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Unified Diff: generated/googleapis_beta/lib/genomics/v1beta.dart

Issue 595873002: Api roll 1: 2014-09-23 (Closed) Base URL: git@github.com:dart-lang/googleapis.git@master
Patch Set: Created 6 years, 3 months ago
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Index: generated/googleapis_beta/lib/genomics/v1beta.dart
diff --git a/generated/googleapis_beta/lib/genomics/v1beta.dart b/generated/googleapis_beta/lib/genomics/v1beta.dart
index c74ffdaaecfac47fa8e9f51d5e0e276505550ecd..e681268668a4bab99784eba07ab0845f517b94cb 100644
--- a/generated/googleapis_beta/lib/genomics/v1beta.dart
+++ b/generated/googleapis_beta/lib/genomics/v1beta.dart
@@ -38,9 +38,10 @@ class GenomicsApi {
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/");
+ _requester = new common_internal.ApiRequester(client, "https://www.googleapis.com/", "genomics/v1beta/");
}
@@ -57,15 +58,15 @@ class BeaconsResourceApi {
*
* Request parameters:
*
- * [variantsetId] - The ID of the variantset to query over. It must be public.
- * Private variantsets will return an unauthorized exception.
+ * [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').
*
- * [contig] - Required. The contig to query over.
- *
* [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
@@ -74,7 +75,7 @@ class BeaconsResourceApi {
* 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 contig, core.String position}) {
+ 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;
@@ -82,21 +83,21 @@ class BeaconsResourceApi {
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
- if (variantsetId == null) {
- throw new core.ArgumentError("Parameter variantsetId is required.");
+ if (variantSetId == null) {
+ throw new core.ArgumentError("Parameter variantSetId is required.");
}
if (allele != null) {
_queryParams["allele"] = [allele];
}
- if (contig != null) {
- _queryParams["contig"] = [contig];
- }
if (position != null) {
_queryParams["position"] = [position];
}
+ if (referenceName != null) {
+ _queryParams["referenceName"] = [referenceName];
+ }
- _url = 'beacons/' + common_internal.Escaper.ecapeVariable('$variantsetId');
+ _url = 'beacons/' + common_internal.Escaper.ecapeVariable('$variantSetId');
var _response = _requester.request(_url,
"GET",
@@ -119,13 +120,13 @@ class CallsetsResourceApi {
_requester = client;
/**
- * Creates a new callset.
+ * Creates a new call set.
*
* [request] - The metadata request object.
*
* Request parameters:
*
- * Completes with a [Callset].
+ * Completes with a [CallSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
@@ -133,7 +134,7 @@ class CallsetsResourceApi {
* 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> create(Callset request) {
+ async.Future<CallSet> create(CallSet request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
@@ -155,15 +156,15 @@ class CallsetsResourceApi {
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
- return _response.then((data) => new Callset.fromJson(data));
+ return _response.then((data) => new CallSet.fromJson(data));
}
/**
- * Deletes a callset.
+ * Deletes a call set.
*
* Request parameters:
*
- * [callsetId] - The ID of the callset to be deleted.
+ * [callSetId] - The ID of the callset to be deleted.
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
@@ -171,7 +172,7 @@ class CallsetsResourceApi {
* 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) {
+ async.Future delete(core.String callSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
@@ -179,13 +180,13 @@ class CallsetsResourceApi {
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
- if (callsetId == null) {
- throw new core.ArgumentError("Parameter callsetId is required.");
+ if (callSetId == null) {
+ throw new core.ArgumentError("Parameter callSetId is required.");
}
_downloadOptions = null;
- _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId');
+ _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callSetId');
var _response = _requester.request(_url,
"DELETE",
@@ -198,13 +199,13 @@ class CallsetsResourceApi {
}
/**
- * Gets a callset by ID.
+ * Gets a call set by ID.
*
* Request parameters:
*
- * [callsetId] - The ID of the callset.
+ * [callSetId] - The ID of the callset.
*
- * Completes with a [Callset].
+ * Completes with a [CallSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
@@ -212,7 +213,7 @@ class CallsetsResourceApi {
* 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) {
+ async.Future<CallSet> get(core.String callSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
@@ -220,12 +221,12 @@ class CallsetsResourceApi {
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
- if (callsetId == null) {
- throw new core.ArgumentError("Parameter callsetId is required.");
+ if (callSetId == null) {
+ throw new core.ArgumentError("Parameter callSetId is required.");
}
- _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId');
+ _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callSetId');
var _response = _requester.request(_url,
"GET",
@@ -234,19 +235,19 @@ class CallsetsResourceApi {
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
- return _response.then((data) => new Callset.fromJson(data));
+ return _response.then((data) => new CallSet.fromJson(data));
}
/**
- * Updates a callset. This method supports patch semantics.
+ * 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 callset to be updated.
*
- * Completes with a [Callset].
+ * Completes with a [CallSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
@@ -254,7 +255,7 @@ class CallsetsResourceApi {
* 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) {
+ async.Future<CallSet> patch(CallSet request, core.String callSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
@@ -265,12 +266,12 @@ class CallsetsResourceApi {
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
- if (callsetId == null) {
- throw new core.ArgumentError("Parameter callsetId is required.");
+ if (callSetId == null) {
+ throw new core.ArgumentError("Parameter callSetId is required.");
}
- _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId');
+ _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callSetId');
var _response = _requester.request(_url,
"PATCH",
@@ -279,17 +280,17 @@ class CallsetsResourceApi {
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
- return _response.then((data) => new Callset.fromJson(data));
+ return _response.then((data) => new CallSet.fromJson(data));
}
/**
- * Gets a list of callsets matching the criteria.
+ * Gets a list of call sets matching the criteria.
*
* [request] - The metadata request object.
*
* Request parameters:
*
- * Completes with a [SearchCallsetsResponse].
+ * Completes with a [SearchCallSetsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
@@ -297,7 +298,7 @@ class CallsetsResourceApi {
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
- async.Future<SearchCallsetsResponse> search(SearchCallsetsRequest request) {
+ async.Future<SearchCallSetsResponse> search(SearchCallSetsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
@@ -319,19 +320,19 @@ class CallsetsResourceApi {
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
- return _response.then((data) => new SearchCallsetsResponse.fromJson(data));
+ return _response.then((data) => new SearchCallSetsResponse.fromJson(data));
}
/**
- * Updates a callset.
+ * 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 callset to be updated.
*
- * Completes with a [Callset].
+ * Completes with a [CallSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
@@ -339,7 +340,7 @@ class CallsetsResourceApi {
* 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) {
+ async.Future<CallSet> update(CallSet request, core.String callSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
@@ -350,12 +351,12 @@ class CallsetsResourceApi {
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
- if (callsetId == null) {
- throw new core.ArgumentError("Parameter callsetId is required.");
+ if (callSetId == null) {
+ throw new core.ArgumentError("Parameter callSetId is required.");
}
- _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId');
+ _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callSetId');
var _response = _requester.request(_url,
"PUT",
@@ -364,7 +365,7 @@ class CallsetsResourceApi {
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
- return _response.then((data) => new Callset.fromJson(data));
+ return _response.then((data) => new CallSet.fromJson(data));
}
}
@@ -505,7 +506,7 @@ class DatasetsResourceApi {
*
* [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.
+ * value of nextPageToken from the previous response.
*
* [projectId] - Only return datasets which belong to this Google Developers
* Console project. Only accepts project numbers.
@@ -1270,23 +1271,23 @@ class ReadsetsCoveragebucketsResourceApi {
*
* [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.
+ * 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_sequenceName] - The reference sequence name, for example "chr1",
- * "1", or "chrX".
+ * [range_sequenceName] - 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.
*
* [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 bucket_width in the response.
+ * 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
- * bucket_width is currently 2048 base pairs; this is subject to change.
+ * bucketWidth is currently 2048 base pairs; this is subject to change.
*
* Completes with a [ListCoverageBucketsResponse].
*
@@ -1509,14 +1510,13 @@ class VariantsResourceApi {
}
/**
- * Gets a summary of all the variant data in a variantset.
+ * Creates variant data by asynchronously importing the provided information.
*
- * Request parameters:
+ * [request] - The metadata request object.
*
- * [variantsetId] - Required. The ID of the variant set to get variant summary
- * information for.
+ * Request parameters:
*
- * Completes with a [GetVariantsSummaryResponse].
+ * Completes with a [ImportVariantsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
@@ -1524,7 +1524,7 @@ class VariantsResourceApi {
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
- async.Future<GetVariantsSummaryResponse> getSummary({core.String variantsetId}) {
+ async.Future<ImportVariantsResponse> import(ImportVariantsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
@@ -1532,31 +1532,31 @@ class VariantsResourceApi {
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
- if (variantsetId != null) {
- _queryParams["variantsetId"] = [variantsetId];
+ if (request != null) {
+ _body = convert.JSON.encode((request).toJson());
}
- _url = 'variants/summary';
+ _url = 'variants/import';
var _response = _requester.request(_url,
- "GET",
+ "POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
- return _response.then((data) => new GetVariantsSummaryResponse.fromJson(data));
+ return _response.then((data) => new ImportVariantsResponse.fromJson(data));
}
/**
- * Creates variant data by asynchronously importing the provided information.
+ * Gets a list of variants matching the criteria.
*
* [request] - The metadata request object.
*
* Request parameters:
*
- * Completes with a [ImportVariantsResponse].
+ * Completes with a [SearchVariantsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
@@ -1564,7 +1564,7 @@ class VariantsResourceApi {
* 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<SearchVariantsResponse> search(SearchVariantsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
@@ -1577,7 +1577,7 @@ class VariantsResourceApi {
}
- _url = 'variants/import';
+ _url = 'variants/search';
var _response = _requester.request(_url,
"POST",
@@ -1586,17 +1586,18 @@ class VariantsResourceApi {
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
- return _response.then((data) => new ImportVariantsResponse.fromJson(data));
+ return _response.then((data) => new SearchVariantsResponse.fromJson(data));
}
/**
- * Updates a variant. This method supports patch semantics.
+ * 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..
+ * [variantId] - The ID of the variant to be updated.
*
* Completes with a [Variant].
*
@@ -1606,7 +1607,7 @@ class VariantsResourceApi {
* 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> patch(Variant request, core.String variantId) {
+ async.Future<Variant> update(Variant request, core.String variantId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
@@ -1625,7 +1626,7 @@ class VariantsResourceApi {
_url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
var _response = _requester.request(_url,
- "PATCH",
+ "PUT",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
@@ -1634,14 +1635,64 @@ class VariantsResourceApi {
return _response.then((data) => new Variant.fromJson(data));
}
+}
+
+
+/** Not documented yet. */
+class VariantsetsResourceApi {
+ final common_internal.ApiRequester _requester;
+
+ VariantsetsResourceApi(common_internal.ApiRequester client) :
+ _requester = client;
+
/**
- * Gets a list of variants matching the criteria.
+ * Deletes the contents of a variant set. The variant set object is not
+ * deleted.
*
- * [request] - The metadata request object.
+ * Request parameters:
+ *
+ * [variantSetId] - The ID of the variant set to be deleted.
+ *
+ * Completes with a [common.ApiRequestError] if the API endpoint returned an
+ * error.
+ *
+ * If the used [http.Client] completes with an error when making a REST call,
+ * this method will complete with the same error.
+ */
+ async.Future delete(core.String variantSetId) {
+ var _url = null;
+ var _queryParams = new core.Map();
+ var _uploadMedia = null;
+ var _uploadOptions = null;
+ var _downloadOptions = common.DownloadOptions.Metadata;
+ var _body = null;
+
+ if (variantSetId == null) {
+ throw new core.ArgumentError("Parameter variantSetId is required.");
+ }
+
+ _downloadOptions = null;
+
+ _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
+
+ var _response = _requester.request(_url,
+ "DELETE",
+ body: _body,
+ queryParams: _queryParams,
+ uploadOptions: _uploadOptions,
+ uploadMedia: _uploadMedia,
+ downloadOptions: _downloadOptions);
+ return _response.then((data) => null);
+ }
+
+ /**
+ * Gets a variant set by ID.
*
* Request parameters:
*
- * Completes with a [SearchVariantsResponse].
+ * [variantSetId] - Required. The ID of the variant set.
+ *
+ * Completes with a [VariantSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
@@ -1649,7 +1700,7 @@ class VariantsResourceApi {
* 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<VariantSet> get(core.String variantSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
@@ -1657,33 +1708,31 @@ class VariantsResourceApi {
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 = 'variants/search';
+ _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
var _response = _requester.request(_url,
- "POST",
+ "GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
- return _response.then((data) => new SearchVariantsResponse.fromJson(data));
+ return _response.then((data) => new VariantSet.fromJson(data));
}
/**
- * Updates a variant.
+ * Returns a list of all variant sets matching search criteria.
*
* [request] - The metadata request object.
*
* Request parameters:
*
- * [variantId] - The ID of the variant to be updated..
- *
- * Completes with a [Variant].
+ * Completes with a [SearchVariantSetsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
@@ -1691,7 +1740,7 @@ class VariantsResourceApi {
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
- async.Future<Variant> update(Variant request, core.String variantId) {
+ async.Future<SearchVariantSetsResponse> search(SearchVariantSetsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
@@ -1702,21 +1751,18 @@ class VariantsResourceApi {
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
- if (variantId == null) {
- throw new core.ArgumentError("Parameter variantId is required.");
- }
- _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
+ _url = 'variantsets/search';
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));
+ return _response.then((data) => new SearchVariantSetsResponse.fromJson(data));
}
}
@@ -1724,7 +1770,7 @@ class VariantsResourceApi {
/**
- * A beacon represents whether any variant call in a variantset has a specific
+ * A beacon represents whether any variant call in a variant set has a specific
* allele at a particular position.
*/
class Beacon {
@@ -1754,25 +1800,24 @@ class Beacon {
* A Call represents the determination of genotype with respect to a particular
* variant. It may include associated information such as quality and phasing.
* For example, a Call might assign a probability of 0.32 to the occurrence of a
- * SNP named rs1234 in a callset with the name NA12345.
+ * SNP named rs1234 in a call set with the name NA12345.
*/
class Call {
- /** The ID of the callset this variant call belongs to. */
- core.String callsetId;
+ /** The ID of the call set this variant call belongs to. */
+ core.String callSetId;
- /** The name of the callset this variant call belongs to. */
- core.String callsetName;
+ /** The name of the call set this variant call belongs to. */
+ core.String callSetName;
/**
* The genotype of this variant call. Each value represents either the value
* of the referenceBases field or a 1-based index into alternateBases. If a
- * variant had a referenceBases field of "T" and an alternateBases value of
+ * variant had a referenceBases value of T and an alternateBases value of
* ["A", "C"], and the genotype was [2, 1], that would mean the call
- * represented the heterozygous value "CA" for this variant. If the genotype
- * was instead [0, 1], the represented value would be "TA". Ordering of the
- * genotype values is important if the phaseset field is present. If a
- * genotype is not called (that is, a "." is present in the GT string) -1 is
- * returned.
+ * represented the heterozygous value CA for this variant. If the genotype was
+ * instead [0, 1], the represented value would be TA. Ordering of the genotype
+ * values is important if the phaseset is present. If a genotype is not called
+ * (that is, a . is present in the GT string) -1 is returned.
*/
core.List<core.int> genotype;
@@ -1788,10 +1833,10 @@ class Call {
/**
* If this field is present, this variant call's genotype ordering implies the
- * phase of the bases and is consistent with any other variant calls on the
- * same contig which have the same phaseset value. When importing data from
- * VCF, if the genotype data was phased but no phase set was specified this
- * field will be set to "*".
+ * phase of the bases and is consistent with any other variant calls in the
+ * same reference sequence which have the same phaseset value. When importing
+ * data from VCF, if the genotype data was phased but no phase set was
+ * specified this field will be set to *.
*/
core.String phaseset;
@@ -1799,11 +1844,11 @@ class Call {
Call();
Call.fromJson(core.Map _json) {
- if (_json.containsKey("callsetId")) {
- callsetId = _json["callsetId"];
+ if (_json.containsKey("callSetId")) {
+ callSetId = _json["callSetId"];
}
- if (_json.containsKey("callsetName")) {
- callsetName = _json["callsetName"];
+ if (_json.containsKey("callSetName")) {
+ callSetName = _json["callSetName"];
}
if (_json.containsKey("genotype")) {
genotype = _json["genotype"];
@@ -1821,11 +1866,11 @@ class Call {
core.Map toJson() {
var _json = new core.Map();
- if (callsetId != null) {
- _json["callsetId"] = callsetId;
+ if (callSetId != null) {
+ _json["callSetId"] = callSetId;
}
- if (callsetName != null) {
- _json["callsetName"] = callsetName;
+ if (callSetName != null) {
+ _json["callSetName"] = callSetName;
}
if (genotype != null) {
_json["genotype"] = genotype;
@@ -1844,12 +1889,12 @@ class Call {
}
-/** A Callset is a collection of Variant Calls. It belongs to a Variantset. */
-class Callset {
- /** The date this callset was created in milliseconds from the epoch. */
+/** A CallSet is a collection of variant calls. 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 callset, immutable. */
+ /** The Google generated ID of the call set, immutable. */
core.String id;
/** A map of additional callset information. */
@@ -1858,13 +1903,16 @@ class Callset {
/** The callset name. */
core.String name;
- /** The ID of the variantset this callset belongs to. */
- core.String variantsetId;
+ /** 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();
+ CallSet();
- Callset.fromJson(core.Map _json) {
+ CallSet.fromJson(core.Map _json) {
if (_json.containsKey("created")) {
created = _json["created"];
}
@@ -1877,8 +1925,11 @@ class Callset {
if (_json.containsKey("name")) {
name = _json["name"];
}
- if (_json.containsKey("variantsetId")) {
- variantsetId = _json["variantsetId"];
+ if (_json.containsKey("sampleId")) {
+ sampleId = _json["sampleId"];
+ }
+ if (_json.containsKey("variantSetIds")) {
+ variantSetIds = _json["variantSetIds"];
}
}
@@ -1896,47 +1947,11 @@ class Callset {
if (name != null) {
_json["name"] = name;
}
- if (variantsetId != null) {
- _json["variantsetId"] = variantsetId;
+ if (sampleId != null) {
+ _json["sampleId"] = sampleId;
}
- return _json;
- }
-}
-
-
-/**
- * ContigBound records an upper bound for the starting coordinate of variants in
- * a particular contig.
- */
-class ContigBound {
- /** The contig the bound is associate with. */
- core.String contig;
-
- /**
- * An upper bound (inclusive) on the starting coordinate of any variant in the
- * contig.
- */
- core.String upperBound;
-
-
- ContigBound();
-
- ContigBound.fromJson(core.Map _json) {
- if (_json.containsKey("contig")) {
- contig = _json["contig"];
- }
- if (_json.containsKey("upperBound")) {
- upperBound = _json["upperBound"];
- }
- }
-
- core.Map toJson() {
- var _json = new core.Map();
- if (contig != null) {
- _json["contig"] = contig;
- }
- if (upperBound != null) {
- _json["upperBound"] = upperBound;
+ if (variantSetIds != null) {
+ _json["variantSetIds"] = variantSetIds;
}
return _json;
}
@@ -2042,28 +2057,28 @@ class Dataset {
class ExperimentalCreateJobRequest {
/**
* Specifies whether or not to run the alignment pipeline. At least one of
- * align or call_variants must be provided.
+ * align or callVariants must be provided.
*/
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 call_variants must be
+ * to the variant caller. At least one of align or callVariants must be
* provided.
*/
core.bool callVariants;
/**
- * Specifies where to copy the results of certain pipelines. This shoud be in
- * the form of "gs://bucket/path".
+ * 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".
+ * file. The first file of each pair should be specified in sourceUris.
*/
core.List<core.String> pairedSourceUris;
@@ -2076,7 +2091,7 @@ class ExperimentalCreateJobRequest {
* 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".
+ * the second of each pair should be listed in pairedSourceUris.
*/
core.List<core.String> sourceUris;
@@ -2173,7 +2188,8 @@ class ExportReadsetsRequest {
/**
* The reference names to export. If this is not specified, all reference
- * sequences are exported. Use '*' to export unmapped reads.
+ * sequences, including unmapped reads, are exported. Use * to export only
+ * unmapped reads.
*/
core.List<core.String> referenceNames;
@@ -2254,10 +2270,10 @@ class ExportVariantsRequest {
core.String bigqueryTable;
/**
- * If provided, only variant call information from the specified callsets will
- * be exported. By default all variant calls are exported.
+ * 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;
+ core.List<core.String> callSetIds;
/**
* The format for the exported data.
@@ -2273,10 +2289,10 @@ class ExportVariantsRequest {
core.String projectId;
/**
- * Required. The ID of the variantset that contains variant data which should
- * be exported. The caller must have READ access to this variantset.
+ * 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 variantSetId;
ExportVariantsRequest();
@@ -2288,8 +2304,8 @@ class ExportVariantsRequest {
if (_json.containsKey("bigqueryTable")) {
bigqueryTable = _json["bigqueryTable"];
}
- if (_json.containsKey("callsetIds")) {
- callsetIds = _json["callsetIds"];
+ if (_json.containsKey("callSetIds")) {
+ callSetIds = _json["callSetIds"];
}
if (_json.containsKey("format")) {
format = _json["format"];
@@ -2297,8 +2313,8 @@ class ExportVariantsRequest {
if (_json.containsKey("projectId")) {
projectId = _json["projectId"];
}
- if (_json.containsKey("variantsetId")) {
- variantsetId = _json["variantsetId"];
+ if (_json.containsKey("variantSetId")) {
+ variantSetId = _json["variantSetId"];
}
}
@@ -2310,8 +2326,8 @@ class ExportVariantsRequest {
if (bigqueryTable != null) {
_json["bigqueryTable"] = bigqueryTable;
}
- if (callsetIds != null) {
- _json["callsetIds"] = callsetIds;
+ if (callSetIds != null) {
+ _json["callSetIds"] = callSetIds;
}
if (format != null) {
_json["format"] = format;
@@ -2319,8 +2335,8 @@ class ExportVariantsRequest {
if (projectId != null) {
_json["projectId"] = projectId;
}
- if (variantsetId != null) {
- _json["variantsetId"] = variantsetId;
+ if (variantSetId != null) {
+ _json["variantSetId"] = variantSetId;
}
return _json;
}
@@ -2361,7 +2377,7 @@ class GenomicRange {
*/
core.String sequenceEnd;
- /** The reference sequence name, for example "chr1", "1", or "chrX". */
+ /** The reference sequence name, for example chr1, 1, or chrX. */
core.String sequenceName;
/**
@@ -2401,42 +2417,6 @@ class GenomicRange {
}
-/** The variants summary response. */
-class GetVariantsSummaryResponse {
- /**
- * A list of all contigs used by the variants in a dataset with associated
- * coordinate upper bounds for each one.
- */
- core.List<ContigBound> contigBounds;
-
- /** The metadata associated with this dataset. */
- core.List<Metadata> metadata;
-
-
- GetVariantsSummaryResponse();
-
- GetVariantsSummaryResponse.fromJson(core.Map _json) {
- if (_json.containsKey("contigBounds")) {
- contigBounds = _json["contigBounds"].map((value) => new ContigBound.fromJson(value)).toList();
- }
- if (_json.containsKey("metadata")) {
- metadata = _json["metadata"].map((value) => new Metadata.fromJson(value)).toList();
- }
- }
-
- core.Map toJson() {
- var _json = new core.Map();
- if (contigBounds != null) {
- _json["contigBounds"] = contigBounds.map((value) => (value).toJson()).toList();
- }
- if (metadata != null) {
- _json["metadata"] = metadata.map((value) => (value).toJson()).toList();
- }
- return _json;
- }
-}
-
-
/** Not documented yet. */
class Header {
/** (SO) Sorting order of alignments. */
@@ -2627,8 +2607,8 @@ class ImportVariantsRequest {
*/
core.List<core.String> sourceUris;
- /** Required. The variantset to which variant data should be imported. */
- core.String variantsetId;
+ /** Required. The variant set to which variant data should be imported. */
+ core.String variantSetId;
ImportVariantsRequest();
@@ -2640,8 +2620,8 @@ class ImportVariantsRequest {
if (_json.containsKey("sourceUris")) {
sourceUris = _json["sourceUris"];
}
- if (_json.containsKey("variantsetId")) {
- variantsetId = _json["variantsetId"];
+ if (_json.containsKey("variantSetId")) {
+ variantSetId = _json["variantSetId"];
}
}
@@ -2653,8 +2633,8 @@ class ImportVariantsRequest {
if (sourceUris != null) {
_json["sourceUris"] = sourceUris;
}
- if (variantsetId != null) {
- _json["variantsetId"] = variantsetId;
+ if (variantSetId != null) {
+ _json["variantSetId"] = variantSetId;
}
return _json;
}
@@ -2862,15 +2842,15 @@ 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
- * target_bucket_width).
+ * targetBucketWidth).
*/
core.String bucketWidth;
/**
* The coverage buckets. The list of buckets is sparse; a bucket with 0
* overlapping reads is not returned. A bucket never crosses more than one
- * reference sequence. Each bucket has width bucket_width, unless its end is
- * is the end of the reference sequence.
+ * reference sequence. Each bucket has width bucketWidth, unless its end is
+ * the end of the reference sequence.
*/
core.List<CoverageBucket> coverageBuckets;
@@ -3476,6 +3456,45 @@ class Readset {
}
+/**
+ * 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;
+
+ /**
+ * An upper bound (inclusive) on the starting coordinate of any variant in the
+ * reference sequence.
+ */
+ core.String upperBound;
+
+
+ ReferenceBound();
+
+ ReferenceBound.fromJson(core.Map _json) {
+ if (_json.containsKey("referenceName")) {
+ referenceName = _json["referenceName"];
+ }
+ if (_json.containsKey("upperBound")) {
+ upperBound = _json["upperBound"];
+ }
+ }
+
+ core.Map toJson() {
+ var _json = new core.Map();
+ if (referenceName != null) {
+ _json["referenceName"] = referenceName;
+ }
+ if (upperBound != null) {
+ _json["upperBound"] = upperBound;
+ }
+ return _json;
+ }
+}
+
+
/** Not documented yet. */
class ReferenceSequence {
/** (AS) Genome assembly identifier. */
@@ -3548,70 +3567,71 @@ class ReferenceSequence {
}
-/** The callset search request. */
-class SearchCallsetsRequest {
- /** The maximum number of callsets to return. */
- core.String maxResults;
-
+/** The call set search request. */
+class SearchCallSetsRequest {
/**
- * Only return callsets for which a substring of the name matches this string.
+ * Only return call sets for which a substring of the name matches this
+ * string.
*/
core.String name;
+ /** The maximum number of call sets to return. */
+ 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.
+ * nextPageToken from the previous response.
*/
core.String pageToken;
/**
- * Restrict the query to callsets within the given variantsets. At least one
+ * Restrict the query to call sets within the given variant sets. At least one
* ID must be provided.
*/
- core.List<core.String> variantsetIds;
+ core.List<core.String> variantSetIds;
- SearchCallsetsRequest();
+ SearchCallSetsRequest();
- SearchCallsetsRequest.fromJson(core.Map _json) {
- if (_json.containsKey("maxResults")) {
- maxResults = _json["maxResults"];
- }
+ SearchCallSetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("name")) {
name = _json["name"];
}
+ if (_json.containsKey("pageSize")) {
+ pageSize = _json["pageSize"];
+ }
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
- if (_json.containsKey("variantsetIds")) {
- variantsetIds = _json["variantsetIds"];
+ if (_json.containsKey("variantSetIds")) {
+ variantSetIds = _json["variantSetIds"];
}
}
core.Map toJson() {
var _json = new core.Map();
- if (maxResults != null) {
- _json["maxResults"] = maxResults;
- }
if (name != null) {
_json["name"] = name;
}
+ if (pageSize != null) {
+ _json["pageSize"] = pageSize;
+ }
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
- if (variantsetIds != null) {
- _json["variantsetIds"] = variantsetIds;
+ if (variantSetIds != null) {
+ _json["variantSetIds"] = variantSetIds;
}
return _json;
}
}
-/** The callset search response. */
-class SearchCallsetsResponse {
- /** The list of matching callsets. */
- core.List<Callset> callsets;
+/** The call set search response. */
+class SearchCallSetsResponse {
+ /** The list of matching call sets. */
+ core.List<CallSet> callSets;
/**
* The continuation token, which is used to page through large result sets.
@@ -3621,11 +3641,11 @@ class SearchCallsetsResponse {
core.String nextPageToken;
- SearchCallsetsResponse();
+ SearchCallSetsResponse();
- SearchCallsetsResponse.fromJson(core.Map _json) {
- if (_json.containsKey("callsets")) {
- callsets = _json["callsets"].map((value) => new Callset.fromJson(value)).toList();
+ SearchCallSetsResponse.fromJson(core.Map _json) {
+ if (_json.containsKey("callSets")) {
+ callSets = _json["callSets"].map((value) => new CallSet.fromJson(value)).toList();
}
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
@@ -3634,8 +3654,8 @@ class SearchCallsetsResponse {
core.Map toJson() {
var _json = new core.Map();
- if (callsets != null) {
- _json["callsets"] = callsets.map((value) => (value).toJson()).toList();
+ if (callSets != null) {
+ _json["callSets"] = callSets.map((value) => (value).toJson()).toList();
}
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
@@ -3668,14 +3688,11 @@ class SearchJobsRequest {
/**
* 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.
+ * nextPageToken from the previous response.
*/
core.String pageToken;
- /**
- * Required. Only return jobs which belong to this Google Developers Console
- * project. Only accepts project numbers.
- */
+ /** Required. Only return jobs which belong to this Google Developers */
core.String projectId;
/** Only return jobs which have a matching status. */
@@ -3778,7 +3795,7 @@ class SearchReadsRequest {
/**
* 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.
+ * nextPageToken from the previous response.
*/
core.String pageToken;
@@ -3791,21 +3808,21 @@ class SearchReadsRequest {
/**
* The end position (1-based, inclusive) of the target range. If specified,
- * "sequenceName" must also be specified. Defaults to the end of the target
+ * sequenceName must also be specified. Defaults to the end of the target
* reference sequence, if any.
*/
core.String sequenceEnd;
/**
- * 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.
+ * 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.
*/
core.String sequenceName;
/**
* The start position (1-based, inclusive) of the target range. If specified,
- * "sequenceName" must also be specified. Defaults to the start of the target
+ * sequenceName must also be specified. Defaults to the start of the target
* reference sequence, if any.
*/
core.String sequenceStart;
@@ -3922,7 +3939,7 @@ class SearchReadsetsRequest {
/**
* 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.
+ * nextPageToken from the previous response.
*/
core.String pageToken;
@@ -4000,114 +4017,201 @@ class SearchReadsetsResponse {
}
-/** The variant search request. */
-class SearchVariantsRequest {
+/** The search variant sets request. */
+class SearchVariantSetsRequest {
/**
- * Only return variant calls which belong to callsets with these ids. Leaving
- * this blank returns all variant calls. At most one of callsetNames or
- * callsetIds should be provided.
+ * Exactly one dataset ID must be provided here. Only variant sets which
+ * belong to this dataset will be returned.
*/
- core.List<core.String> callsetIds;
+ core.List<core.String> datasetIds;
+
+ /** The maximum number of variant sets to return in a request. */
+ 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;
+
+
+ SearchVariantSetsRequest();
+
+ SearchVariantSetsRequest.fromJson(core.Map _json) {
+ if (_json.containsKey("datasetIds")) {
+ datasetIds = _json["datasetIds"];
+ }
+ 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 (pageSize != null) {
+ _json["pageSize"] = pageSize;
+ }
+ if (pageToken != null) {
+ _json["pageToken"] = pageToken;
+ }
+ return _json;
+ }
+}
+
+/** The search variant sets response. */
+class SearchVariantSetsResponse {
/**
- * Only return variant calls which belong to callsets which have exactly these
- * names. Leaving this blank returns all variant calls. At most one of
- * callsetNames or callsetIds should be provided.
+ * 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.List<core.String> callsetNames;
+ core.String nextPageToken;
+
+ /** The variant sets belonging to the requested dataset. */
+ core.List<VariantSet> variantSets;
- /** Required. Only return variants on this contig. */
- core.String contig;
+
+ SearchVariantSetsResponse();
+
+ SearchVariantSetsResponse.fromJson(core.Map _json) {
+ if (_json.containsKey("nextPageToken")) {
+ nextPageToken = _json["nextPageToken"];
+ }
+ if (_json.containsKey("variantSets")) {
+ variantSets = _json["variantSets"].map((value) => new VariantSet.fromJson(value)).toList();
+ }
+ }
+
+ core.Map toJson() {
+ var _json = new core.Map();
+ if (nextPageToken != null) {
+ _json["nextPageToken"] = nextPageToken;
+ }
+ if (variantSets != null) {
+ _json["variantSets"] = variantSets.map((value) => (value).toJson()).toList();
+ }
+ return _json;
+ }
+}
+
+
+/** The variant search request. */
+class SearchVariantsRequest {
+ /**
+ * Only return variant calls which belong to call sets with these ids. Leaving
+ * this blank returns all variant calls.
+ */
+ core.List<core.String> callSetIds;
/**
* Required. The end of the window (0-based, exclusive) for which overlapping
* variants should be returned.
*/
- core.String endPosition;
+ core.String end;
+
+ /**
+ * The maximum number of calls to return. However, at least one variant will
+ * always be returned, even if it has more calls than this limit.
+ */
+ core.int maxCalls;
/** The maximum number of variants to return. */
- 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.
+ * nextPageToken from the previous response.
*/
core.String pageToken;
+ /** Required. Only return variants in this reference sequence. */
+ core.String referenceName;
+
/**
* Required. The beginning of the window (0-based, inclusive) for which
* overlapping variants should be returned.
*/
- core.String startPosition;
+ core.String start;
/** Only return variants which have exactly this name. */
core.String variantName;
- /** Required. The ID of the variantset to search. */
- core.String variantsetId;
+ /**
+ * Exactly one variant set ID must be provided. Only variants from this
+ * variant set will be returned.
+ */
+ core.List<core.String> variantSetIds;
SearchVariantsRequest();
SearchVariantsRequest.fromJson(core.Map _json) {
- if (_json.containsKey("callsetIds")) {
- callsetIds = _json["callsetIds"];
+ if (_json.containsKey("callSetIds")) {
+ callSetIds = _json["callSetIds"];
}
- if (_json.containsKey("callsetNames")) {
- callsetNames = _json["callsetNames"];
- }
- if (_json.containsKey("contig")) {
- contig = _json["contig"];
+ if (_json.containsKey("end")) {
+ end = _json["end"];
}
- if (_json.containsKey("endPosition")) {
- endPosition = _json["endPosition"];
+ if (_json.containsKey("maxCalls")) {
+ maxCalls = _json["maxCalls"];
}
- if (_json.containsKey("maxResults")) {
- maxResults = _json["maxResults"];
+ if (_json.containsKey("pageSize")) {
+ pageSize = _json["pageSize"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
- if (_json.containsKey("startPosition")) {
- startPosition = _json["startPosition"];
+ if (_json.containsKey("referenceName")) {
+ referenceName = _json["referenceName"];
+ }
+ if (_json.containsKey("start")) {
+ start = _json["start"];
}
if (_json.containsKey("variantName")) {
variantName = _json["variantName"];
}
- if (_json.containsKey("variantsetId")) {
- variantsetId = _json["variantsetId"];
+ if (_json.containsKey("variantSetIds")) {
+ variantSetIds = _json["variantSetIds"];
}
}
core.Map toJson() {
var _json = new core.Map();
- if (callsetIds != null) {
- _json["callsetIds"] = callsetIds;
- }
- if (callsetNames != null) {
- _json["callsetNames"] = callsetNames;
+ if (callSetIds != null) {
+ _json["callSetIds"] = callSetIds;
}
- if (contig != null) {
- _json["contig"] = contig;
+ if (end != null) {
+ _json["end"] = end;
}
- if (endPosition != null) {
- _json["endPosition"] = endPosition;
+ if (maxCalls != null) {
+ _json["maxCalls"] = maxCalls;
}
- if (maxResults != null) {
- _json["maxResults"] = maxResults;
+ if (pageSize != null) {
+ _json["pageSize"] = pageSize;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
- if (startPosition != null) {
- _json["startPosition"] = startPosition;
+ if (referenceName != null) {
+ _json["referenceName"] = referenceName;
+ }
+ if (start != null) {
+ _json["start"] = start;
}
if (variantName != null) {
_json["variantName"] = variantName;
}
- if (variantsetId != null) {
- _json["variantsetId"] = variantsetId;
+ if (variantSetIds != null) {
+ _json["variantSetIds"] = variantSetIds;
}
return _json;
}
@@ -4154,7 +4258,7 @@ class SearchVariantsResponse {
/**
* 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 Variantset.
+ * a variant set.
*/
class Variant {
/** The bases that appear instead of the reference bases. */
@@ -4166,17 +4270,14 @@ class Variant {
*/
core.List<Call> calls;
- /** The contig on which this variant occurs. (such as 'chr20' or 'X') */
- core.String contig;
-
/** The date this variant was created, in milliseconds from the epoch. */
core.String created;
/**
* The end position (0-based) of this variant. This corresponds to the first
* base after the last base in the reference allele. So, the length of the
- * reference allele is (end - position). This is useful for variants that
- * don't explicitly give alternate bases, for example large deletions.
+ * reference allele is (end - start). This is useful for variants that don't
+ * explicitly give alternate bases, for example large deletions.
*/
core.String end;
@@ -4190,18 +4291,21 @@ class Variant {
core.List<core.String> names;
/**
- * The position at which this variant occurs (0-based). This corresponds to
- * the first base of the string of reference bases.
+ * The reference bases for this variant. They start at the given position.
*/
- core.String position;
+ core.String referenceBases;
+
+ /** The reference on which this variant occurs. (such as chr20 or X) */
+ core.String referenceName;
/**
- * The reference bases for this variant. They start at the given position.
+ * The position at which this variant occurs (0-based). This corresponds to
+ * the first base of the string of reference bases.
*/
- core.String referenceBases;
+ core.String start;
- /** The ID of the variantset this variant belongs to. */
- core.String variantsetId;
+ /** The ID of the variant set this variant belongs to. */
+ core.String variantSetId;
Variant();
@@ -4213,9 +4317,6 @@ class Variant {
if (_json.containsKey("calls")) {
calls = _json["calls"].map((value) => new Call.fromJson(value)).toList();
}
- if (_json.containsKey("contig")) {
- contig = _json["contig"];
- }
if (_json.containsKey("created")) {
created = _json["created"];
}
@@ -4231,14 +4332,17 @@ class Variant {
if (_json.containsKey("names")) {
names = _json["names"];
}
- if (_json.containsKey("position")) {
- position = _json["position"];
- }
if (_json.containsKey("referenceBases")) {
referenceBases = _json["referenceBases"];
}
- if (_json.containsKey("variantsetId")) {
- variantsetId = _json["variantsetId"];
+ if (_json.containsKey("referenceName")) {
+ referenceName = _json["referenceName"];
+ }
+ if (_json.containsKey("start")) {
+ start = _json["start"];
+ }
+ if (_json.containsKey("variantSetId")) {
+ variantSetId = _json["variantSetId"];
}
}
@@ -4250,9 +4354,6 @@ class Variant {
if (calls != null) {
_json["calls"] = calls.map((value) => (value).toJson()).toList();
}
- if (contig != null) {
- _json["contig"] = contig;
- }
if (created != null) {
_json["created"] = created;
}
@@ -4268,14 +4369,74 @@ class Variant {
if (names != null) {
_json["names"] = names;
}
- if (position != null) {
- _json["position"] = position;
- }
if (referenceBases != null) {
_json["referenceBases"] = referenceBases;
}
- if (variantsetId != null) {
- _json["variantsetId"] = variantsetId;
+ if (referenceName != null) {
+ _json["referenceName"] = referenceName;
+ }
+ if (start != null) {
+ _json["start"] = start;
+ }
+ if (variantSetId != null) {
+ _json["variantSetId"] = variantSetId;
+ }
+ return _json;
+ }
+}
+
+
+/**
+ * A VariantSet represents a collection of Variants and their summary
+ * statistics.
+ */
+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;
+
+ /**
+ * A list of all references used by the variants in a variant set with
+ * associated coordinate upper bounds for each one.
+ */
+ core.List<ReferenceBound> referenceBounds;
+
+
+ VariantSet();
+
+ VariantSet.fromJson(core.Map _json) {
+ if (_json.containsKey("datasetId")) {
+ datasetId = _json["datasetId"];
+ }
+ if (_json.containsKey("id")) {
+ id = _json["id"];
+ }
+ if (_json.containsKey("metadata")) {
+ metadata = _json["metadata"].map((value) => new Metadata.fromJson(value)).toList();
+ }
+ if (_json.containsKey("referenceBounds")) {
+ referenceBounds = _json["referenceBounds"].map((value) => new ReferenceBound.fromJson(value)).toList();
+ }
+ }
+
+ core.Map toJson() {
+ var _json = new core.Map();
+ if (datasetId != null) {
+ _json["datasetId"] = datasetId;
+ }
+ if (id != null) {
+ _json["id"] = id;
+ }
+ if (metadata != null) {
+ _json["metadata"] = metadata.map((value) => (value).toJson()).toList();
+ }
+ if (referenceBounds != null) {
+ _json["referenceBounds"] = referenceBounds.map((value) => (value).toJson()).toList();
}
return _json;
}
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