Api roll 5: 2014-11-05

generated/googleapis_beta/lib/genomics/v1beta.dart

 library googleapis_beta.genomics.v1beta;
 
 import "dart:core" as core;
 import "dart:collection" as collection;
 import "dart:async" as async;
 import "dart:convert" as convert;
 
 import "package:crypto/crypto.dart" as crypto;
 import 'package:http/http.dart' as http;
 import '../src/common_internal.dart' as common_internal;
@@ skipping 12 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);
   ReadsResourceApi get reads => new ReadsResourceApi(_requester);
   ReadsetsResourceApi get readsets => new ReadsetsResourceApi(_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/");
 }
 
 
 /** 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.
    *
    * [request] - The metadata request object.
@@ skipping 31 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 1167 matching lines @@
   }
 
   /**
    * 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.
+   * to the metadata already in a variant set.
    *
    * [request] - The metadata request object.
    *
    * Request parameters:
    *
    * Completes with a [ImportVariantsResponse].
    *
    * Completes with a [common.ApiRequestError] if the API endpoint returned an
    * error.
    *
@@ skipping 21 matching lines @@
                                        queryParams: _queryParams,
                                        uploadOptions: _uploadOptions,
                                        uploadMedia: _uploadMedia,
                                        downloadOptions: _downloadOptions);
     return _response.then((data) => new ImportVariantsResponse.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,
@@ skipping 206 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 28 matching lines @@
                                        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;
-
-
-  Beacon();
-
-  Beacon.fromJson(core.Map _json) {
-    if (_json.containsKey("exists")) {
-      exists = _json["exists"];
-    }
-  }
-
-  core.Map toJson() {
-    var _json = new core.Map();
-    if (exists != null) {
-      _json["exists"] = exists;
-    }
-    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. */
+/**
+ * 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 135 matching lines @@
       _json["projectId"] = projectId;
     }
     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;
 
   /**
@@ skipping 707 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:
+   * - "alignReadsets"
+   * - "callReadsets"
    * - "experimentalCreateJob"
    * - "exportReadsets"
    * - "exportVariants"
    * - "importReadsets"
    * - "importVariants"
    * - "unknownType"
    */
   core.String type;
 
 
@@ skipping 1466 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;
   }
 }