
+    if (_json.containsKey("info")) {
+      info = _json["info"];
+    }
+    if (_json.containsKey("nextMatePosition")) {
+      nextMatePosition = new Position.fromJson(_json["nextMatePosition"]);
+    }
+    if (_json.containsKey("numberReads")) {
+      numberReads = _json["numberReads"];
+    }
+    if (_json.containsKey("properPlacement")) {
+      properPlacement = _json["properPlacement"];
+    }
+    if (_json.containsKey("readGroupId")) {
+      readGroupId = _json["readGroupId"];
+    }
+    if (_json.containsKey("readGroupSetId")) {
+      readGroupSetId = _json["readGroupSetId"];
+    }
+    if (_json.containsKey("readNumber")) {
+      readNumber = _json["readNumber"];
+    }
+    if (_json.containsKey("secondaryAlignment")) {
+      secondaryAlignment = _json["secondaryAlignment"];
+    }
+    if (_json.containsKey("supplementaryAlignment")) {
+      supplementaryAlignment = _json["supplementaryAlignment"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (alignedQuality != null) {
+      _json["alignedQuality"] = alignedQuality;
+    }
+    if (alignedSequence != null) {
+      _json["alignedSequence"] = alignedSequence;
+    }
+    if (alignment != null) {
+      _json["alignment"] = (alignment).toJson();
+    }
+    if (duplicateFragment != null) {
+      _json["duplicateFragment"] = duplicateFragment;
+    }
+    if (failedVendorQualityChecks != null) {
+      _json["failedVendorQualityChecks"] = failedVendorQualityChecks;
+    }
+    if (fragmentLength != null) {
+      _json["fragmentLength"] = fragmentLength;
+    }
+    if (fragmentName != null) {
+      _json["fragmentName"] = fragmentName;
+    }
+    if (id != null) {
+      _json["id"] = id;
+    }
+    if (info != null) {
+      _json["info"] = info;
+    }
+    if (nextMatePosition != null) {
+      _json["nextMatePosition"] = (nextMatePosition).toJson();
+    }
+    if (numberReads != null) {
+      _json["numberReads"] = numberReads;
+    }
+    if (properPlacement != null) {
+      _json["properPlacement"] = properPlacement;
+    }
+    if (readGroupId != null) {
+      _json["readGroupId"] = readGroupId;
+    }
+    if (readGroupSetId != null) {
+      _json["readGroupSetId"] = readGroupSetId;
+    }
+    if (readNumber != null) {
+      _json["readNumber"] = readNumber;
+    }
+    if (secondaryAlignment != null) {
+      _json["secondaryAlignment"] = secondaryAlignment;
+    }
+    if (supplementaryAlignment != null) {
+      _json["supplementaryAlignment"] = supplementaryAlignment;
+    }
+    return _json;
+  }
+}
+
+
+/**
+ * A read group is all the data that's processed the same way by the sequencer.
+ */
+class ReadGroup {
+  /** The ID of the dataset this read group belongs to. */
+  core.String datasetId;
+
+  /** A free-form text description of this read group. */
+  core.String description;
+
+  /** The experiment used to generate this read group. */
+  ReadGroupExperiment experiment;
+
+  /**
+   * 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.
+   */
+  core.String id;
+
+  /** A map of additional read group information. */
+  core.Map<core.String, core.List<core.String>> info;
+
+  /**
+   * The read group name. This corresponds to the @RG ID field in the SAM spec.
+   */
+  core.String name;
+
+  /**
+   * 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.
+   */
+  core.int predictedInsertSize;
+
+  /**
+   * 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.
+   */
+  core.List<ReadGroupProgram> programs;
+
+  /**
+   * The reference set the reads in this read group are aligned to. Required if
+   * there are any read alignments.
+   */
+  core.String referenceSetId;
+
+  /**
+   * 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.
+   */
+  core.String sampleId;
+
+
+  ReadGroup();
+
+  ReadGroup.fromJson(core.Map _json) {
+    if (_json.containsKey("datasetId")) {
+      datasetId = _json["datasetId"];
+    }
+    if (_json.containsKey("description")) {
+      description = _json["description"];
+    }
+    if (_json.containsKey("experiment")) {
+      experiment = new ReadGroupExperiment.fromJson(_json["experiment"]);
+    }
+    if (_json.containsKey("id")) {
+      id = _json["id"];
+    }
+    if (_json.containsKey("info")) {
+      info = _json["info"];
     }
     if (_json.containsKey("name")) {
       name = _json["name"];
     }
-    if (_json.containsKey("originalBases")) {
-      originalBases = _json["originalBases"];
-    }
-    if (_json.containsKey("position")) {
-      position = _json["position"];
-    }
-    if (_json.containsKey("readsetId")) {
-      readsetId = _json["readsetId"];
-    }
-    if (_json.containsKey("referenceSequenceName")) {
-      referenceSequenceName = _json["referenceSequenceName"];
-    }
-    if (_json.containsKey("tags")) {
-      tags = _json["tags"];
-    }
-    if (_json.containsKey("templateLength")) {
-      templateLength = _json["templateLength"];
+    if (_json.containsKey("predictedInsertSize")) {
+      predictedInsertSize = _json["predictedInsertSize"];
+    }
+    if (_json.containsKey("programs")) {
+      programs = _json["programs"].map((value) => new ReadGroupProgram.fromJson(value)).toList();
+    }
+    if (_json.containsKey("referenceSetId")) {
+      referenceSetId = _json["referenceSetId"];
+    }
+    if (_json.containsKey("sampleId")) {
+      sampleId = _json["sampleId"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
-    if (alignedBases != null) {
-      _json["alignedBases"] = alignedBases;
-    }
-    if (baseQuality != null) {
-      _json["baseQuality"] = baseQuality;
-    }
-    if (cigar != null) {
-      _json["cigar"] = cigar;
-    }
-    if (flags != null) {
-      _json["flags"] = flags;
+    if (datasetId != null) {
+      _json["datasetId"] = datasetId;
+    }
+    if (description != null) {
+      _json["description"] = description;
+    }
+    if (experiment != null) {
+      _json["experiment"] = (experiment).toJson();
     }
     if (id != null) {
       _json["id"] = id;
     }
-    if (mappingQuality != null) {
-      _json["mappingQuality"] = mappingQuality;
-    }
-    if (matePosition != null) {
-      _json["matePosition"] = matePosition;
-    }
-    if (mateReferenceSequenceName != null) {
-      _json["mateReferenceSequenceName"] = mateReferenceSequenceName;
+    if (info != null) {
+      _json["info"] = info;
     }
     if (name != null) {
       _json["name"] = name;
     }
-    if (originalBases != null) {
-      _json["originalBases"] = originalBases;
-    }
-    if (position != null) {
-      _json["position"] = position;
-    }
-    if (readsetId != null) {
-      _json["readsetId"] = readsetId;
-    }
-    if (referenceSequenceName != null) {
-      _json["referenceSequenceName"] = referenceSequenceName;
-    }
-    if (tags != null) {
-      _json["tags"] = tags;
-    }
-    if (templateLength != null) {
-      _json["templateLength"] = templateLength;
+    if (predictedInsertSize != null) {
+      _json["predictedInsertSize"] = predictedInsertSize;
+    }
+    if (programs != null) {
+      _json["programs"] = programs.map((value) => (value).toJson()).toList();
+    }
+    if (referenceSetId != null) {
+      _json["referenceSetId"] = referenceSetId;
+    }
+    if (sampleId != null) {
+      _json["sampleId"] = sampleId;
     }
     return _json;
   }
 }
 
 
 /** Not documented yet. */
-class ReadGroup {
-  /** (DT) Date the run was produced (ISO8601 date or date/time). */
-  core.String date;
-
-  /** (DS) Description. */
-  core.String description;
-
-  /**
-   * (FO) Flow order. The array of nucleotide bases that correspond to the
-   * nucleotides used for each flow of each read.
-   */
-  core.String flowOrder;
-
-  /** (ID) Read group identifier. */
+class ReadGroupExperiment {
+  /**
+   * The instrument model used as part of this experiment. This maps to
+   * sequencing technology in BAM.
+   */
+  core.String instrumentModel;
+
+  /**
+   * 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.
+   */
+  core.String libraryId;
+
+  /**
+   * The platform unit used as part of this experiment e.g.
+   * flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
+   */
+  core.String platformUnit;
+
+  /** The sequencing center used as part of this experiment. */
+  core.String sequencingCenter;
+
+
+  ReadGroupExperiment();
+
+  ReadGroupExperiment.fromJson(core.Map _json) {
+    if (_json.containsKey("instrumentModel")) {
+      instrumentModel = _json["instrumentModel"];
+    }
+    if (_json.containsKey("libraryId")) {
+      libraryId = _json["libraryId"];
+    }
+    if (_json.containsKey("platformUnit")) {
+      platformUnit = _json["platformUnit"];
+    }
+    if (_json.containsKey("sequencingCenter")) {
+      sequencingCenter = _json["sequencingCenter"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (instrumentModel != null) {
+      _json["instrumentModel"] = instrumentModel;
+    }
+    if (libraryId != null) {
+      _json["libraryId"] = libraryId;
+    }
+    if (platformUnit != null) {
+      _json["platformUnit"] = platformUnit;
+    }
+    if (sequencingCenter != null) {
+      _json["sequencingCenter"] = sequencingCenter;
+    }
+    return _json;
+  }
+}
+
+
+/** Not documented yet. */
+class ReadGroupProgram {
+  /** The command line used to run this program. */
+  core.String commandLine;
+
+  /**
+   * The user specified locally unique ID of the program. Used along with
+   * prevProgramId to define an ordering between programs.
+   */
   core.String id;
 
-  /**
-   * (KS) The array of nucleotide bases that correspond to the key sequence of
-   * each read.
-   */
-  core.String keySequence;
-
-  /** (LS) Library. */
-  core.String library;
-
-  /** (PU) Platform unit. */
-  core.String platformUnit;
-
-  /** (PI) Predicted median insert size. */
-  core.int predictedInsertSize;
-
-  /** (PG) Programs used for processing the read group. */
-  core.String processingProgram;
-
-  /** (SM) Sample. */
-  core.String sample;
-
-  /** (CN) Name of sequencing center producing the read. */
-  core.String sequencingCenterName;
-
-  /** (PL) Platform/technology used to produce the reads. */
-  core.String sequencingTechnology;
-
-
-  ReadGroup();
-
-  ReadGroup.fromJson(core.Map _json) {
-    if (_json.containsKey("date")) {
-      date = _json["date"];
-    }
-    if (_json.containsKey("description")) {
-      description = _json["description"];
-    }
-    if (_json.containsKey("flowOrder")) {
-      flowOrder = _json["flowOrder"];
+  /** The name of the program. */
+  core.String name;
+
+  /** The ID of the program run before this one. */
+  core.String prevProgramId;
+
+  /** The version of the program run. */
+  core.String version;
+
+
+  ReadGroupProgram();
+
+  ReadGroupProgram.fromJson(core.Map _json) {
+    if (_json.containsKey("commandLine")) {
+      commandLine = _json["commandLine"];
     }
     if (_json.containsKey("id")) {
       id = _json["id"];
     }
-    if (_json.containsKey("keySequence")) {
-      keySequence = _json["keySequence"];
-    }
-    if (_json.containsKey("library")) {
-      library = _json["library"];
-    }
-    if (_json.containsKey("platformUnit")) {
-      platformUnit = _json["platformUnit"];
-    }
-    if (_json.containsKey("predictedInsertSize")) {
-      predictedInsertSize = _json["predictedInsertSize"];
-    }
-    if (_json.containsKey("processingProgram")) {
-      processingProgram = _json["processingProgram"];
-    }
-    if (_json.containsKey("sample")) {
-      sample = _json["sample"];
-    }
-    if (_json.containsKey("sequencingCenterName")) {
-      sequencingCenterName = _json["sequencingCenterName"];
-    }
-    if (_json.containsKey("sequencingTechnology")) {
-      sequencingTechnology = _json["sequencingTechnology"];
+    if (_json.containsKey("name")) {
+      name = _json["name"];
+    }
+    if (_json.containsKey("prevProgramId")) {
+      prevProgramId = _json["prevProgramId"];
+    }
+    if (_json.containsKey("version")) {
+      version = _json["version"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
-    if (date != null) {
-      _json["date"] = date;
-    }
-    if (description != null) {
-      _json["description"] = description;
-    }
-    if (flowOrder != null) {
-      _json["flowOrder"] = flowOrder;
+    if (commandLine != null) {
+      _json["commandLine"] = commandLine;
     }
     if (id != null) {
       _json["id"] = id;
     }
-    if (keySequence != null) {
-      _json["keySequence"] = keySequence;
-    }
-    if (library != null) {
-      _json["library"] = library;
-    }
-    if (platformUnit != null) {
-      _json["platformUnit"] = platformUnit;
-    }
-    if (predictedInsertSize != null) {
-      _json["predictedInsertSize"] = predictedInsertSize;
-    }
-    if (processingProgram != null) {
-      _json["processingProgram"] = processingProgram;
-    }
-    if (sample != null) {
-      _json["sample"] = sample;
-    }
-    if (sequencingCenterName != null) {
-      _json["sequencingCenterName"] = sequencingCenterName;
-    }
-    if (sequencingTechnology != null) {
-      _json["sequencingTechnology"] = sequencingTechnology;
+    if (name != null) {
+      _json["name"] = name;
+    }
+    if (prevProgramId != null) {
+      _json["prevProgramId"] = prevProgramId;
+    }
+    if (version != null) {
+      _json["version"] = version;
     }
     return _json;
   }
 }
 
 
-/** A Readset is a collection of Reads. */
-class Readset {
-  /** The ID of the dataset this readset belongs to. */
+/**
+ * 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.
+ * - A read group set belongs to one dataset.
+ * - A read group belongs to one read group set.
+ * - A read belongs to one read group.
+ */
+class ReadGroupSet {
+  /** The dataset ID. */
   core.String datasetId;
 
   /**
-   * File information from the original BAM import. See the BAM format
-   * specification for additional information on each field.
-   */
-  core.List<HeaderSection> fileData;
-
-  /** The Google generated ID of the readset, immutable. */
+   * The filename of the original source file for this read group set, if any.
+   */
+  core.String filename;
+
+  /** The read group set ID. */
   core.String id;
 
-  /** The readset name, typically this is the sample name. */
+  /**
+   * The read group set name. By default this will be initialized to the sample
+   * name of the sequenced data contained in this set.
+   */
   core.String name;
 
-
-  Readset();
-
-  Readset.fromJson(core.Map _json) {
+  /**
+   * The read groups in this set. There are typically 1-10 read groups in a read
+   * group set.
+   */
+  core.List<ReadGroup> readGroups;
+
+  /** The reference set the reads in this read group set are aligned to. */
+  core.String referenceSetId;
+
+
+  ReadGroupSet();
+
+  ReadGroupSet.fromJson(core.Map _json) {
     if (_json.containsKey("datasetId")) {
       datasetId = _json["datasetId"];
     }
-    if (_json.containsKey("fileData")) {
-      fileData = _json["fileData"].map((value) => new HeaderSection.fromJson(value)).toList();
+    if (_json.containsKey("filename")) {
+      filename = _json["filename"];
     }
     if (_json.containsKey("id")) {
       id = _json["id"];
     }
     if (_json.containsKey("name")) {
       name = _json["name"];
     }
+    if (_json.containsKey("readGroups")) {
+      readGroups = _json["readGroups"].map((value) => new ReadGroup.fromJson(value)).toList();
+    }
+    if (_json.containsKey("referenceSetId")) {
+      referenceSetId = _json["referenceSetId"];
+    }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (datasetId != null) {
       _json["datasetId"] = datasetId;
     }
-    if (fileData != null) {
-      _json["fileData"] = fileData.map((value) => (value).toJson()).toList();
+    if (filename != null) {
+      _json["filename"] = filename;
     }
     if (id != null) {
       _json["id"] = id;
     }
     if (name != null) {
       _json["name"] = name;
     }
+    if (readGroups != null) {
+      _json["readGroups"] = readGroups.map((value) => (value).toJson()).toList();
+    }
+    if (referenceSetId != null) {
+      _json["referenceSetId"] = referenceSetId;
+    }
     return _json;
   }
 }
+
+
+/**
+ * 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.
+ */
+class Reference {
+  /** The Google generated immutable ID of the reference. */
+  core.String id;
+
+  /** The length of this reference's sequence. */
+  core.String length;
+
+  /**
+   * 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.
+   */
+  core.String md5checksum;
+
+  /** The name of this reference, for example 22. */
+  core.String name;
+
+  /**
+   * ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not
+   * specified by the containing reference set.
+   */
+  core.int ncbiTaxonId;
+
+  /**
+   * All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
+   * with a version number, for example GCF_000001405.26.
+   */
+  core.List<core.String> sourceAccessions;
+
+  /**
+   * The URI from which the sequence was obtained. Specifies a FASTA format
+   * file/string with one name, sequence pair.
+   */
+  core.String sourceURI;
+
+
+  Reference();
+
+  Reference.fromJson(core.Map _json) {
+    if (_json.containsKey("id")) {
+      id = _json["id"];
+    }
+    if (_json.containsKey("length")) {
+      length = _json["length"];
+    }
+    if (_json.containsKey("md5checksum")) {
+      md5checksum = _json["md5checksum"];
+    }
+    if (_json.containsKey("name")) {
+      name = _json["name"];
+    }
+    if (_json.containsKey("ncbiTaxonId")) {
+      ncbiTaxonId = _json["ncbiTaxonId"];
+    }
+    if (_json.containsKey("sourceAccessions")) {
+      sourceAccessions = _json["sourceAccessions"];
+    }
+    if (_json.containsKey("sourceURI")) {
+      sourceURI = _json["sourceURI"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (id != null) {
+      _json["id"] = id;
+    }
+    if (length != null) {
+      _json["length"] = length;
+    }
+    if (md5checksum != null) {
+      _json["md5checksum"] = md5checksum;
+    }
+    if (name != null) {
+      _json["name"] = name;
+    }
+    if (ncbiTaxonId != null) {
+      _json["ncbiTaxonId"] = ncbiTaxonId;
+    }
+    if (sourceAccessions != null) {
+      _json["sourceAccessions"] = sourceAccessions;
+    }
+    if (sourceURI != null) {
+      _json["sourceURI"] = sourceURI;
+    }
+    return _json;
+  }
+}
 
 
 /**
  * ReferenceBound records an upper bound for the starting coordinate of variants
  * in a particular reference.
  */
 class ReferenceBound {
   /** The reference the bound is associate with. */
   core.String referenceName;
 
@@ skipping 21 matching lines @@
       _json["referenceName"] = referenceName;
     }
     if (upperBound != null) {
       _json["upperBound"] = upperBound;
     }
     return _json;
   }
 }
 
 
-/** Not documented yet. */
-class ReferenceSequence {
-  /** (AS) Genome assembly identifier. */
+/**
+ * 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.
+ */
+class ReferenceSet {
+  /** Public id of this reference set, such as GRCh37. */
   core.String assemblyId;
 
-  /** (LN) Reference sequence length. */
-  core.int length;
+  /** Optional free text description of this reference set. */
+  core.String description;
+
+  /** The Google generated immutable ID of the reference set. */
+  core.String id;
 
   /**
-   * (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but
-   * including pads as *.
+   * 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.
    */
-  core.String md5Checksum;
+  core.String md5checksum;
 
-  /** (SN) Reference sequence name. */
-  core.String name;
+  /**
+   * 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.
+   */
+  core.int ncbiTaxonId;
 
-  /** (SP) Species. */
-  core.String species;
+  /**
+   * The IDs of the reference objects that are part of this set.
+   * Reference.md5checksum must be unique within this set.
+   */
+  core.List<core.String> referenceIds;
 
-  /** (UR) URI of the sequence. */
-  core.String uri;
+  /**
+   * All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
+   * with a version number, for example NC_000001.11.
+   */
+  core.List<core.String> sourceAccessions;
+
+  /** The URI from which the references were obtained. */
+  core.String sourceURI;
 
 
-  ReferenceSequence();
+  ReferenceSet();
 
-  ReferenceSequence.fromJson(core.Map _json) {
+  ReferenceSet.fromJson(core.Map _json) {
     if (_json.containsKey("assemblyId")) {
       assemblyId = _json["assemblyId"];
     }
-    if (_json.containsKey("length")) {
-      length = _json["length"];
+    if (_json.containsKey("description")) {
+      description = _json["description"];
     }
-    if (_json.containsKey("md5Checksum")) {
-      md5Checksum = _json["md5Checksum"];
+    if (_json.containsKey("id")) {
+      id = _json["id"];
     }
-    if (_json.containsKey("name")) {
-      name = _json["name"];
+    if (_json.containsKey("md5checksum")) {
+      md5checksum = _json["md5checksum"];
     }
-    if (_json.containsKey("species")) {
-      species = _json["species"];
+    if (_json.containsKey("ncbiTaxonId")) {
+      ncbiTaxonId = _json["ncbiTaxonId"];
     }
-    if (_json.containsKey("uri")) {
-      uri = _json["uri"];
+    if (_json.containsKey("referenceIds")) {
+      referenceIds = _json["referenceIds"];
+    }
+    if (_json.containsKey("sourceAccessions")) {
+      sourceAccessions = _json["sourceAccessions"];
+    }
+    if (_json.containsKey("sourceURI")) {
+      sourceURI = _json["sourceURI"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (assemblyId != null) {
       _json["assemblyId"] = assemblyId;
     }
-    if (length != null) {
-      _json["length"] = length;
+    if (description != null) {
+      _json["description"] = description;
     }
-    if (md5Checksum != null) {
-      _json["md5Checksum"] = md5Checksum;
+    if (id != null) {
+      _json["id"] = id;
     }
-    if (name != null) {
-      _json["name"] = name;
+    if (md5checksum != null) {
+      _json["md5checksum"] = md5checksum;
     }
-    if (species != null) {
-      _json["species"] = species;
+    if (ncbiTaxonId != null) {
+      _json["ncbiTaxonId"] = ncbiTaxonId;
     }
-    if (uri != null) {
-      _json["uri"] = uri;
+    if (referenceIds != null) {
+      _json["referenceIds"] = referenceIds;
+    }
+    if (sourceAccessions != null) {
+      _json["sourceAccessions"] = sourceAccessions;
+    }
+    if (sourceURI != null) {
+      _json["sourceURI"] = sourceURI;
     }
     return _json;
   }
 }
 
 
 /** The call set search request. */
 class SearchCallSetsRequest {
   /**
    * Only return call sets for which a substring of the name matches this
@@ skipping 102 matching lines @@
   /**
    * If specified, only jobs created prior to this date, given in milliseconds
    * since Unix epoch, will be returned.
    */
   core.String createdBefore;
 
   /**
    * Specifies the number of results to return in a single page. Defaults to
    * 128. The maximum value is 256.
    */
-  core.String maxResults;
+  core.int pageSize;
 
   /**
    * 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.
    */
   core.String pageToken;
 
   /** Required. Only return jobs which belong to this Google Developers */
-  core.String projectId;
+  core.String projectNumber;
 
   /** Only return jobs which have a matching status. */
   core.List<core.String> status;
 
 
   SearchJobsRequest();
 
   SearchJobsRequest.fromJson(core.Map _json) {
     if (_json.containsKey("createdAfter")) {
       createdAfter = _json["createdAfter"];
     }
     if (_json.containsKey("createdBefore")) {
       createdBefore = _json["createdBefore"];
     }
-    if (_json.containsKey("maxResults")) {
-      maxResults = _json["maxResults"];
+    if (_json.containsKey("pageSize")) {
+      pageSize = _json["pageSize"];
     }
     if (_json.containsKey("pageToken")) {
       pageToken = _json["pageToken"];
     }
-    if (_json.containsKey("projectId")) {
-      projectId = _json["projectId"];
+    if (_json.containsKey("projectNumber")) {
+      projectNumber = _json["projectNumber"];
     }
     if (_json.containsKey("status")) {
       status = _json["status"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (createdAfter != null) {
       _json["createdAfter"] = createdAfter;
     }
     if (createdBefore != null) {
       _json["createdBefore"] = createdBefore;
     }
-    if (maxResults != null) {
-      _json["maxResults"] = maxResults;
+    if (pageSize != null) {
+      _json["pageSize"] = pageSize;
     }
     if (pageToken != null) {
       _json["pageToken"] = pageToken;
     }
-    if (projectId != null) {
-      _json["projectId"] = projectId;
+    if (projectNumber != null) {
+      _json["projectNumber"] = projectNumber;
     }
     if (status != null) {
       _json["status"] = status;
     }
     return _json;
   }
 }
 
 
 /** The job search response. */
@@ skipping 26 matching lines @@
       _json["jobs"] = jobs.map((value) => (value).toJson()).toList();
     }
     if (nextPageToken != null) {
       _json["nextPageToken"] = nextPageToken;
     }
     return _json;
   }
 }
 
 
+/** The read group set search request. */
+class SearchReadGroupSetsRequest {
+  /**
+   * Restricts this query to read group sets within the given datasets. At least
+   * one ID must be provided.
+   */
+  core.List<core.String> datasetIds;
+
+  /**
+   * Only return read group sets for which a substring of the name matches this
+   * string.
+   */
+  core.String name;
+
+  /**
+   * Specifies number of results to return in a single page. If unspecified, it
+   * will default to 128. The maximum value is 1024.
+   */
+  core.int pageSize;
+
+  /**
+   * 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.
+   */
+  core.String pageToken;
+
+
+  SearchReadGroupSetsRequest();
+
+  SearchReadGroupSetsRequest.fromJson(core.Map _json) {
+    if (_json.containsKey("datasetIds")) {
+      datasetIds = _json["datasetIds"];
+    }
+    if (_json.containsKey("name")) {
+      name = _json["name"];
+    }
+    if (_json.containsKey("pageSize")) {
+      pageSize = _json["pageSize"];
+    }
+    if (_json.containsKey("pageToken")) {
+      pageToken = _json["pageToken"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (datasetIds != null) {
+      _json["datasetIds"] = datasetIds;
+    }
+    if (name != null) {
+      _json["name"] = name;
+    }
+    if (pageSize != null) {
+      _json["pageSize"] = pageSize;
+    }
+    if (pageToken != null) {
+      _json["pageToken"] = pageToken;
+    }
+    return _json;
+  }
+}
+
+
+/** The read group set search response. */
+class SearchReadGroupSetsResponse {
+  /**
+   * 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.
+   */
+  core.String nextPageToken;
+
+  /** The list of matching read group sets. */
+  core.List<ReadGroupSet> readGroupSets;
+
+
+  SearchReadGroupSetsResponse();
+
+  SearchReadGroupSetsResponse.fromJson(core.Map _json) {
+    if (_json.containsKey("nextPageToken")) {
+      nextPageToken = _json["nextPageToken"];
+    }
+    if (_json.containsKey("readGroupSets")) {
+      readGroupSets = _json["readGroupSets"].map((value) => new ReadGroupSet.fromJson(value)).toList();
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (nextPageToken != null) {
+      _json["nextPageToken"] = nextPageToken;
+    }
+    if (readGroupSets != null) {
+      _json["readGroupSets"] = readGroupSets.map((value) => (value).toJson()).toList();
+    }
+    return _json;
+  }
+}
+
+
 /** The read search request. */
 class SearchReadsRequest {
   /**
+   * The end position of the range on the reference, 0-based exclusive. If
+   * specified, referenceName must also be specified.
+   */
+  core.String end;
+
+  /**
    * Specifies number of results to return in a single page. If unspecified, it
    * will default to 256. The maximum value is 2048.
    */
-  core.String maxResults;
+  core.int pageSize;
 
   /**
    * 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.
    */
   core.String pageToken;
 
   /**
-   * 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.
+   * 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.
    */
-  core.List<core.String> readsetIds;
+  core.List<core.String> readGroupIds;
 
   /**
-   * 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.
+   * 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.
    */
-  core.String sequenceEnd;
+  core.List<core.String> readGroupSetIds;
 
   /**
-   * 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.
+   * The reference sequence name, for example chr1, 1, or chrX. If set to *,
+   * only unmapped reads are returned.
    */
-  core.String sequenceName;
+  core.String referenceName;
 
   /**
-   * 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.
+   * The start position of the range on the reference, 0-based inclusive. If
+   * specified, referenceName must also be specified.
    */
-  core.String sequenceStart;
+  core.String start;
 
 
   SearchReadsRequest();
 
   SearchReadsRequest.fromJson(core.Map _json) {
-    if (_json.containsKey("maxResults")) {
-      maxResults = _json["maxResults"];
+    if (_json.containsKey("end")) {
+      end = _json["end"];
+    }
+    if (_json.containsKey("pageSize")) {
+      pageSize = _json["pageSize"];
     }
     if (_json.containsKey("pageToken")) {
       pageToken = _json["pageToken"];
     }
-    if (_json.containsKey("readsetIds")) {
-      readsetIds = _json["readsetIds"];
+    if (_json.containsKey("readGroupIds")) {
+      readGroupIds = _json["readGroupIds"];
     }
-    if (_json.containsKey("sequenceEnd")) {
-      sequenceEnd = _json["sequenceEnd"];
+    if (_json.containsKey("readGroupSetIds")) {
+      readGroupSetIds = _json["readGroupSetIds"];
     }
-    if (_json.containsKey("sequenceName")) {
-      sequenceName = _json["sequenceName"];
+    if (_json.containsKey("referenceName")) {
+      referenceName = _json["referenceName"];
     }
-    if (_json.containsKey("sequenceStart")) {
-      sequenceStart = _json["sequenceStart"];
+    if (_json.containsKey("start")) {
+      start = _json["start"];
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
-    if (maxResults != null) {
-      _json["maxResults"] = maxResults;
+    if (end != null) {
+      _json["end"] = end;
+    }
+    if (pageSize != null) {
+      _json["pageSize"] = pageSize;
     }
     if (pageToken != null) {
       _json["pageToken"] = pageToken;
     }
-    if (readsetIds != null) {
-      _json["readsetIds"] = readsetIds;
+    if (readGroupIds != null) {
+      _json["readGroupIds"] = readGroupIds;
     }
-    if (sequenceEnd != null) {
-      _json["sequenceEnd"] = sequenceEnd;
+    if (readGroupSetIds != null) {
+      _json["readGroupSetIds"] = readGroupSetIds;
     }
-    if (sequenceName != null) {
-      _json["sequenceName"] = sequenceName;
+    if (referenceName != null) {
+      _json["referenceName"] = referenceName;
     }
-    if (sequenceStart != null) {
-      _json["sequenceStart"] = sequenceStart;
+    if (start != null) {
+      _json["start"] = start;
     }
     return _json;
   }
 }
 
 
 /** The read search response. */
 class SearchReadsResponse {
   /**
+   * 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.
+   */
+  core.List<Read> alignments;
+
+  /**
    * 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.
    */
   core.String nextPageToken;
 
-  /**
-   * 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.
-   */
-  core.List<Read> reads;
-
 
   SearchReadsResponse();
 
   SearchReadsResponse.fromJson(core.Map _json) {
+    if (_json.containsKey("alignments")) {
+      alignments = _json["alignments"].map((value) => new Read.fromJson(value)).toList();
+    }
     if (_json.containsKey("nextPageToken")) {
       nextPageToken = _json["nextPageToken"];
     }
-    if (_json.containsKey("reads")) {
-      reads = _json["reads"].map((value) => new Read.fromJson(value)).toList();
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (alignments != null) {
+      _json["alignments"] = alignments.map((value) => (value).toJson()).toList();
+    }
+    if (nextPageToken != null) {
+      _json["nextPageToken"] = nextPageToken;
+    }
+    return _json;
+  }
+}
+
+
+/** Not documented yet. */
+class SearchReferenceSetsRequest {
+  /**
+   * 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.
+   */
+  core.List<core.String> accessions;
+
+  /**
+   * If present, return references for which the md5checksum matches. See
+   * ReferenceSet.md5checksum for details.
+   */
+  core.List<core.String> md5checksums;
+
+  /** Specifies the maximum number of results to return in a single page. */
+  core.int pageSize;
+
+  /**
+   * 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.
+   */
+  core.String pageToken;
+
+
+  SearchReferenceSetsRequest();
+
+  SearchReferenceSetsRequest.fromJson(core.Map _json) {
+    if (_json.containsKey("accessions")) {
+      accessions = _json["accessions"];
+    }
+    if (_json.containsKey("md5checksums")) {
+      md5checksums = _json["md5checksums"];
+    }
+    if (_json.containsKey("pageSize")) {
+      pageSize = _json["pageSize"];
+    }
+    if (_json.containsKey("pageToken")) {
+      pageToken = _json["pageToken"];
+    }
+  }
+
+  core.Map toJson() {
+    var _json = new core.Map();
+    if (accessions != null) {
+      _json["accessions"] = accessions;
+    }
+    if (md5checksums != null) {
+      _json["md5checksums"] = md5checksums;
+    }
+    if (pageSize != null) {
+      _json["pageSize"] = pageSize;
+    }
+    if (pageToken != null) {
+      _json["pageToken"] = pageToken;
+    }
+    return _json;
+  }
+}
+
+
+/** Not documented yet. */
+class SearchReferenceSetsResponse {
+  /**
+   * 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.
+   */
+  core.String nextPageToken;
+
+  /** The matching references sets. */
+  core.List<ReferenceSet> referenceSets;
+
+
+  SearchReferenceSetsResponse();
+
+  SearchReferenceSetsResponse.fromJson(core.Map _json) {
+    if (_json.containsKey("nextPageToken")) {
+      nextPageToken = _json["nextPageToken"];
+    }
+    if (_json.containsKey("referenceSets")) {
+      referenceSets = _json["referenceSets"].map((value) => new ReferenceSet.fromJson(value)).toList();
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (nextPageToken != null) {
       _json["nextPageToken"] = nextPageToken;
     }
-    if (reads != null) {
-      _json["reads"] = reads.map((value) => (value).toJson()).toList();
+    if (referenceSets != null) {
+      _json["referenceSets"] = referenceSets.map((value) => (value).toJson()).toList();
     }
     return _json;
   }
 }
 
 
-/** The readset search request. */
-class SearchReadsetsRequest {
+/** Not documented yet. */
+class SearchReferencesRequest {
   /**
-   * Restricts this query to readsets within the given datasets. At least one ID
-   * must be provided.
+   * 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.
    */
-  core.List<core.String> datasetIds;
+  core.List<core.String> accessions;
 
   /**
-   * Specifies number of results to return in a single page. If unspecified, it
-   * will default to 128. The maximum value is 1024.
+   * If present, return references for which the md5checksum matches. See
+   * Reference.md5checksum for construction details.
    */
-  core.String maxResults;
+  core.List<core.String> md5checksums;
 
-  /**
-   * Only return readsets for which a substring of the name matches this string.
-   */
-  core.String name;
+  /** Specifies the maximum number of results to return in a single page. */
+  core.int pageSize;
 
   /**
    * 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.
    */
   core.String pageToken;
 
+  /** If present, return only references which belong to this reference set. */
+  core.String referenceSetId;
 
-  SearchReadsetsRequest();
 
-  SearchReadsetsRequest.fromJson(core.Map _json) {
-    if (_json.containsKey("datasetIds")) {
-      datasetIds = _json["datasetIds"];
+  SearchReferencesRequest();
+
+  SearchReferencesRequest.fromJson(core.Map _json) {
+    if (_json.containsKey("accessions")) {
+      accessions = _json["accessions"];
     }
-    if (_json.containsKey("maxResults")) {
-      maxResults = _json["maxResults"];
+    if (_json.containsKey("md5checksums")) {
+      md5checksums = _json["md5checksums"];
     }
-    if (_json.containsKey("name")) {
-      name = _json["name"];
+    if (_json.containsKey("pageSize")) {
+      pageSize = _json["pageSize"];
     }
     if (_json.containsKey("pageToken")) {
       pageToken = _json["pageToken"];
     }
+    if (_json.containsKey("referenceSetId")) {
+      referenceSetId = _json["referenceSetId"];
+    }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
-    if (datasetIds != null) {
-      _json["datasetIds"] = datasetIds;
+    if (accessions != null) {
+      _json["accessions"] = accessions;
     }
-    if (maxResults != null) {
-      _json["maxResults"] = maxResults;
+    if (md5checksums != null) {
+      _json["md5checksums"] = md5checksums;
     }
-    if (name != null) {
-      _json["name"] = name;
+    if (pageSize != null) {
+      _json["pageSize"] = pageSize;
     }
     if (pageToken != null) {
       _json["pageToken"] = pageToken;
     }
+    if (referenceSetId != null) {
+      _json["referenceSetId"] = referenceSetId;
+    }
     return _json;
   }
 }
 
 
-/** The readset search response. */
-class SearchReadsetsResponse {
+/** Not documented yet. */
+class SearchReferencesResponse {
   /**
    * 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.
    */
   core.String nextPageToken;
 
-  /** The list of matching Readsets. */
-  core.List<Readset> readsets;
+  /** The matching references. */
+  core.List<Reference> references;
 
 
-  SearchReadsetsResponse();
+  SearchReferencesResponse();
 
-  SearchReadsetsResponse.fromJson(core.Map _json) {
+  SearchReferencesResponse.fromJson(core.Map _json) {
     if (_json.containsKey("nextPageToken")) {
       nextPageToken = _json["nextPageToken"];
     }
-    if (_json.containsKey("readsets")) {
-      readsets = _json["readsets"].map((value) => new Readset.fromJson(value)).toList();
+    if (_json.containsKey("references")) {
+      references = _json["references"].map((value) => new Reference.fromJson(value)).toList();
     }
   }
 
   core.Map toJson() {
     var _json = new core.Map();
     if (nextPageToken != null) {
       _json["nextPageToken"] = nextPageToken;
     }
-    if (readsets != null) {
-      _json["readsets"] = readsets.map((value) => (value).toJson()).toList();
+    if (references != null) {
+      _json["references"] = references.map((value) => (value).toJson()).toList();
     }
     return _json;
   }
 }
 
 
 /** The search variant sets request. */
 class SearchVariantSetsRequest {
   /**
    * Exactly one dataset ID must be provided here. Only variant sets which
@@ skipping 227 matching lines @@
     }
     if (variants != null) {
       _json["variants"] = variants.map((value) => (value).toJson()).toList();
     }
     return _json;
   }
 }
 
 
 /**
- * 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.
+ * 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.
  */
 class Variant {
   /** The bases that appear instead of the reference bases. */
   core.List<core.String> alternateBases;
 
   /**
    * The variant calls for this particular variant. Each one represents the
    * determination of genotype with respect to this variant.
    */
   core.List<Call> calls;
@@ skipping 132 matching lines @@
     }
     if (variantSetId != null) {
       _json["variantSetId"] = variantSetId;
     }
     return _json;
   }
 }
 
 
 /**
- * A VariantSet represents a collection of Variants and their summary
- * statistics.
+ * 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.
  */
 class VariantSet {
   /** The dataset to which this variant set belongs. Immutable. */
   core.String datasetId;
 
   /** The Google-generated ID of the variant set. Immutable. */
   core.String id;
 
   /** The metadata associated with this variant set. */
   core.List<Metadata> metadata;
@@ skipping 34 matching lines @@
       _json["metadata"] = metadata.map((value) => (value).toJson()).toList();
     }
     if (referenceBounds != null) {
       _json["referenceBounds"] = referenceBounds.map((value) => (value).toJson()).toList();
     }
     return _json;
   }
 }