| Index: generated/googleapis/lib/genomics/v1.dart
|
| diff --git a/generated/googleapis/lib/genomics/v1.dart b/generated/googleapis/lib/genomics/v1.dart
|
| index a981d8a13c56d9bc0009872e5ebc383dcedb08df..b4d2809f5b7431ebd4c76e8f780275d8fca49c09 100644
|
| --- a/generated/googleapis/lib/genomics/v1.dart
|
| +++ b/generated/googleapis/lib/genomics/v1.dart
|
| @@ -14,7 +14,7 @@ export 'package:_discoveryapis_commons/_discoveryapis_commons.dart' show
|
|
|
| const core.String USER_AGENT = 'dart-api-client genomics/v1';
|
|
|
| -/** Stores, processes, explores and shares genomic data. */
|
| +/** Upload, process, query, and search Genomics data in the cloud. */
|
| class GenomicsApi {
|
| /** View and manage your data in Google BigQuery */
|
| static const BigqueryScope = "https://www.googleapis.com/auth/bigquery";
|
| @@ -58,15 +58,20 @@ class AnnotationsResourceApi {
|
| _requester = client;
|
|
|
| /**
|
| - * Creates one or more new annotations atomically. All annotations must belong
|
| - * to the same annotation set. Caller must have WRITE permission for this
|
| - * annotation set. For optimal performance, batch positionally adjacent
|
| - * annotations together. If the request has a systemic issue, such as an
|
| - * attempt to write to an inaccessible annotation set, the entire RPC will
|
| - * fail accordingly. For lesser data issues, when possible an error will be
|
| - * isolated to the corresponding batch entry in the response; the remaining
|
| - * well formed annotations will be created normally. For details on the
|
| - * requirements for each individual annotation resource, see CreateAnnotation.
|
| + * Creates one or more new annotations atomically. All annotations must
|
| + * belong to the same annotation set. Caller must have WRITE
|
| + * permission for this annotation set. For optimal performance, batch
|
| + * positionally adjacent annotations together.
|
| + *
|
| + * If the request has a systemic issue, such as an attempt to write to
|
| + * an inaccessible annotation set, the entire RPC will fail accordingly. For
|
| + * lesser data issues, when possible an error will be isolated to the
|
| + * corresponding batch entry in the response; the remaining well formed
|
| + * annotations will be created normally.
|
| + *
|
| + * For details on the requirements for each individual annotation resource,
|
| + * see
|
| + * CreateAnnotation.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| @@ -105,15 +110,28 @@ class AnnotationsResourceApi {
|
| }
|
|
|
| /**
|
| - * Creates a new annotation. Caller must have WRITE permission for the
|
| - * associated annotation set. The following fields are required: *
|
| - * annotationSetId * referenceName or referenceId ### Transcripts For
|
| - * annotations of type TRANSCRIPT, the following fields of transcript must be
|
| - * provided: * exons.start * exons.end All other fields may be optionally
|
| - * specified, unless documented as being server-generated (for example, the
|
| - * `id` field). The annotated range must be no longer than 100Mbp (mega base
|
| - * pairs). See the Annotation resource for additional restrictions on each
|
| - * field.
|
| + * Creates a new annotation. Caller must have WRITE permission
|
| + * for the associated annotation set.
|
| + *
|
| + * The following fields are required:
|
| + *
|
| + * * annotationSetId
|
| + * * referenceName or
|
| + * referenceId
|
| + *
|
| + * ### Transcripts
|
| + *
|
| + * For annotations of type TRANSCRIPT, the following fields of
|
| + * transcript must be provided:
|
| + *
|
| + * * exons.start
|
| + * * exons.end
|
| + *
|
| + * All other fields may be optionally specified, unless documented as being
|
| + * server-generated (for example, the `id` field). The annotated
|
| + * range must be no longer than 100Mbp (mega base pairs). See the
|
| + * Annotation resource
|
| + * for additional restrictions on each field.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| @@ -152,8 +170,8 @@ class AnnotationsResourceApi {
|
| }
|
|
|
| /**
|
| - * Deletes an annotation. Caller must have WRITE permission for the associated
|
| - * annotation set.
|
| + * Deletes an annotation. Caller must have WRITE permission for
|
| + * the associated annotation set.
|
| *
|
| * Request parameters:
|
| *
|
| @@ -192,8 +210,8 @@ class AnnotationsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets an annotation. Caller must have READ permission for the associated
|
| - * annotation set.
|
| + * Gets an annotation. Caller must have READ permission
|
| + * for the associated annotation set.
|
| *
|
| * Request parameters:
|
| *
|
| @@ -232,13 +250,13 @@ class AnnotationsResourceApi {
|
| }
|
|
|
| /**
|
| - * Searches for annotations that match the given criteria. Results are ordered
|
| - * by genomic coordinate (by reference sequence, then position). Annotations
|
| - * with equivalent genomic coordinates are returned in an unspecified order.
|
| - * This order is consistent, such that two queries for the same content
|
| - * (regardless of page size) yield annotations in the same order across their
|
| - * respective streams of paginated responses. Caller must have READ permission
|
| - * for the queried annotation sets.
|
| + * Searches for annotations that match the given criteria. Results are
|
| + * ordered by genomic coordinate (by reference sequence, then position).
|
| + * Annotations with equivalent genomic coordinates are returned in an
|
| + * unspecified order. This order is consistent, such that two queries for the
|
| + * same content (regardless of page size) yield annotations in the same order
|
| + * across their respective streams of paginated responses. Caller must have
|
| + * READ permission for the queried annotation sets.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| @@ -277,8 +295,8 @@ class AnnotationsResourceApi {
|
| }
|
|
|
| /**
|
| - * Updates an annotation. Caller must have WRITE permission for the associated
|
| - * dataset.
|
| + * Updates an annotation. Caller must have
|
| + * WRITE permission for the associated dataset.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| @@ -287,7 +305,11 @@ class AnnotationsResourceApi {
|
| * [annotationId] - The ID of the annotation to be updated.
|
| *
|
| * [updateMask] - An optional mask specifying which fields to update. Mutable
|
| - * fields are name, variant, transcript, and info. If unspecified, all mutable
|
| + * fields are
|
| + * name,
|
| + * variant,
|
| + * transcript, and
|
| + * info. If unspecified, all mutable
|
| * fields will be updated.
|
| *
|
| * Completes with a [Annotation].
|
| @@ -339,9 +361,15 @@ class AnnotationsetsResourceApi {
|
|
|
| /**
|
| * Creates a new annotation set. Caller must have WRITE permission for the
|
| - * associated dataset. The following fields are required: * datasetId *
|
| - * referenceSetId All other fields may be optionally specified, unless
|
| - * documented as being server-generated (for example, the `id` field).
|
| + * associated dataset.
|
| + *
|
| + * The following fields are required:
|
| + *
|
| + * * datasetId
|
| + * * referenceSetId
|
| + *
|
| + * All other fields may be optionally specified, unless documented as being
|
| + * server-generated (for example, the `id` field).
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| @@ -380,8 +408,8 @@ class AnnotationsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Deletes an annotation set. Caller must have WRITE permission for the
|
| - * associated annotation set.
|
| + * Deletes an annotation set. Caller must have WRITE permission
|
| + * for the associated annotation set.
|
| *
|
| * Request parameters:
|
| *
|
| @@ -420,8 +448,8 @@ class AnnotationsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets an annotation set. Caller must have READ permission for the associated
|
| - * dataset.
|
| + * Gets an annotation set. Caller must have READ permission for
|
| + * the associated dataset.
|
| *
|
| * Request parameters:
|
| *
|
| @@ -514,8 +542,11 @@ class AnnotationsetsResourceApi {
|
| * [annotationSetId] - The ID of the annotation set to be updated.
|
| *
|
| * [updateMask] - An optional mask specifying which fields to update. Mutable
|
| - * fields are name, source_uri, and info. If unspecified, all mutable fields
|
| - * will be updated.
|
| + * fields are
|
| + * name,
|
| + * source_uri, and
|
| + * info. If unspecified, all
|
| + * mutable fields will be updated.
|
| *
|
| * Completes with a [AnnotationSet].
|
| *
|
| @@ -565,8 +596,10 @@ class CallsetsResourceApi {
|
| _requester = client;
|
|
|
| /**
|
| - * Creates a new call set. For the definitions of call sets and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Creates a new call set.
|
| + *
|
| + * For the definitions of call sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * [request] - The metadata request object.
|
| @@ -606,8 +639,10 @@ class CallsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Deletes a call set. For the definitions of call sets and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Deletes a call set.
|
| + *
|
| + * For the definitions of call sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * Request parameters:
|
| @@ -647,8 +682,10 @@ class CallsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets a call set by ID. For the definitions of call sets and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Gets a call set by ID.
|
| + *
|
| + * For the definitions of call sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * Request parameters:
|
| @@ -688,9 +725,12 @@ class CallsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Updates a call set. For the definitions of call sets and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Updates a call set.
|
| + *
|
| + * For the definitions of call sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * This method supports patch semantics.
|
| *
|
| * [request] - The metadata request object.
|
| @@ -700,8 +740,10 @@ class CallsetsResourceApi {
|
| * [callSetId] - The ID of the call set to be updated.
|
| *
|
| * [updateMask] - An optional mask specifying which fields to update. At this
|
| - * time, the only mutable field is name. The only acceptable value is "name".
|
| - * If unspecified, all mutable fields will be updated.
|
| + * time, the only
|
| + * mutable field is name. The only
|
| + * acceptable value is "name". If unspecified, all mutable fields will be
|
| + * updated.
|
| *
|
| * Completes with a [CallSet].
|
| *
|
| @@ -742,9 +784,12 @@ class CallsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets a list of call sets matching the criteria. For the definitions of call
|
| - * sets and other genomics resources, see [Fundamentals of Google
|
| + * Gets a list of call sets matching the criteria.
|
| + *
|
| + * For the definitions of call sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * Implements
|
| * [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).
|
| *
|
| @@ -794,8 +839,10 @@ class DatasetsResourceApi {
|
| _requester = client;
|
|
|
| /**
|
| - * Creates a new dataset. For the definitions of datasets and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Creates a new dataset.
|
| + *
|
| + * For the definitions of datasets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * [request] - The metadata request object.
|
| @@ -835,9 +882,13 @@ class DatasetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Deletes a dataset and all of its contents (all read group sets, reference
|
| - * sets, variant sets, call sets, annotation sets, etc.) This is reversible
|
| - * (up to one week after the deletion) via the datasets.undelete operation.
|
| + * Deletes a dataset and all of its contents (all read group sets,
|
| + * reference sets, variant sets, call sets, annotation sets, etc.)
|
| + * This is reversible (up to one week after the deletion) via
|
| + * the
|
| + * datasets.undelete
|
| + * operation.
|
| + *
|
| * For the definitions of datasets and other genomics resources, see
|
| * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| @@ -879,8 +930,10 @@ class DatasetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets a dataset by ID. For the definitions of datasets and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Gets a dataset by ID.
|
| + *
|
| + * For the definitions of datasets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * Request parameters:
|
| @@ -920,10 +973,14 @@ class DatasetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets the access control policy for the dataset. This is empty if the policy
|
| - * or resource does not exist. See Getting a Policy for more information. For
|
| - * the definitions of datasets and other genomics resources, see [Fundamentals
|
| - * of Google
|
| + * Gets the access control policy for the dataset. This is empty if the
|
| + * policy or resource does not exist.
|
| + *
|
| + * See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
|
| + * Policy</a> for more information.
|
| + *
|
| + * For the definitions of datasets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * [request] - The metadata request object.
|
| @@ -931,7 +988,8 @@ class DatasetsResourceApi {
|
| * Request parameters:
|
| *
|
| * [resource] - REQUIRED: The resource for which policy is being specified.
|
| - * Format is `datasets/`.
|
| + * Format is
|
| + * `datasets/<dataset ID>`.
|
| * Value must have pattern "^datasets/[^/]+$".
|
| *
|
| * Completes with a [Policy].
|
| @@ -970,20 +1028,24 @@ class DatasetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Lists datasets within a project. For the definitions of datasets and other
|
| - * genomics resources, see [Fundamentals of Google
|
| + * Lists datasets within a project.
|
| + *
|
| + * For the definitions of datasets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * Request parameters:
|
| *
|
| - * [projectId] - Required. The Google Cloud project ID to list datasets for.
|
| - *
|
| * [pageSize] - The maximum number of results to return in a single page. If
|
| - * unspecified, defaults to 50. The maximum value is 1024.
|
| + * unspecified,
|
| + * defaults to 50. The maximum value is 1024.
|
| + *
|
| + * [projectId] - Required. The Google Cloud project ID to list datasets for.
|
| *
|
| * [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.
|
| + * result sets.
|
| + * To get the next page of results, set this parameter to the value of
|
| + * `nextPageToken` from the previous response.
|
| *
|
| * Completes with a [ListDatasetsResponse].
|
| *
|
| @@ -993,7 +1055,7 @@ class DatasetsResourceApi {
|
| * 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 projectId, core.int pageSize, core.String pageToken}) {
|
| + async.Future<ListDatasetsResponse> list({core.int pageSize, core.String projectId, core.String pageToken}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1001,12 +1063,12 @@ class DatasetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (projectId != null) {
|
| - _queryParams["projectId"] = [projectId];
|
| - }
|
| if (pageSize != null) {
|
| _queryParams["pageSize"] = ["${pageSize}"];
|
| }
|
| + if (projectId != null) {
|
| + _queryParams["projectId"] = [projectId];
|
| + }
|
| if (pageToken != null) {
|
| _queryParams["pageToken"] = [pageToken];
|
| }
|
| @@ -1024,9 +1086,12 @@ class DatasetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Updates a dataset. For the definitions of datasets and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Updates a dataset.
|
| + *
|
| + * For the definitions of datasets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * This method supports patch semantics.
|
| *
|
| * [request] - The metadata request object.
|
| @@ -1036,8 +1101,10 @@ class DatasetsResourceApi {
|
| * [datasetId] - The ID of the dataset to be updated.
|
| *
|
| * [updateMask] - An optional mask specifying which fields to update. At this
|
| - * time, the only mutable field is name. The only acceptable value is "name".
|
| - * If unspecified, all mutable fields will be updated.
|
| + * time, the only
|
| + * mutable field is name. The only
|
| + * acceptable value is "name". If unspecified, all mutable fields will be
|
| + * updated.
|
| *
|
| * Completes with a [Dataset].
|
| *
|
| @@ -1079,17 +1146,22 @@ class DatasetsResourceApi {
|
|
|
| /**
|
| * Sets the access control policy on the specified dataset. Replaces any
|
| - * existing policy. For the definitions of datasets and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * existing policy.
|
| + *
|
| + * For the definitions of datasets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - * See Setting a Policy for more information.
|
| + *
|
| + * See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
|
| + * Policy</a> for more information.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| * [resource] - REQUIRED: The resource for which policy is being specified.
|
| - * Format is `datasets/`.
|
| + * Format is
|
| + * `datasets/<dataset ID>`.
|
| * Value must have pattern "^datasets/[^/]+$".
|
| *
|
| * Completes with a [Policy].
|
| @@ -1128,9 +1200,12 @@ class DatasetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Returns permissions that a caller has on the specified resource. See
|
| - * Testing Permissions for more information. For the definitions of datasets
|
| - * and other genomics resources, see [Fundamentals of Google
|
| + * Returns permissions that a caller has on the specified resource.
|
| + * See <a href="/iam/docs/managing-policies#testing_permissions">Testing
|
| + * Permissions</a> for more information.
|
| + *
|
| + * For the definitions of datasets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * [request] - The metadata request object.
|
| @@ -1138,7 +1213,8 @@ class DatasetsResourceApi {
|
| * Request parameters:
|
| *
|
| * [resource] - REQUIRED: The resource for which policy is being specified.
|
| - * Format is `datasets/`.
|
| + * Format is
|
| + * `datasets/<dataset ID>`.
|
| * Value must have pattern "^datasets/[^/]+$".
|
| *
|
| * Completes with a [TestIamPermissionsResponse].
|
| @@ -1178,9 +1254,11 @@ class DatasetsResourceApi {
|
|
|
| /**
|
| * Undeletes a dataset by restoring a dataset which was deleted via this API.
|
| + *
|
| * For the definitions of datasets and other genomics resources, see
|
| * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * This operation is only possible for a week after the deletion occurred.
|
| *
|
| * [request] - The metadata request object.
|
| @@ -1283,7 +1361,7 @@ class OperationsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets the latest state of a long-running operation. Clients can use this
|
| + * Gets the latest state of a long-running operation. Clients can use this
|
| * method to poll the operation result at intervals as recommended by the API
|
| * service.
|
| *
|
| @@ -1332,17 +1410,29 @@ class OperationsResourceApi {
|
| * [name] - The name of the operation collection.
|
| * Value must have pattern "^operations$".
|
| *
|
| - * [filter] - A string for filtering Operations. The following filter fields
|
| - * are supported: * projectId: Required. Corresponds to
|
| - * OperationMetadata.projectId. * createTime: The time this job was created,
|
| - * in seconds from the [epoch](http://en.wikipedia.org/wiki/Unix_time). Can
|
| - * use `>=` and/or `= 1432140000` * `projectId = my-project AND createTime >=
|
| - * 1432140000 AND createTime <= 1432150000 AND status = RUNNING` * `projectId
|
| - * = my-project AND labels.color = *` * `projectId = my-project AND
|
| - * labels.color = red`
|
| - *
|
| * [pageSize] - The maximum number of results to return. If unspecified,
|
| - * defaults to 256. The maximum value is 2048.
|
| + * defaults to
|
| + * 256. The maximum value is 2048.
|
| + *
|
| + * [filter] - A string for filtering Operations.
|
| + * The following filter fields are supported:
|
| + *
|
| + * * projectId: Required. Corresponds to
|
| + * OperationMetadata.projectId.
|
| + * * createTime: The time this job was created, in seconds from the
|
| + * [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`
|
| + * operators.
|
| + * * status: Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only
|
| + * one status may be specified.
|
| + * * labels.key where key is a label key.
|
| + *
|
| + * Examples:
|
| + *
|
| + * * `projectId = my-project AND createTime >= 1432140000`
|
| + * * `projectId = my-project AND createTime >= 1432140000 AND createTime <=
|
| + * 1432150000 AND status = RUNNING`
|
| + * * `projectId = my-project AND labels.color = *`
|
| + * * `projectId = my-project AND labels.color = red`
|
| *
|
| * [pageToken] - The standard list page token.
|
| *
|
| @@ -1354,7 +1444,7 @@ class OperationsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<ListOperationsResponse> list(core.String name, {core.String filter, core.int pageSize, core.String pageToken}) {
|
| + async.Future<ListOperationsResponse> list(core.String name, {core.int pageSize, core.String filter, core.String pageToken}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1365,12 +1455,12 @@ class OperationsResourceApi {
|
| if (name == null) {
|
| throw new core.ArgumentError("Parameter name is required.");
|
| }
|
| - if (filter != null) {
|
| - _queryParams["filter"] = [filter];
|
| - }
|
| if (pageSize != null) {
|
| _queryParams["pageSize"] = ["${pageSize}"];
|
| }
|
| + if (filter != null) {
|
| + _queryParams["filter"] = [filter];
|
| + }
|
| if (pageToken != null) {
|
| _queryParams["pageToken"] = [pageToken];
|
| }
|
| @@ -1399,15 +1489,17 @@ class ReadgroupsetsResourceApi {
|
| _requester = client;
|
|
|
| /**
|
| - * Deletes a read group set. For the definitions of read group sets and other
|
| - * genomics resources, see [Fundamentals of Google
|
| + * Deletes a read group set.
|
| + *
|
| + * For the definitions of read group sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * 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.
|
| + * must have WRITE
|
| + * permissions to the dataset associated with this read group set.
|
| *
|
| * Completes with a [Empty].
|
| *
|
| @@ -1442,20 +1534,24 @@ class ReadgroupsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Exports a read group set to a BAM file in Google Cloud Storage. For the
|
| - * definitions of read group sets and other genomics resources, see
|
| + * Exports a read group set to a BAM file in Google Cloud Storage.
|
| + *
|
| + * For the definitions of read group sets and other genomics resources, see
|
| * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * Note that currently there may be some differences between exported BAM
|
| * files and the original BAM file at the time of import. See
|
| - * ImportReadGroupSets for caveats.
|
| + * ImportReadGroupSets
|
| + * for caveats.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| * [readGroupSetId] - Required. The ID of the read group set to export. The
|
| - * caller must have READ access to this read group set.
|
| + * caller must have
|
| + * READ access to this read group set.
|
| *
|
| * Completes with a [Operation].
|
| *
|
| @@ -1493,8 +1589,10 @@ class ReadgroupsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets a read group set by ID. For the definitions of read group sets and
|
| - * other genomics resources, see [Fundamentals of Google
|
| + * Gets a read group set by ID.
|
| + *
|
| + * For the definitions of read group sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * Request parameters:
|
| @@ -1535,17 +1633,23 @@ class ReadgroupsetsResourceApi {
|
|
|
| /**
|
| * Creates read group sets by asynchronously importing the provided
|
| - * information. For the definitions of read group sets and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * information.
|
| + *
|
| + * For the definitions of read group sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - * The caller must have WRITE permissions to the dataset. ## Notes on
|
| - * [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import - Tags will be
|
| - * converted to strings - tag types are not preserved - Comments (`@CO`) in
|
| - * the input file header will not be preserved - Original header order of
|
| - * references (`@SQ`) will not be preserved - Any reverse stranded unmapped
|
| - * reads will be reverse complemented, and their qualities (also the "BQ" and
|
| - * "OQ" tags, if any) will be reversed - Unmapped reads will be stripped of
|
| - * positional information (reference name and position)
|
| + *
|
| + * The caller must have WRITE permissions to the dataset.
|
| + *
|
| + * ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
|
| + *
|
| + * - Tags will be converted to strings - tag types are not preserved
|
| + * - Comments (`@CO`) in the input file header will not be preserved
|
| + * - Original header order of references (`@SQ`) will not be preserved
|
| + * - Any reverse stranded unmapped reads will be reverse complemented, and
|
| + * their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
|
| + * - Unmapped reads will be stripped of positional information (reference name
|
| + * and position)
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| @@ -1584,9 +1688,12 @@ class ReadgroupsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Updates a read group set. For the definitions of read group sets and other
|
| - * genomics resources, see [Fundamentals of Google
|
| + * Updates a read group set.
|
| + *
|
| + * For the definitions of read group sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * This method supports patch semantics.
|
| *
|
| * [request] - The metadata request object.
|
| @@ -1594,12 +1701,17 @@ class ReadgroupsetsResourceApi {
|
| * Request parameters:
|
| *
|
| * [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.
|
| + * must have WRITE
|
| + * permissions to the dataset associated with this read group set.
|
| *
|
| * [updateMask] - An optional mask specifying which fields to update.
|
| - * Supported fields: * name. * referenceSetId. Leaving `updateMask` unset is
|
| - * equivalent to specifying all mutable fields.
|
| + * Supported fields:
|
| + *
|
| + * * name.
|
| + * * referenceSetId.
|
| + *
|
| + * Leaving `updateMask` unset is equivalent to specifying all mutable
|
| + * fields.
|
| *
|
| * Completes with a [ReadGroupSet].
|
| *
|
| @@ -1640,9 +1752,12 @@ class ReadgroupsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Searches for read group sets matching the criteria. For the definitions of
|
| - * read group sets and other genomics resources, see [Fundamentals of Google
|
| + * Searches for read group sets matching the criteria.
|
| + *
|
| + * For the definitions of read group sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * Implements
|
| * [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
|
| *
|
| @@ -1694,10 +1809,12 @@ class ReadgroupsetsCoveragebucketsResourceApi {
|
| /**
|
| * 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. For the
|
| - * definitions of read group sets and other genomics resources, see
|
| + * coverage information across its corresponding genomic range.
|
| + *
|
| + * For the definitions of read group sets and other genomics resources, see
|
| * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * 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
|
| @@ -1709,30 +1826,36 @@ class ReadgroupsetsCoveragebucketsResourceApi {
|
| * [readGroupSetId] - Required. The ID of the read group set over which
|
| * coverage is requested.
|
| *
|
| - * [referenceName] - The name of the reference to query, within the reference
|
| - * set associated with this query. Optional.
|
| + * [pageSize] - The maximum number of results to return in a single page. If
|
| + * unspecified,
|
| + * defaults to 1024. The maximum value is 2048.
|
| *
|
| * [start] - The start position of the range on the reference, 0-based
|
| - * inclusive. If specified, `referenceName` must also be specified. Defaults
|
| - * to 0.
|
| - *
|
| - * [end] - The end position of the range on the reference, 0-based exclusive.
|
| - * If specified, `referenceName` must also be specified. If unset or 0,
|
| - * defaults to the length of the reference.
|
| + * inclusive. If
|
| + * specified, `referenceName` must also be specified. Defaults to 0.
|
| *
|
| * [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.
|
| + * 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.
|
| *
|
| - * [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.
|
| + * [referenceName] - The name of the reference to query, within the reference
|
| + * set associated
|
| + * with this query. Optional.
|
| *
|
| - * [pageSize] - The maximum number of results to return in a single page. If
|
| - * unspecified, defaults to 1024. The maximum value is 2048.
|
| + * [end] - The end position of the range on the reference, 0-based exclusive.
|
| + * If
|
| + * specified, `referenceName` must also be specified. If unset or 0, defaults
|
| + * to the length of the reference.
|
| + *
|
| + * [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.
|
| *
|
| * Completes with a [ListCoverageBucketsResponse].
|
| *
|
| @@ -1742,7 +1865,7 @@ class ReadgroupsetsCoveragebucketsResourceApi {
|
| * 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 readGroupSetId, {core.String referenceName, core.String start, core.String end, core.String targetBucketWidth, core.String pageToken, core.int pageSize}) {
|
| + async.Future<ListCoverageBucketsResponse> list(core.String readGroupSetId, {core.int pageSize, core.String start, core.String targetBucketWidth, core.String referenceName, core.String end, core.String pageToken}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1753,24 +1876,24 @@ class ReadgroupsetsCoveragebucketsResourceApi {
|
| if (readGroupSetId == null) {
|
| throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
| - if (referenceName != null) {
|
| - _queryParams["referenceName"] = [referenceName];
|
| + if (pageSize != null) {
|
| + _queryParams["pageSize"] = ["${pageSize}"];
|
| }
|
| if (start != null) {
|
| _queryParams["start"] = [start];
|
| }
|
| - if (end != null) {
|
| - _queryParams["end"] = [end];
|
| - }
|
| if (targetBucketWidth != null) {
|
| _queryParams["targetBucketWidth"] = [targetBucketWidth];
|
| }
|
| + if (referenceName != null) {
|
| + _queryParams["referenceName"] = [referenceName];
|
| + }
|
| + if (end != null) {
|
| + _queryParams["end"] = [end];
|
| + }
|
| if (pageToken != null) {
|
| _queryParams["pageToken"] = [pageToken];
|
| }
|
| - if (pageSize != null) {
|
| - _queryParams["pageSize"] = ["${pageSize}"];
|
| - }
|
|
|
| _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId') + '/coveragebuckets';
|
|
|
| @@ -1794,22 +1917,29 @@ class ReadsResourceApi {
|
| _requester = client;
|
|
|
| /**
|
| - * Gets a list of reads for one or more read group sets. For the definitions
|
| - * of read group sets and other genomics resources, see [Fundamentals of
|
| - * Google
|
| + * Gets a list of reads for one or more read group sets.
|
| + *
|
| + * For the definitions of read group sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * 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 (by
|
| - * reference sequence, then position). Reads with equivalent genomic
|
| - * coordinates are returned in an unspecified order. This order is consistent,
|
| - * such that two queries for the same content (regardless of page size) yield
|
| - * reads in the same order across their respective streams of paginated
|
| - * responses. Implements
|
| + * & 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 (by reference sequence, then position). Reads with
|
| + * equivalent genomic coordinates are returned in an unspecified order. This
|
| + * order is consistent, such that two queries for the same content (regardless
|
| + * of page size) yield reads in the same order across their respective streams
|
| + * of paginated responses.
|
| + *
|
| + * Implements
|
| * [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
|
| *
|
| * [request] - The metadata request object.
|
| @@ -1848,46 +1978,6 @@ class ReadsResourceApi {
|
| return _response.then((data) => new SearchReadsResponse.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Returns a stream of all the reads matching the search request, ordered by
|
| - * reference name, position, and ID.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [StreamReadsResponse].
|
| - *
|
| - * Completes with a [commons.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<StreamReadsResponse> stream(StreamReadsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'v1/reads:stream';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new StreamReadsResponse.fromJson(data));
|
| - }
|
| -
|
| }
|
|
|
|
|
| @@ -1900,9 +1990,12 @@ class ReferencesResourceApi {
|
| _requester = client;
|
|
|
| /**
|
| - * Gets a reference. For the definitions of references and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Gets a reference.
|
| + *
|
| + * For the definitions of references and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * Implements
|
| * [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
|
| *
|
| @@ -1943,9 +2036,12 @@ class ReferencesResourceApi {
|
| }
|
|
|
| /**
|
| - * Searches for references which match the given criteria. For the definitions
|
| - * of references and other genomics resources, see [Fundamentals of Google
|
| + * Searches for references which match the given criteria.
|
| + *
|
| + * For the definitions of references and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * Implements
|
| * [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
|
| *
|
| @@ -1995,10 +2091,12 @@ class ReferencesBasesResourceApi {
|
| _requester = client;
|
|
|
| /**
|
| - * Lists the bases in a reference, optionally restricted to a range. For the
|
| - * definitions of references and other genomics resources, see [Fundamentals
|
| - * of Google
|
| + * Lists the bases in a reference, optionally restricted to a range.
|
| + *
|
| + * For the definitions of references and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * Implements
|
| * [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
|
| *
|
| @@ -2006,18 +2104,21 @@ class ReferencesBasesResourceApi {
|
| *
|
| * [referenceId] - The ID of the reference.
|
| *
|
| + * [pageSize] - The maximum number of bases to return in a single page. If
|
| + * unspecified,
|
| + * defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base
|
| + * pairs).
|
| + *
|
| * [start] - The start position (0-based) of this query. Defaults to 0.
|
| *
|
| * [end] - The end position (0-based, exclusive) of this query. Defaults to
|
| - * the length of this reference.
|
| + * the length
|
| + * of this reference.
|
| *
|
| * [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.
|
| - *
|
| - * [pageSize] - The maximum number of bases to return in a single page. If
|
| - * unspecified, defaults to 200Kbp (kilo base pairs). The maximum value is
|
| - * 10Mbp (mega base pairs).
|
| + * result sets.
|
| + * To get the next page of results, set this parameter to the value of
|
| + * `nextPageToken` from the previous response.
|
| *
|
| * Completes with a [ListBasesResponse].
|
| *
|
| @@ -2027,7 +2128,7 @@ class ReferencesBasesResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<ListBasesResponse> list(core.String referenceId, {core.String start, core.String end, core.String pageToken, core.int pageSize}) {
|
| + async.Future<ListBasesResponse> list(core.String referenceId, {core.int pageSize, core.String start, core.String end, core.String pageToken}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -2038,6 +2139,9 @@ class ReferencesBasesResourceApi {
|
| if (referenceId == null) {
|
| throw new core.ArgumentError("Parameter referenceId is required.");
|
| }
|
| + if (pageSize != null) {
|
| + _queryParams["pageSize"] = ["${pageSize}"];
|
| + }
|
| if (start != null) {
|
| _queryParams["start"] = [start];
|
| }
|
| @@ -2047,9 +2151,6 @@ class ReferencesBasesResourceApi {
|
| if (pageToken != null) {
|
| _queryParams["pageToken"] = [pageToken];
|
| }
|
| - if (pageSize != null) {
|
| - _queryParams["pageSize"] = ["${pageSize}"];
|
| - }
|
|
|
| _url = 'v1/references/' + commons.Escaper.ecapeVariable('$referenceId') + '/bases';
|
|
|
| @@ -2073,9 +2174,12 @@ class ReferencesetsResourceApi {
|
| _requester = client;
|
|
|
| /**
|
| - * Gets a reference set. For the definitions of references and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Gets a reference set.
|
| + *
|
| + * For the definitions of references and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * Implements
|
| * [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
|
| *
|
| @@ -2116,10 +2220,12 @@ class ReferencesetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Searches for reference sets which match the given criteria. For the
|
| - * definitions of references and other genomics resources, see [Fundamentals
|
| - * of Google
|
| + * Searches for reference sets which match the given criteria.
|
| + *
|
| + * For the definitions of references and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * Implements
|
| * [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
|
| *
|
| @@ -2169,8 +2275,10 @@ class VariantsResourceApi {
|
| _requester = client;
|
|
|
| /**
|
| - * Creates a new variant. For the definitions of variants and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Creates a new variant.
|
| + *
|
| + * For the definitions of variants and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * [request] - The metadata request object.
|
| @@ -2210,8 +2318,10 @@ class VariantsResourceApi {
|
| }
|
|
|
| /**
|
| - * Deletes a variant. For the definitions of variants and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Deletes a variant.
|
| + *
|
| + * For the definitions of variants and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * Request parameters:
|
| @@ -2251,8 +2361,10 @@ class VariantsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets a variant by ID. For the definitions of variants and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Gets a variant by ID.
|
| + *
|
| + * For the definitions of variants and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * Request parameters:
|
| @@ -2293,18 +2405,23 @@ class VariantsResourceApi {
|
|
|
| /**
|
| * Creates variant data by asynchronously importing the provided information.
|
| + *
|
| * For the definitions of variant sets and other genomics resources, see
|
| * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * The variants for import will be merged with any 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 Variant info fields are merged as
|
| - * specified in infoMergeConfig. 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.
|
| + *
|
| + * When variants are merged, the call information from the new variant
|
| + * is added to the existing variant, and Variant info fields are merged
|
| + * as specified in
|
| + * infoMergeConfig.
|
| + * 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.
|
| *
|
| @@ -2343,34 +2460,97 @@ class VariantsResourceApi {
|
| }
|
|
|
| /**
|
| - * Merges the given variants with existing variants. For the definitions of
|
| - * variants and other genomics resources, see [Fundamentals of Google
|
| + * Merges the given variants with existing variants.
|
| + *
|
| + * For the definitions of variants and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - * 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. Variant info fields are merged as specified in the infoMergeConfig
|
| - * field of the MergeVariantsRequest. Please exercise caution when using this
|
| - * method! It is easy to introduce mistakes in existing variants and difficult
|
| - * to back out of them. For example, suppose you were trying to merge a new
|
| - * variant with an existing one and both variants contain calls that belong to
|
| - * callsets with the same callset ID. // Existing variant - irrelevant fields
|
| - * trimmed for clarity { "variantSetId": "10473108253681171589",
|
| - * "referenceName": "1", "start": "10582", "referenceBases": "G",
|
| - * "alternateBases": [ "A" ], "calls": [ { "callSetId":
|
| - * "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 0, 1 ],
|
| - * } ] } // New variant with conflicting call information { "variantSetId":
|
| - * "10473108253681171589", "referenceName": "1", "start": "10582",
|
| - * "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId":
|
| - * "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ],
|
| - * } ] } The resulting merged variant would overwrite the existing calls with
|
| - * those from the new variant: { "variantSetId": "10473108253681171589",
|
| - * "referenceName": "1", "start": "10582", "referenceBases": "G",
|
| - * "alternateBases": [ "A" ], "calls": [ { "callSetId":
|
| - * "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ],
|
| - * } ] } This may be the desired outcome, but it is up to the user to
|
| - * determine if if that is indeed the case.
|
| + *
|
| + * 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. Variant info fields are merged as
|
| + * specified in the
|
| + * infoMergeConfig
|
| + * field of the MergeVariantsRequest.
|
| + *
|
| + * Please exercise caution when using this method! It is easy to introduce
|
| + * mistakes in existing variants and difficult to back out of them. For
|
| + * example,
|
| + * suppose you were trying to merge a new variant with an existing one and
|
| + * both
|
| + * variants contain calls that belong to callsets with the same callset ID.
|
| + *
|
| + * // Existing variant - irrelevant fields trimmed for clarity
|
| + * {
|
| + * "variantSetId": "10473108253681171589",
|
| + * "referenceName": "1",
|
| + * "start": "10582",
|
| + * "referenceBases": "G",
|
| + * "alternateBases": [
|
| + * "A"
|
| + * ],
|
| + * "calls": [
|
| + * {
|
| + * "callSetId": "10473108253681171589-0",
|
| + * "callSetName": "CALLSET0",
|
| + * "genotype": [
|
| + * 0,
|
| + * 1
|
| + * ],
|
| + * }
|
| + * ]
|
| + * }
|
| + *
|
| + * // New variant with conflicting call information
|
| + * {
|
| + * "variantSetId": "10473108253681171589",
|
| + * "referenceName": "1",
|
| + * "start": "10582",
|
| + * "referenceBases": "G",
|
| + * "alternateBases": [
|
| + * "A"
|
| + * ],
|
| + * "calls": [
|
| + * {
|
| + * "callSetId": "10473108253681171589-0",
|
| + * "callSetName": "CALLSET0",
|
| + * "genotype": [
|
| + * 1,
|
| + * 1
|
| + * ],
|
| + * }
|
| + * ]
|
| + * }
|
| + *
|
| + * The resulting merged variant would overwrite the existing calls with those
|
| + * from the new variant:
|
| + *
|
| + * {
|
| + * "variantSetId": "10473108253681171589",
|
| + * "referenceName": "1",
|
| + * "start": "10582",
|
| + * "referenceBases": "G",
|
| + * "alternateBases": [
|
| + * "A"
|
| + * ],
|
| + * "calls": [
|
| + * {
|
| + * "callSetId": "10473108253681171589-0",
|
| + * "callSetName": "CALLSET0",
|
| + * "genotype": [
|
| + * 1,
|
| + * 1
|
| + * ],
|
| + * }
|
| + * ]
|
| + * }
|
| + *
|
| + * This may be the desired outcome, but it is up to the user to determine if
|
| + * if that is indeed the case.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| @@ -2409,9 +2589,12 @@ class VariantsResourceApi {
|
| }
|
|
|
| /**
|
| - * Updates a variant. For the definitions of variants and other genomics
|
| - * resources, see [Fundamentals of Google
|
| + * Updates a variant.
|
| + *
|
| + * For the definitions of variants and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * This method supports patch semantics. Returns the modified variant without
|
| * its calls.
|
| *
|
| @@ -2422,7 +2605,9 @@ class VariantsResourceApi {
|
| * [variantId] - The ID of the variant to be updated.
|
| *
|
| * [updateMask] - An optional mask specifying which fields to update. At this
|
| - * time, mutable fields are names and info. Acceptable values are "names" and
|
| + * time, mutable
|
| + * fields are names and
|
| + * info. Acceptable values are "names" and
|
| * "info". If unspecified, all mutable fields will be updated.
|
| *
|
| * Completes with a [Variant].
|
| @@ -2464,9 +2649,12 @@ class VariantsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets a list of variants matching the criteria. For the definitions of
|
| - * variants and other genomics resources, see [Fundamentals of Google
|
| + * Gets a list of variants matching the criteria.
|
| + *
|
| + * For the definitions of variants and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * Implements
|
| * [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
|
| *
|
| @@ -2506,46 +2694,6 @@ class VariantsResourceApi {
|
| return _response.then((data) => new SearchVariantsResponse.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Returns a stream of all the variants matching the search request, ordered
|
| - * by reference name, position, and ID.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [StreamVariantsResponse].
|
| - *
|
| - * Completes with a [commons.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<StreamVariantsResponse> stream(StreamVariantsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'v1/variants:stream';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new StreamVariantsResponse.fromJson(data));
|
| - }
|
| -
|
| }
|
|
|
|
|
| @@ -2556,9 +2704,12 @@ class VariantsetsResourceApi {
|
| _requester = client;
|
|
|
| /**
|
| - * Creates a new variant set. For the definitions of variant sets and other
|
| - * genomics resources, see [Fundamentals of Google
|
| + * Creates a new variant set.
|
| + *
|
| + * For the definitions of variant sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * The provided variant set must have a valid `datasetId` set - all other
|
| * fields are optional. Note that the `id` field will be ignored, as this is
|
| * assigned by the server.
|
| @@ -2601,8 +2752,10 @@ class VariantsetsResourceApi {
|
|
|
| /**
|
| * Deletes a variant set including all variants, call sets, and calls within.
|
| - * This is not reversible. For the definitions of variant sets and other
|
| - * genomics resources, see [Fundamentals of Google
|
| + * This is not reversible.
|
| + *
|
| + * For the definitions of variant sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * Request parameters:
|
| @@ -2642,8 +2795,10 @@ class VariantsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Exports variant set data to an external destination. For the definitions of
|
| - * variant sets and other genomics resources, see [Fundamentals of Google
|
| + * Exports variant set data to an external destination.
|
| + *
|
| + * For the definitions of variant sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * [request] - The metadata request object.
|
| @@ -2651,8 +2806,8 @@ class VariantsetsResourceApi {
|
| * 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.
|
| + * data which
|
| + * should be exported. The caller must have READ access to this variant set.
|
| *
|
| * Completes with a [Operation].
|
| *
|
| @@ -2690,8 +2845,10 @@ class VariantsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets a variant set by ID. For the definitions of variant sets and other
|
| - * genomics resources, see [Fundamentals of Google
|
| + * Gets a variant set by ID.
|
| + *
|
| + * For the definitions of variant sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * Request parameters:
|
| @@ -2731,8 +2888,10 @@ class VariantsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Updates a variant set using patch semantics. For the definitions of variant
|
| - * sets and other genomics resources, see [Fundamentals of Google
|
| + * Updates a variant set using patch semantics.
|
| + *
|
| + * For the definitions of variant sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| *
|
| * [request] - The metadata request object.
|
| @@ -2742,8 +2901,14 @@ class VariantsetsResourceApi {
|
| * [variantSetId] - The ID of the variant to be updated (must already exist).
|
| *
|
| * [updateMask] - An optional mask specifying which fields to update.
|
| - * Supported fields: * metadata. * name. * description. Leaving `updateMask`
|
| - * unset is equivalent to specifying all mutable fields.
|
| + * Supported fields:
|
| + *
|
| + * * metadata.
|
| + * * name.
|
| + * * description.
|
| + *
|
| + * Leaving `updateMask` unset is equivalent to specifying all mutable
|
| + * fields.
|
| *
|
| * Completes with a [VariantSet].
|
| *
|
| @@ -2784,10 +2949,12 @@ class VariantsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Returns a list of all variant sets matching search criteria. For the
|
| - * definitions of variant sets and other genomics resources, see [Fundamentals
|
| - * of Google
|
| + * Returns a list of all variant sets matching search criteria.
|
| + *
|
| + * For the definitions of variant sets and other genomics resources, see
|
| + * [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * Implements
|
| * [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
|
| *
|
| @@ -2834,9 +3001,10 @@ class VariantsetsResourceApi {
|
| /**
|
| * An annotation describes a region of reference genome. The value of an
|
| * annotation may be one of several canonical types, supplemented by arbitrary
|
| - * info tags. An annotation is not inherently associated with a specific sample
|
| - * or individual (though a client could choose to use annotations in this way).
|
| - * Example canonical annotation types are `GENE` and `VARIANT`.
|
| + * info tags. An annotation is not inherently associated with a specific
|
| + * sample or individual (though a client could choose to use annotations in
|
| + * this way). Example canonical annotation types are `GENE` and
|
| + * `VARIANT`.
|
| */
|
| class Annotation {
|
| /** The annotation set to which this annotation belongs. */
|
| @@ -2847,7 +3015,7 @@ class Annotation {
|
| core.String id;
|
| /**
|
| * A map of additional read alignment information. This must be of the form
|
| - * map (string key mapping to a list of string values).
|
| + * map<string, string[]> (string key mapping to a list of string values).
|
| *
|
| * The values for Object must be JSON objects. It can consist of `num`,
|
| * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| @@ -2858,8 +3026,8 @@ class Annotation {
|
| /** The ID of the Google Genomics reference associated with this range. */
|
| core.String referenceId;
|
| /**
|
| - * The display name corresponding to the reference specified by `referenceId`,
|
| - * for example `chr1`, `1`, or `chrX`.
|
| + * The display name corresponding to the reference specified by
|
| + * `referenceId`, for example `chr1`, `1`, or `chrX`.
|
| */
|
| core.String referenceName;
|
| /**
|
| @@ -2871,21 +3039,30 @@ class Annotation {
|
| /** The start position of the range on the reference, 0-based inclusive. */
|
| core.String start;
|
| /**
|
| - * A transcript value represents the assertion that a particular region of the
|
| - * reference genome may be transcribed as RNA. An alternative splicing pattern
|
| - * would be represented as a separate transcript object. This field is only
|
| - * set for annotations of type `TRANSCRIPT`.
|
| + * A transcript value represents the assertion that a particular region of
|
| + * the reference genome may be transcribed as RNA. An alternative splicing
|
| + * pattern would be represented as a separate transcript object. This field
|
| + * is only set for annotations of type `TRANSCRIPT`.
|
| */
|
| Transcript transcript;
|
| /**
|
| * The data type for this annotation. Must match the containing annotation
|
| * set's type.
|
| * Possible string values are:
|
| - * - "ANNOTATION_TYPE_UNSPECIFIED" : A ANNOTATION_TYPE_UNSPECIFIED.
|
| - * - "GENERIC" : A GENERIC.
|
| - * - "VARIANT" : A VARIANT.
|
| - * - "GENE" : A GENE.
|
| - * - "TRANSCRIPT" : A TRANSCRIPT.
|
| + * - "ANNOTATION_TYPE_UNSPECIFIED"
|
| + * - "GENERIC" : A `GENERIC` annotation type should be used when no other
|
| + * annotation
|
| + * type will suffice. This represents an untyped annotation of the reference
|
| + * genome.
|
| + * - "VARIANT" : A `VARIANT` annotation type.
|
| + * - "GENE" : A `GENE` annotation type represents the existence of a gene at
|
| + * the
|
| + * associated reference coordinates. The start coordinate is typically the
|
| + * gene's transcription start site and the end is typically the end of the
|
| + * gene's last exon.
|
| + * - "TRANSCRIPT" : A `TRANSCRIPT` annotation type represents the assertion
|
| + * that a
|
| + * particular region of the reference genome may be transcribed as RNA.
|
| */
|
| core.String type;
|
| /**
|
| @@ -2993,7 +3170,7 @@ class AnnotationSet {
|
| core.String id;
|
| /**
|
| * A map of additional read alignment information. This must be of the form
|
| - * map (string key mapping to a list of string values).
|
| + * map<string, string[]> (string key mapping to a list of string values).
|
| *
|
| * The values for Object must be JSON objects. It can consist of `num`,
|
| * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| @@ -3014,11 +3191,20 @@ class AnnotationSet {
|
| /**
|
| * The type of annotations contained within this set.
|
| * Possible string values are:
|
| - * - "ANNOTATION_TYPE_UNSPECIFIED" : A ANNOTATION_TYPE_UNSPECIFIED.
|
| - * - "GENERIC" : A GENERIC.
|
| - * - "VARIANT" : A VARIANT.
|
| - * - "GENE" : A GENE.
|
| - * - "TRANSCRIPT" : A TRANSCRIPT.
|
| + * - "ANNOTATION_TYPE_UNSPECIFIED"
|
| + * - "GENERIC" : A `GENERIC` annotation type should be used when no other
|
| + * annotation
|
| + * type will suffice. This represents an untyped annotation of the reference
|
| + * genome.
|
| + * - "VARIANT" : A `VARIANT` annotation type.
|
| + * - "GENE" : A `GENE` annotation type represents the existence of a gene at
|
| + * the
|
| + * associated reference coordinates. The start coordinate is typically the
|
| + * gene's transcription start site and the end is typically the end of the
|
| + * gene's last exon.
|
| + * - "TRANSCRIPT" : A `TRANSCRIPT` annotation type represents the assertion
|
| + * that a
|
| + * particular region of the reference genome may be transcribed as RNA.
|
| */
|
| core.String type;
|
|
|
| @@ -3086,9 +3272,9 @@ class BatchCreateAnnotationsRequest {
|
| * If provided, duplicated requests will result in the same response; if not
|
| * provided, duplicated requests may result in duplicated data. For a given
|
| * annotation set, callers should not reuse `request_id`s when writing
|
| - * different batches of annotations - behavior in this case is undefined. A
|
| - * common approach is to use a UUID. For batch jobs where worker crashes are a
|
| - * possibility, consider using some unique variant of a worker or run ID.
|
| + * different batches of annotations - behavior in this case is undefined.
|
| + * A common approach is to use a UUID. For batch jobs where worker crashes are
|
| + * a possibility, consider using some unique variant of a worker or run ID.
|
| */
|
| core.String requestId;
|
|
|
| @@ -3143,23 +3329,32 @@ class BatchCreateAnnotationsResponse {
|
| class Binding {
|
| /**
|
| * Specifies the identities requesting access for a Cloud Platform resource.
|
| - * `members` can have the following values: * `allUsers`: A special identifier
|
| - * that represents anyone who is on the internet; with or without a Google
|
| - * account. * `allAuthenticatedUsers`: A special identifier that represents
|
| - * anyone who is authenticated with a Google account or a service account. *
|
| - * `user:{emailid}`: An email address that represents a specific Google
|
| - * account. For example, `alice@gmail.com` or `joe@example.com`. *
|
| - * `serviceAccount:{emailid}`: An email address that represents a service
|
| - * account. For example, `my-other-app@appspot.gserviceaccount.com`. *
|
| - * `group:{emailid}`: An email address that represents a Google group. For
|
| - * example, `admins@example.com`. * `domain:{domain}`: A Google Apps domain
|
| - * name that represents all the users of that domain. For example,
|
| - * `google.com` or `example.com`.
|
| + * `members` can have the following values:
|
| + *
|
| + * * `allUsers`: A special identifier that represents anyone who is
|
| + * on the internet; with or without a Google account.
|
| + *
|
| + * * `allAuthenticatedUsers`: A special identifier that represents anyone
|
| + * who is authenticated with a Google account or a service account.
|
| + *
|
| + * * `user:{emailid}`: An email address that represents a specific Google
|
| + * account. For example, `alice@gmail.com` or `joe@example.com`.
|
| + *
|
| + *
|
| + * * `serviceAccount:{emailid}`: An email address that represents a service
|
| + * account. For example, `my-other-app@appspot.gserviceaccount.com`.
|
| + *
|
| + * * `group:{emailid}`: An email address that represents a Google group.
|
| + * For example, `admins@example.com`.
|
| + *
|
| + * * `domain:{domain}`: A Google Apps domain name that represents all the
|
| + * users of that domain. For example, `google.com` or `example.com`.
|
| */
|
| core.List<core.String> members;
|
| /**
|
| - * Role that is assigned to `members`. For example, `roles/viewer`,
|
| - * `roles/editor`, or `roles/owner`. Required
|
| + * Role that is assigned to `members`.
|
| + * For example, `roles/viewer`, `roles/editor`, or `roles/owner`.
|
| + * Required
|
| */
|
| core.String role;
|
|
|
| @@ -3188,8 +3383,9 @@ class Binding {
|
|
|
| /**
|
| * A call set is a collection of variant calls, typically for one sample. It
|
| - * belongs to a variant set. For more genomics resource definitions, see
|
| - * [Fundamentals of Google
|
| + * belongs to a variant set.
|
| + *
|
| + * For more genomics resource definitions, see [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| */
|
| class CallSet {
|
| @@ -3198,8 +3394,8 @@ class CallSet {
|
| /** The server-generated call set ID, unique across all call sets. */
|
| core.String id;
|
| /**
|
| - * A map of additional call set information. This must be of the form map
|
| - * (string key mapping to a list of string values).
|
| + * A map of additional call set information. This must be of the form
|
| + * map<string, string[]> (string key mapping to a list of string values).
|
| *
|
| * The values for Object must be JSON objects. It can consist of `num`,
|
| * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| @@ -3210,9 +3406,10 @@ class CallSet {
|
| /** The sample ID this call set corresponds to. */
|
| core.String sampleId;
|
| /**
|
| - * The IDs of the variant sets this call set belongs to. This field must have
|
| - * exactly length one, as a call set belongs to a single variant set. This
|
| - * field is repeated for compatibility with the [GA4GH 0.5.1
|
| + * The IDs of the variant sets this call set belongs to. This field must
|
| + * have exactly length one, as a call set belongs to a single variant set.
|
| + * This field is repeated for compatibility with the
|
| + * [GA4GH 0.5.1
|
| * API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variants.avdl#L76).
|
| */
|
| core.List<core.String> variantSetIds;
|
| @@ -3283,24 +3480,60 @@ class CigarUnit {
|
| /**
|
| *
|
| * Possible string values are:
|
| - * - "OPERATION_UNSPECIFIED" : A OPERATION_UNSPECIFIED.
|
| - * - "ALIGNMENT_MATCH" : A ALIGNMENT_MATCH.
|
| - * - "INSERT" : A INSERT.
|
| - * - "DELETE" : A DELETE.
|
| - * - "SKIP" : A SKIP.
|
| - * - "CLIP_SOFT" : A CLIP_SOFT.
|
| - * - "CLIP_HARD" : A CLIP_HARD.
|
| - * - "PAD" : A PAD.
|
| - * - "SEQUENCE_MATCH" : A SEQUENCE_MATCH.
|
| - * - "SEQUENCE_MISMATCH" : A SEQUENCE_MISMATCH.
|
| + * - "OPERATION_UNSPECIFIED"
|
| + * - "ALIGNMENT_MATCH" : An alignment match indicates that a sequence can be
|
| + * aligned to the
|
| + * reference without evidence of an INDEL. Unlike the
|
| + * `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators,
|
| + * the `ALIGNMENT_MATCH` operator does not indicate whether the
|
| + * reference and read sequences are an exact match. This operator is
|
| + * equivalent to SAM's `M`.
|
| + * - "INSERT" : The insert operator indicates that the read contains evidence
|
| + * of bases
|
| + * being inserted into the reference. This operator is equivalent to SAM's
|
| + * `I`.
|
| + * - "DELETE" : The delete operator indicates that the read contains evidence
|
| + * of bases
|
| + * being deleted from the reference. This operator is equivalent to SAM's
|
| + * `D`.
|
| + * - "SKIP" : The skip operator indicates that this read skips a long segment
|
| + * of the
|
| + * reference, but the bases have not been deleted. This operator is commonly
|
| + * used when working with RNA-seq data, where reads may skip long segments
|
| + * of the reference between exons. This operator is equivalent to SAM's
|
| + * `N`.
|
| + * - "CLIP_SOFT" : The soft clip operator indicates that bases at the
|
| + * start/end of a read
|
| + * have not been considered during alignment. This may occur if the majority
|
| + * of a read maps, except for low quality bases at the start/end of a read.
|
| + * This operator is equivalent to SAM's `S`. Bases that are soft
|
| + * clipped will still be stored in the read.
|
| + * - "CLIP_HARD" : The hard clip operator indicates that bases at the
|
| + * start/end of a read
|
| + * have been omitted from this alignment. This may occur if this linear
|
| + * alignment is part of a chimeric alignment, or if the read has been
|
| + * trimmed (for example, during error correction or to trim poly-A tails for
|
| + * RNA-seq). This operator is equivalent to SAM's `H`.
|
| + * - "PAD" : The pad operator indicates that there is padding in an alignment.
|
| + * This
|
| + * operator is equivalent to SAM's `P`.
|
| + * - "SEQUENCE_MATCH" : This operator indicates that this portion of the
|
| + * aligned sequence exactly
|
| + * matches the reference. This operator is equivalent to SAM's `=`.
|
| + * - "SEQUENCE_MISMATCH" : This operator indicates that this portion of the
|
| + * aligned sequence is an
|
| + * alignment match to the reference, but a sequence mismatch. This can
|
| + * indicate a SNP or a read error. This operator is equivalent to SAM's
|
| + * `X`.
|
| */
|
| core.String operation;
|
| /** The number of genomic 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.
|
| + * `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;
|
|
|
| @@ -3335,8 +3568,8 @@ class CigarUnit {
|
|
|
| class ClinicalCondition {
|
| /**
|
| - * The MedGen concept id associated with this gene. Search for these IDs at
|
| - * http://www.ncbi.nlm.nih.gov/medgen/
|
| + * The MedGen concept id associated with this gene.
|
| + * Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
|
| */
|
| core.String conceptId;
|
| /** The set of external IDs for this condition. */
|
| @@ -3344,7 +3577,8 @@ class ClinicalCondition {
|
| /** A set of names for the condition. */
|
| core.List<core.String> names;
|
| /**
|
| - * The OMIM id for this condition. Search for these IDs at http://omim.org/
|
| + * The OMIM id for this condition.
|
| + * Search for these IDs at http://omim.org/
|
| */
|
| core.String omimId;
|
|
|
| @@ -3475,8 +3709,8 @@ class ComputeEngine {
|
| */
|
| class CoverageBucket {
|
| /**
|
| - * The average number of reads which are aligned to each individual reference
|
| - * base in this bucket.
|
| + * 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. */
|
| @@ -3506,8 +3740,9 @@ class CoverageBucket {
|
| }
|
|
|
| /**
|
| - * A Dataset is a collection of genomic data. For more genomics resource
|
| - * definitions, see [Fundamentals of Google
|
| + * A Dataset is a collection of genomic data.
|
| + *
|
| + * For more genomics resource definitions, see [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| */
|
| class Dataset {
|
| @@ -3557,10 +3792,14 @@ class Dataset {
|
|
|
| /**
|
| * A generic empty message that you can re-use to avoid defining duplicated
|
| - * empty messages in your APIs. A typical example is to use it as the request or
|
| - * the response type of an API method. For instance: service Foo { rpc
|
| - * Bar(google.protobuf.Empty) returns (google.protobuf.Empty); } The JSON
|
| - * representation for `Empty` is empty JSON object `{}`.
|
| + * empty messages in your APIs. A typical example is to use it as the request
|
| + * or the response type of an API method. For instance:
|
| + *
|
| + * service Foo {
|
| + * rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty);
|
| + * }
|
| + *
|
| + * The JSON representation for `Empty` is empty JSON object `{}`.
|
| */
|
| class Empty {
|
|
|
| @@ -3612,14 +3851,19 @@ class Exon {
|
| */
|
| core.String end;
|
| /**
|
| - * The frame of this exon. Contains a value of 0, 1, or 2, which indicates the
|
| - * offset of the first coding base of the exon within the reading frame of the
|
| - * coding DNA sequence, if any. This field is dependent on the strandedness of
|
| - * this annotation (see Annotation.reverse_strand). For forward stranded
|
| - * annotations, this offset is relative to the exon.start. For reverse strand
|
| - * annotations, this offset is relative to the exon.end `- 1`. Unset if this
|
| - * exon does not intersect the coding sequence. Upon creation of a transcript,
|
| - * the frame must be populated for all or none of the coding exons.
|
| + * The frame of this exon. Contains a value of 0, 1, or 2, which indicates
|
| + * the offset of the first coding base of the exon within the reading frame
|
| + * of the coding DNA sequence, if any. This field is dependent on the
|
| + * strandedness of this annotation (see
|
| + * Annotation.reverse_strand).
|
| + * For forward stranded annotations, this offset is relative to the
|
| + * exon.start. For reverse
|
| + * strand annotations, this offset is relative to the
|
| + * exon.end `- 1`.
|
| + *
|
| + * Unset if this exon does not intersect the coding sequence. Upon creation
|
| + * of a transcript, the frame must be populated for all or none of the
|
| + * coding exons.
|
| */
|
| core.int frame;
|
| /**
|
| @@ -3666,9 +3910,9 @@ class Experiment {
|
| core.String instrumentModel;
|
| /**
|
| * A client-supplied library identifier; a library is a collection of DNA
|
| - * fragments which have been prepared for sequencing from a sample. This field
|
| - * is important for quality control as error or bias can be introduced during
|
| - * sample preparation.
|
| + * fragments which have been prepared for sequencing from a sample. This
|
| + * field is important for quality control as error or bias can be introduced
|
| + * during sample preparation.
|
| */
|
| core.String libraryId;
|
| /**
|
| @@ -3718,20 +3962,20 @@ class Experiment {
|
| /** The read group set export request. */
|
| class ExportReadGroupSetRequest {
|
| /**
|
| - * Required. A Google Cloud Storage URI for the exported BAM file. The
|
| - * currently authenticated user must have write access to the new file. An
|
| - * error will be returned if the URI already contains data.
|
| + * Required. A Google Cloud Storage URI for the exported BAM file.
|
| + * The currently authenticated user must have write access to the new file.
|
| + * An error will be returned if the URI already contains data.
|
| */
|
| core.String exportUri;
|
| /**
|
| - * Required. The Google Cloud project ID that owns this export. The caller
|
| - * must have WRITE access to this project.
|
| + * Required. The Google Cloud project ID that owns this
|
| + * export. The caller must have WRITE access to this project.
|
| */
|
| core.String projectId;
|
| /**
|
| * The reference names to export. If this is not specified, all reference
|
| - * sequences, including unmapped reads, are exported. Use `*` to export only
|
| - * unmapped reads.
|
| + * sequences, including unmapped reads, are exported.
|
| + * Use `*` to export only unmapped reads.
|
| */
|
| core.List<core.String> referenceNames;
|
|
|
| @@ -3772,8 +4016,9 @@ class ExportVariantSetRequest {
|
| */
|
| core.String bigqueryDataset;
|
| /**
|
| - * Required. 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.
|
| + * Required. 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;
|
| /**
|
| @@ -3784,14 +4029,14 @@ class ExportVariantSetRequest {
|
| /**
|
| * The format for the exported data.
|
| * Possible string values are:
|
| - * - "FORMAT_UNSPECIFIED" : A FORMAT_UNSPECIFIED.
|
| - * - "FORMAT_BIGQUERY" : A FORMAT_BIGQUERY.
|
| + * - "FORMAT_UNSPECIFIED"
|
| + * - "FORMAT_BIGQUERY" : Export the data to Google BigQuery.
|
| */
|
| core.String format;
|
| /**
|
| - * Required. The Google Cloud project ID that owns the destination BigQuery
|
| - * dataset. The caller must have WRITE access to this project. This project
|
| - * will also own the resulting export job.
|
| + * Required. The Google Cloud project ID 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;
|
|
|
| @@ -3890,9 +4135,20 @@ class ImportReadGroupSetsRequest {
|
| * The partition strategy describes how read groups are partitioned into read
|
| * group sets.
|
| * Possible string values are:
|
| - * - "PARTITION_STRATEGY_UNSPECIFIED" : A PARTITION_STRATEGY_UNSPECIFIED.
|
| - * - "PER_FILE_PER_SAMPLE" : A PER_FILE_PER_SAMPLE.
|
| - * - "MERGE_ALL" : A MERGE_ALL.
|
| + * - "PARTITION_STRATEGY_UNSPECIFIED"
|
| + * - "PER_FILE_PER_SAMPLE" : In most cases, this strategy yields one read
|
| + * group set per file. This is
|
| + * the default behavior.
|
| + *
|
| + * Allocate one read group set per file per sample. For BAM files, read
|
| + * groups are considered to share a sample if they have identical sample
|
| + * names. Furthermore, all reads for each file which do not belong to a read
|
| + * group, if any, will be grouped into a single read group set per-file.
|
| + * - "MERGE_ALL" : Includes all read groups in all imported files into a
|
| + * single read group
|
| + * set. Requires that the headers for all imported files are equivalent. All
|
| + * reads which do not belong to a read group, if any, will be grouped into a
|
| + * separate read group set.
|
| */
|
| core.String partitionStrategy;
|
| /**
|
| @@ -3904,8 +4160,15 @@ class ImportReadGroupSetsRequest {
|
| core.String referenceSetId;
|
| /**
|
| * A list of URIs pointing at [BAM
|
| - * files](https://samtools.github.io/hts-specs/SAMv1.pdf) in Google Cloud
|
| - * Storage.
|
| + * files](https://samtools.github.io/hts-specs/SAMv1.pdf)
|
| + * in Google Cloud Storage.
|
| + * Those URIs can include wildcards (*), but do not add or remove
|
| + * matching files before import has completed.
|
| + *
|
| + * Note that Google Cloud Storage object listing is only eventually
|
| + * consistent: files added may be not be immediately visible to
|
| + * everyone. Thus, if using a wildcard it is preferable not to start
|
| + * the import immediately after the files are created.
|
| */
|
| core.List<core.String> sourceUris;
|
|
|
| @@ -3972,25 +4235,30 @@ class ImportVariantsRequest {
|
| * The format of the variant data being imported. If unspecified, defaults to
|
| * to `VCF`.
|
| * Possible string values are:
|
| - * - "FORMAT_UNSPECIFIED" : A FORMAT_UNSPECIFIED.
|
| - * - "FORMAT_VCF" : A FORMAT_VCF.
|
| - * - "FORMAT_COMPLETE_GENOMICS" : A FORMAT_COMPLETE_GENOMICS.
|
| + * - "FORMAT_UNSPECIFIED"
|
| + * - "FORMAT_VCF" : VCF (Variant Call Format). The VCF files may be gzip
|
| + * compressed. gVCF is
|
| + * also supported.
|
| + * - "FORMAT_COMPLETE_GENOMICS" : Complete Genomics masterVarBeta format. The
|
| + * masterVarBeta files may
|
| + * be bzip2 compressed.
|
| */
|
| core.String format;
|
| /**
|
| - * A mapping between info field keys and the InfoMergeOperations to be
|
| - * performed on them. This is plumbed down to the MergeVariantRequests
|
| + * A mapping between info field keys and the InfoMergeOperations to
|
| + * be performed on them. This is plumbed down to the MergeVariantRequests
|
| * generated by the resulting import job.
|
| */
|
| core.Map<core.String, core.String> infoMergeConfig;
|
| /**
|
| - * Convert reference names to the canonical representation. hg19 haploytypes
|
| - * (those reference names containing "_hap") are not modified in any way. All
|
| - * other reference names are modified according to the following rules: The
|
| - * reference name is capitalized. The "chr" prefix is dropped for all
|
| - * autosomes and sex chromsomes. For example "chr17" becomes "17" and "chrX"
|
| - * becomes "X". All mitochondrial chromosomes ("chrM", "chrMT", etc) become
|
| - * "MT".
|
| + * Convert reference names to the canonical representation.
|
| + * hg19 haploytypes (those reference names containing "_hap")
|
| + * are not modified in any way.
|
| + * All other reference names are modified according to the following rules:
|
| + * The reference name is capitalized.
|
| + * The "chr" prefix is dropped for all autosomes and sex chromsomes.
|
| + * For example "chr17" becomes "17" and "chrX" becomes "X".
|
| + * All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
|
| */
|
| core.bool normalizeReferenceNames;
|
| /**
|
| @@ -4077,9 +4345,11 @@ class LinearAlignment {
|
| */
|
| core.List<CigarUnit> cigar;
|
| /**
|
| - * The mapping quality of this alignment. Represents how likely the read maps
|
| - * to this position as opposed to other locations. Specifically, this is -10
|
| - * log10 Pr(mapping position is wrong), rounded to the nearest integer.
|
| + * The mapping quality of this alignment. Represents how likely
|
| + * the read maps to this position as opposed to other locations.
|
| + *
|
| + * Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
|
| + * the nearest integer.
|
| */
|
| core.int mappingQuality;
|
| /** The position of this alignment. */
|
| @@ -4122,9 +4392,9 @@ class ListBasesResponse {
|
| */
|
| 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.
|
| + * 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. */
|
| @@ -4170,8 +4440,8 @@ class ListCoverageBucketsResponse {
|
| /**
|
| * 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 `bucketWidth`, unless its end 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;
|
| /**
|
| @@ -4276,8 +4546,8 @@ class ListOperationsResponse {
|
|
|
| class MergeVariantsRequest {
|
| /**
|
| - * A mapping between info field keys and the InfoMergeOperations to be
|
| - * performed on them.
|
| + * A mapping between info field keys and the InfoMergeOperations to
|
| + * be performed on them.
|
| */
|
| core.Map<core.String, core.String> infoMergeConfig;
|
| /** The destination variant set. */
|
| @@ -4320,8 +4590,8 @@ class MergeVariantsRequest {
|
| */
|
| class Operation {
|
| /**
|
| - * If the value is `false`, it means the operation is still in progress. If
|
| - * true, the operation is completed, and either `error` or `response` is
|
| + * If the value is `false`, it means the operation is still in progress.
|
| + * If true, the operation is completed, and either `error` or `response` is
|
| * available.
|
| */
|
| core.bool done;
|
| @@ -4337,14 +4607,14 @@ class Operation {
|
| core.Map<core.String, core.Object> metadata;
|
| /**
|
| * The server-assigned name, which is only unique within the same service that
|
| - * originally returns it. For example:
|
| + * originally returns it. For example:
|
| * `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
|
| */
|
| core.String name;
|
| /**
|
| * If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If
|
| - * importing Variants, an ImportVariantsResponse is returned. For exports, an
|
| - * empty response is returned.
|
| + * importing Variants, an ImportVariantsResponse is returned. For pipelines
|
| + * and exports, an empty response is returned.
|
| *
|
| * The values for Object must be JSON objects. It can consist of `num`,
|
| * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| @@ -4446,8 +4716,8 @@ class OperationMetadata {
|
| core.String endTime;
|
| /**
|
| * Optional event messages that were generated during the job's execution.
|
| - * This also contains any warnings that were generated during import or
|
| - * export.
|
| + * This also contains any warnings that were generated during import
|
| + * or export.
|
| */
|
| core.List<OperationEvent> events;
|
| /**
|
| @@ -4542,33 +4812,54 @@ class OperationMetadata {
|
| }
|
|
|
| /**
|
| - * Defines an Identity and Access Management (IAM) policy. It is used to specify
|
| - * access control policies for Cloud Platform resources. A `Policy` consists of
|
| - * a list of `bindings`. A `Binding` binds a list of `members` to a `role`,
|
| - * where the members can be user accounts, Google groups, Google domains, and
|
| - * service accounts. A `role` is a named list of permissions defined by IAM.
|
| - * **Example** { "bindings": [ { "role": "roles/owner", "members": [
|
| - * "user:mike@example.com", "group:admins@example.com", "domain:google.com",
|
| - * "serviceAccount:my-other-app@appspot.gserviceaccount.com", ] }, { "role":
|
| - * "roles/viewer", "members": ["user:sean@example.com"] } ] } For a description
|
| - * of IAM and its features, see the [IAM developer's
|
| - * guide](https://cloud.google.com/iam).
|
| + * Defines an Identity and Access Management (IAM) policy. It is used to
|
| + * specify access control policies for Cloud Platform resources.
|
| + *
|
| + *
|
| + * A `Policy` consists of a list of `bindings`. A `Binding` binds a list of
|
| + * `members` to a `role`, where the members can be user accounts, Google groups,
|
| + * Google domains, and service accounts. A `role` is a named list of permissions
|
| + * defined by IAM.
|
| + *
|
| + * **Example**
|
| + *
|
| + * {
|
| + * "bindings": [
|
| + * {
|
| + * "role": "roles/owner",
|
| + * "members": [
|
| + * "user:mike@example.com",
|
| + * "group:admins@example.com",
|
| + * "domain:google.com",
|
| + * "serviceAccount:my-other-app@appspot.gserviceaccount.com",
|
| + * ]
|
| + * },
|
| + * {
|
| + * "role": "roles/viewer",
|
| + * "members": ["user:sean@example.com"]
|
| + * }
|
| + * ]
|
| + * }
|
| + *
|
| + * For a description of IAM and its features, see the
|
| + * [IAM developer's guide](https://cloud.google.com/iam).
|
| */
|
| class Policy {
|
| /**
|
| - * Associates a list of `members` to a `role`. Multiple `bindings` must not be
|
| - * specified for the same `role`. `bindings` with no members will result in an
|
| - * error.
|
| + * Associates a list of `members` to a `role`.
|
| + * Multiple `bindings` must not be specified for the same `role`.
|
| + * `bindings` with no members will result in an error.
|
| */
|
| core.List<Binding> bindings;
|
| /**
|
| - * `etag` is used for optimistic concurrency control as a way to help prevent
|
| - * simultaneous updates of a policy from overwriting each other. It is
|
| - * strongly suggested that systems make use of the `etag` in the
|
| + * `etag` is used for optimistic concurrency control as a way to help
|
| + * prevent simultaneous updates of a policy from overwriting each other.
|
| + * It is strongly suggested that systems make use of the `etag` in the
|
| * read-modify-write cycle to perform policy updates in order to avoid race
|
| * conditions: An `etag` is returned in the response to `getIamPolicy`, and
|
| * systems are expected to put that etag in the request to `setIamPolicy` to
|
| * ensure that their change will be applied to the same version of the policy.
|
| + *
|
| * If no `etag` is provided in the call to `setIamPolicy`, then the existing
|
| * policy is overwritten blindly.
|
| */
|
| @@ -4723,7 +5014,10 @@ class Program {
|
| class Range {
|
| /** The end position of the range on the reference, 0-based exclusive. */
|
| core.String end;
|
| - /** The reference sequence name, for example `chr1`, `1`, or `chrX`. */
|
| + /**
|
| + * 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. */
|
| core.String start;
|
| @@ -4759,63 +5053,108 @@ class Range {
|
|
|
| /**
|
| * 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. For more genomics resource
|
| - * definitions, see [Fundamentals of Google
|
| + * 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.
|
| + *
|
| + * For more genomics resource definitions, see [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - * ### Reverse-stranded reads Mapped reads (reads having a non-null `alignment`)
|
| - * can be aligned to either the forward or the reverse strand of their
|
| - * associated reference. Strandedness of a mapped read is encoded by
|
| - * `alignment.position.reverseStrand`. If we consider the reference to be a
|
| - * forward-stranded coordinate space of `[0, reference.length)` with `0` as the
|
| - * left-most position and `reference.length` as the right-most position, reads
|
| - * are always aligned left to right. That is, `alignment.position.position`
|
| - * always refers to the left-most reference coordinate and `alignment.cigar`
|
| - * describes the alignment of this read to the reference from left to right. All
|
| - * per-base fields such as `alignedSequence` and `alignedQuality` share this
|
| - * same left-to-right orientation; this is true of reads which are aligned to
|
| - * either strand. For reverse-stranded reads, this means that `alignedSequence`
|
| - * is the reverse complement of the bases that were originally reported by the
|
| - * sequencing machine. ### Generating a reference-aligned sequence string When
|
| - * interacting with mapped reads, it's often useful to produce a string
|
| + *
|
| + * ### Reverse-stranded reads
|
| + *
|
| + * Mapped reads (reads having a non-null `alignment`) can be aligned to either
|
| + * the forward or the reverse strand of their associated reference. Strandedness
|
| + * of a mapped read is encoded by `alignment.position.reverseStrand`.
|
| + *
|
| + * If we consider the reference to be a forward-stranded coordinate space of
|
| + * `[0, reference.length)` with `0` as the left-most position and
|
| + * `reference.length` as the right-most position, reads are always aligned left
|
| + * to right. That is, `alignment.position.position` always refers to the
|
| + * left-most reference coordinate and `alignment.cigar` describes the alignment
|
| + * of this read to the reference from left to right. All per-base fields such as
|
| + * `alignedSequence` and `alignedQuality` share this same left-to-right
|
| + * orientation; this is true of reads which are aligned to either strand. For
|
| + * reverse-stranded reads, this means that `alignedSequence` is the reverse
|
| + * complement of the bases that were originally reported by the sequencing
|
| + * machine.
|
| + *
|
| + * ### Generating a reference-aligned sequence string
|
| + *
|
| + * When interacting with mapped reads, it's often useful to produce a string
|
| * representing the local alignment of the read to reference. The following
|
| - * pseudocode demonstrates one way of doing this: out = "" offset = 0 for c in
|
| - * read.alignment.cigar { switch c.operation { case "ALIGNMENT_MATCH",
|
| - * "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out +=
|
| - * read.alignedSequence[offset:offset+c.operationLength] offset +=
|
| - * c.operationLength break case "CLIP_SOFT", "INSERT": offset +=
|
| - * c.operationLength break case "PAD": out += repeat("*", c.operationLength)
|
| - * break case "DELETE": out += repeat("-", c.operationLength) break case "SKIP":
|
| - * out += repeat(" ", c.operationLength) break case "CLIP_HARD": break } }
|
| - * return out ### Converting to SAM's CIGAR string The following pseudocode
|
| - * generates a SAM CIGAR string from the `cigar` field. Note that this is a
|
| - * lossy conversion (`cigar.referenceSequence` is lost). cigarMap = {
|
| - * "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N",
|
| - * "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=",
|
| - * "SEQUENCE_MISMATCH": "X", } cigarStr = "" for c in read.alignment.cigar {
|
| - * cigarStr += c.operationLength + cigarMap[c.operation] } return cigarStr
|
| + * pseudocode demonstrates one way of doing this:
|
| + *
|
| + * out = ""
|
| + * offset = 0
|
| + * for c in read.alignment.cigar {
|
| + * switch c.operation {
|
| + * case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH":
|
| + * out += read.alignedSequence[offset:offset+c.operationLength]
|
| + * offset += c.operationLength
|
| + * break
|
| + * case "CLIP_SOFT", "INSERT":
|
| + * offset += c.operationLength
|
| + * break
|
| + * case "PAD":
|
| + * out += repeat("*", c.operationLength)
|
| + * break
|
| + * case "DELETE":
|
| + * out += repeat("-", c.operationLength)
|
| + * break
|
| + * case "SKIP":
|
| + * out += repeat(" ", c.operationLength)
|
| + * break
|
| + * case "CLIP_HARD":
|
| + * break
|
| + * }
|
| + * }
|
| + * return out
|
| + *
|
| + * ### Converting to SAM's CIGAR string
|
| + *
|
| + * The following pseudocode generates a SAM CIGAR string from the
|
| + * `cigar` field. Note that this is a lossy conversion
|
| + * (`cigar.referenceSequence` is lost).
|
| + *
|
| + * cigarMap = {
|
| + * "ALIGNMENT_MATCH": "M",
|
| + * "INSERT": "I",
|
| + * "DELETE": "D",
|
| + * "SKIP": "N",
|
| + * "CLIP_SOFT": "S",
|
| + * "CLIP_HARD": "H",
|
| + * "PAD": "P",
|
| + * "SEQUENCE_MATCH": "=",
|
| + * "SEQUENCE_MISMATCH": "X",
|
| + * }
|
| + * cigarStr = ""
|
| + * for c in read.alignment.cigar {
|
| + * cigarStr += c.operationLength + cigarMap[c.operation]
|
| + * }
|
| + * return cigarStr
|
| */
|
| class Read {
|
| /**
|
| * The quality of the read sequence contained in this alignment record
|
| - * (equivalent to QUAL in SAM). `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,
|
| - * **without CIGAR operations applied** (equivalent to SEQ in SAM).
|
| + * (equivalent to QUAL in SAM).
|
| * `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,
|
| + * **without CIGAR operations applied** (equivalent to SEQ in SAM).
|
| + * `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 is null for
|
| @@ -4840,15 +5179,16 @@ class Read {
|
| core.String id;
|
| /**
|
| * A map of additional read alignment information. This must be of the form
|
| - * map (string key mapping to a list of string values).
|
| + * map<string, string[]> (string key mapping to a list of string values).
|
| *
|
| * The values for Object must be JSON objects. It can consist of `num`,
|
| * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| */
|
| core.Map<core.String, core.List<core.Object>> 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.
|
| + * 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). */
|
| @@ -4861,7 +5201,8 @@ class Read {
|
| /**
|
| * The ID of the read group this read belongs to. A read belongs to exactly
|
| * one read group. This is a server-generated ID which is distinct from SAM's
|
| - * RG tag (for that value, see ReadGroup.name).
|
| + * RG tag (for that value, see
|
| + * ReadGroup.name).
|
| */
|
| core.String readGroupId;
|
| /**
|
| @@ -4875,25 +5216,26 @@ class Read {
|
| */
|
| 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
|
| + * 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.
|
| + * 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.
|
| + * 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;
|
|
|
| @@ -5021,14 +5363,14 @@ class ReadGroup {
|
| /** The experiment used to generate this read group. */
|
| Experiment experiment;
|
| /**
|
| - * The server-generated read group ID, unique for all read groups. Note: This
|
| - * is different than the @RG ID field in the SAM spec. For that value, see
|
| - * name.
|
| + * The server-generated read group ID, unique for all read groups.
|
| + * Note: This is different than the @RG ID field in the SAM spec. For that
|
| + * value, see name.
|
| */
|
| core.String id;
|
| /**
|
| - * A map of additional read group information. This must be of the form map
|
| - * (string key mapping to a list of string values).
|
| + * A map of additional read group information. This must be of the form
|
| + * map<string, string[]> (string key mapping to a list of string values).
|
| *
|
| * The values for Object must be JSON objects. It can consist of `num`,
|
| * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| @@ -5046,7 +5388,8 @@ class ReadGroup {
|
| /**
|
| * 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.
|
| + * only the first read group in a returned set will have this field
|
| + * populated.
|
| */
|
| core.List<Program> programs;
|
| /** The reference set the reads in this read group are aligned to. */
|
| @@ -5129,9 +5472,13 @@ class ReadGroup {
|
| * 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. For more genomics
|
| - * resource definitions, see [Fundamentals of Google
|
| + * 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.
|
| + *
|
| + * For more genomics resource definitions, see [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| */
|
| class ReadGroupSet {
|
| @@ -5224,8 +5571,9 @@ class ReadGroupSet {
|
| * 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. For more genomics resource
|
| - * definitions, see [Fundamentals of Google
|
| + * reference belongs to one or more reference sets.
|
| + *
|
| + * For more genomics resource definitions, see [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| */
|
| class Reference {
|
| @@ -5234,8 +5582,8 @@ class Reference {
|
| /** 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
|
| + * 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;
|
| @@ -5310,15 +5658,15 @@ class Reference {
|
| }
|
|
|
| /**
|
| - * ReferenceBound records an upper bound for the starting coordinate of variants
|
| - * in a particular reference.
|
| + * ReferenceBound records an upper bound for the starting coordinate of
|
| + * variants in a particular reference.
|
| */
|
| class ReferenceBound {
|
| /** The name of the reference associated with this reference bound. */
|
| core.String referenceName;
|
| /**
|
| - * An upper bound (inclusive) on the starting coordinate of any variant in the
|
| - * reference sequence.
|
| + * An upper bound (inclusive) on the starting coordinate of any
|
| + * variant in the reference sequence.
|
| */
|
| core.String upperBound;
|
|
|
| @@ -5347,11 +5695,12 @@ class ReferenceBound {
|
|
|
| /**
|
| * 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. For more genomics resource definitions, see [Fundamentals of
|
| - * Google
|
| + * 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.
|
| + *
|
| + * For more genomics resource definitions, see [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| */
|
| class ReferenceSet {
|
| @@ -5366,9 +5715,9 @@ class ReferenceSet {
|
| /**
|
| * 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.
|
| + * `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;
|
| /**
|
| @@ -5452,8 +5801,9 @@ class ReferenceSet {
|
| }
|
|
|
| /**
|
| - * Runtime metadata that will be populated in the runtimeMetadata field of the
|
| - * Operation associated with a RunPipeline execution.
|
| + * Runtime metadata that will be populated in the
|
| + * runtimeMetadata
|
| + * field of the Operation associated with a RunPipeline execution.
|
| */
|
| class RuntimeMetadata {
|
| /** Execution information specific to Google Compute Engine. */
|
| @@ -5493,8 +5843,8 @@ class SearchAnnotationSetsRequest {
|
| */
|
| 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 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;
|
| @@ -5591,15 +5941,16 @@ class SearchAnnotationSetsResponse {
|
|
|
| class SearchAnnotationsRequest {
|
| /**
|
| - * Required. The annotation sets to search within. The caller must have `READ`
|
| - * access to these annotation sets. All queried annotation sets must have the
|
| - * same type.
|
| + * Required. The annotation sets to search within. The caller must have
|
| + * `READ` access to these annotation sets.
|
| + * All queried annotation sets must have the same type.
|
| */
|
| core.List<core.String> annotationSetIds;
|
| /**
|
| * The end position of the range on the reference, 0-based exclusive. If
|
| - * referenceId or referenceName must be specified, Defaults to the length of
|
| - * the reference.
|
| + * referenceId or
|
| + * referenceName
|
| + * must be specified, Defaults to the length of the reference.
|
| */
|
| core.String end;
|
| /**
|
| @@ -5608,8 +5959,8 @@ class SearchAnnotationsRequest {
|
| */
|
| 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 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;
|
| @@ -5622,7 +5973,10 @@ class SearchAnnotationsRequest {
|
| core.String referenceName;
|
| /**
|
| * The start position of the range on the reference, 0-based inclusive. If
|
| - * specified, referenceId or referenceName must be specified. Defaults to 0.
|
| + * specified,
|
| + * referenceId or
|
| + * referenceName
|
| + * must be specified. Defaults to 0.
|
| */
|
| core.String start;
|
|
|
| @@ -5725,8 +6079,8 @@ class SearchCallSetsRequest {
|
| */
|
| 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 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;
|
| @@ -5823,8 +6177,8 @@ class SearchReadGroupSetsRequest {
|
| */
|
| 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 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;
|
| @@ -5911,8 +6265,8 @@ class SearchReadsRequest {
|
| */
|
| 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 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;
|
| @@ -5997,10 +6351,10 @@ class SearchReadsRequest {
|
| /** 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 contiguously and are sorted in ascending
|
| - * lexicographic order by fragment name.
|
| + * 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 contiguously and are sorted in
|
| + * ascending lexicographic order by fragment name.
|
| */
|
| core.List<Read> alignments;
|
| /**
|
| @@ -6036,8 +6390,9 @@ class SearchReadsResponse {
|
| class SearchReferenceSetsRequest {
|
| /**
|
| * If present, return reference sets for which a prefix of any of
|
| - * sourceAccessions match any of these strings. Accession numbers typically
|
| - * have a main number and a version, for example `NC_000001.11`.
|
| + * sourceAccessions
|
| + * match any of these strings. Accession numbers typically have a main number
|
| + * and a version, for example `NC_000001.11`.
|
| */
|
| core.List<core.String> accessions;
|
| /**
|
| @@ -6046,8 +6401,8 @@ class SearchReferenceSetsRequest {
|
| */
|
| core.String assemblyId;
|
| /**
|
| - * If present, return reference sets for which the md5checksum matches
|
| - * exactly.
|
| + * If present, return reference sets for which the
|
| + * md5checksum matches exactly.
|
| */
|
| core.List<core.String> md5checksums;
|
| /**
|
| @@ -6056,8 +6411,8 @@ class SearchReferenceSetsRequest {
|
| */
|
| 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 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;
|
| @@ -6138,13 +6493,15 @@ class SearchReferenceSetsResponse {
|
|
|
| class SearchReferencesRequest {
|
| /**
|
| - * If present, return references for which a prefix of any of sourceAccessions
|
| - * match any of these strings. Accession numbers typically have a main number
|
| - * and a version, for example `GCF_000001405.26`.
|
| + * If present, return references for which a prefix of any of
|
| + * sourceAccessions match
|
| + * any of these strings. Accession numbers typically have a main number and a
|
| + * version, for example `GCF_000001405.26`.
|
| */
|
| core.List<core.String> accessions;
|
| /**
|
| - * If present, return references for which the md5checksum matches exactly.
|
| + * If present, return references for which the
|
| + * md5checksum matches exactly.
|
| */
|
| core.List<core.String> md5checksums;
|
| /**
|
| @@ -6153,8 +6510,8 @@ class SearchReferencesRequest {
|
| */
|
| 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 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;
|
| @@ -6248,8 +6605,8 @@ class SearchVariantSetsRequest {
|
| */
|
| 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 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;
|
| @@ -6320,9 +6677,9 @@ class SearchVariantSetsResponse {
|
| /** 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. If a variant has no calls belonging
|
| - * to any of these call sets, it won't be returned at all.
|
| + * Only return variant calls which belong to call sets with these ids.
|
| + * Leaving this blank returns all variant calls. If a variant has no
|
| + * calls belonging to any of these call sets, it won't be returned at all.
|
| */
|
| core.List<core.String> callSetIds;
|
| /**
|
| @@ -6343,16 +6700,16 @@ class SearchVariantsRequest {
|
| */
|
| 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 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;
|
| /** Required. Only return variants in this reference sequence. */
|
| core.String referenceName;
|
| /**
|
| - * The beginning of the window (0-based, inclusive) for which overlapping
|
| - * variants should be returned. If unspecified, defaults to 0.
|
| + * The beginning of the window (0-based, inclusive) for which
|
| + * overlapping variants should be returned. If unspecified, defaults to 0.
|
| */
|
| core.String start;
|
| /** Only return variants which have exactly this name. */
|
| @@ -6467,8 +6824,9 @@ class SearchVariantsResponse {
|
| class SetIamPolicyRequest {
|
| /**
|
| * REQUIRED: The complete policy to be applied to the `resource`. The size of
|
| - * the policy is limited to a few 10s of KB. An empty policy is a valid policy
|
| - * but certain Cloud Platform services (such as Projects) might reject them.
|
| + * the policy is limited to a few 10s of KB. An empty policy is a
|
| + * valid policy but certain Cloud Platform services (such as Projects)
|
| + * might reject them.
|
| */
|
| Policy policy;
|
|
|
| @@ -6491,45 +6849,66 @@ class SetIamPolicyRequest {
|
|
|
| /**
|
| * The `Status` type defines a logical error model that is suitable for
|
| - * different programming environments, including REST APIs and RPC APIs. It is
|
| - * used by [gRPC](https://github.com/grpc). The error model is designed to be: -
|
| - * Simple to use and understand for most users - Flexible enough to meet
|
| - * unexpected needs # Overview The `Status` message contains three pieces of
|
| - * data: error code, error message, and error details. The error code should be
|
| - * an enum value of google.rpc.Code, but it may accept additional error codes if
|
| - * needed. The error message should be a developer-facing English message that
|
| - * helps developers *understand* and *resolve* the error. If a localized
|
| - * user-facing error message is needed, put the localized message in the error
|
| - * details or localize it in the client. The optional error details may contain
|
| - * arbitrary information about the error. There is a predefined set of error
|
| - * detail types in the package `google.rpc` which can be used for common error
|
| - * conditions. # Language mapping The `Status` message is the logical
|
| - * representation of the error model, but it is not necessarily the actual wire
|
| - * format. When the `Status` message is exposed in different client libraries
|
| - * and different wire protocols, it can be mapped differently. For example, it
|
| - * will likely be mapped to some exceptions in Java, but more likely mapped to
|
| - * some error codes in C. # Other uses The error model and the `Status` message
|
| - * can be used in a variety of environments, either with or without APIs, to
|
| - * provide a consistent developer experience across different environments.
|
| - * Example uses of this error model include: - Partial errors. If a service
|
| - * needs to return partial errors to the client, it may embed the `Status` in
|
| - * the normal response to indicate the partial errors. - Workflow errors. A
|
| - * typical workflow has multiple steps. Each step may have a `Status` message
|
| - * for error reporting purpose. - Batch operations. If a client uses batch
|
| - * request and batch response, the `Status` message should be used directly
|
| - * inside batch response, one for each error sub-response. - Asynchronous
|
| - * operations. If an API call embeds asynchronous operation results in its
|
| - * response, the status of those operations should be represented directly using
|
| - * the `Status` message. - Logging. If some API errors are stored in logs, the
|
| - * message `Status` could be used directly after any stripping needed for
|
| - * security/privacy reasons.
|
| + * different
|
| + * programming environments, including REST APIs and RPC APIs. It is used by
|
| + * [gRPC](https://github.com/grpc). The error model is designed to be:
|
| + *
|
| + * - Simple to use and understand for most users
|
| + * - Flexible enough to meet unexpected needs
|
| + *
|
| + * # Overview
|
| + *
|
| + * The `Status` message contains three pieces of data: error code, error
|
| + * message,
|
| + * and error details. The error code should be an enum value of
|
| + * google.rpc.Code, but it may accept additional error codes if needed. The
|
| + * error message should be a developer-facing English message that helps
|
| + * developers *understand* and *resolve* the error. If a localized user-facing
|
| + * error message is needed, put the localized message in the error details or
|
| + * localize it in the client. The optional error details may contain arbitrary
|
| + * information about the error. There is a predefined set of error detail types
|
| + * in the package `google.rpc` which can be used for common error conditions.
|
| + *
|
| + * # Language mapping
|
| + *
|
| + * The `Status` message is the logical representation of the error model, but it
|
| + * is not necessarily the actual wire format. When the `Status` message is
|
| + * exposed in different client libraries and different wire protocols, it can be
|
| + * mapped differently. For example, it will likely be mapped to some exceptions
|
| + * in Java, but more likely mapped to some error codes in C.
|
| + *
|
| + * # Other uses
|
| + *
|
| + * The error model and the `Status` message can be used in a variety of
|
| + * environments, either with or without APIs, to provide a
|
| + * consistent developer experience across different environments.
|
| + *
|
| + * Example uses of this error model include:
|
| + *
|
| + * - Partial errors. If a service needs to return partial errors to the client,
|
| + * it may embed the `Status` in the normal response to indicate the partial
|
| + * errors.
|
| + *
|
| + * - Workflow errors. A typical workflow has multiple steps. Each step may
|
| + * have a `Status` message for error reporting purpose.
|
| + *
|
| + * - Batch operations. If a client uses batch request and batch response, the
|
| + * `Status` message should be used directly inside batch response, one for
|
| + * each error sub-response.
|
| + *
|
| + * - Asynchronous operations. If an API call embeds asynchronous operation
|
| + * results in its response, the status of those operations should be
|
| + * represented directly using the `Status` message.
|
| + *
|
| + * - Logging. If some API errors are stored in logs, the message `Status` could
|
| + * be used directly after any stripping needed for security/privacy reasons.
|
| */
|
| class Status {
|
| /** The status code, which should be an enum value of google.rpc.Code. */
|
| core.int code;
|
| /**
|
| - * A list of messages that carry the error details. There will be a common set
|
| - * of message types for APIs to use.
|
| + * A list of messages that carry the error details. There will be a
|
| + * common set of message types for APIs to use.
|
| *
|
| * The values for Object must be JSON objects. It can consist of `num`,
|
| * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| @@ -6571,229 +6950,20 @@ class Status {
|
| }
|
| }
|
|
|
| -/** The stream reads request. */
|
| -class StreamReadsRequest {
|
| - /**
|
| - * The end position of the range on the reference, 0-based exclusive. If
|
| - * specified, `referenceName` must also be specified.
|
| - */
|
| - core.String end;
|
| - /**
|
| - * The Google Cloud project ID which will be billed for this access. The
|
| - * caller must have WRITE access to this project. Required.
|
| - */
|
| - core.String projectId;
|
| - /** The ID of the read group set from which to stream reads. */
|
| - core.String readGroupSetId;
|
| - /**
|
| - * The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to
|
| - * *, only unmapped reads are returned.
|
| - */
|
| - core.String referenceName;
|
| - /**
|
| - * Restricts results to a shard containing approximately `1/totalShards` of
|
| - * the normal response payload for this query. Results from a sharded request
|
| - * are disjoint from those returned by all queries which differ only in their
|
| - * shard parameter. A shard may yield 0 results; this is especially likely for
|
| - * large values of `totalShards`. Valid values are `[0, totalShards)`.
|
| - */
|
| - core.int shard;
|
| - /**
|
| - * The start position of the range on the reference, 0-based inclusive. If
|
| - * specified, `referenceName` must also be specified.
|
| - */
|
| - core.String start;
|
| - /**
|
| - * Specifying `totalShards` causes a disjoint subset of the normal response
|
| - * payload to be returned for each query with a unique `shard` parameter
|
| - * specified. A best effort is made to yield equally sized shards. Sharding
|
| - * can be used to distribute processing amongst workers, where each worker is
|
| - * assigned a unique `shard` number and all workers specify the same
|
| - * `totalShards` number. The union of reads returned for all sharded queries
|
| - * `[0, totalShards)` is equal to those returned by a single unsharded query.
|
| - * Queries for different values of `totalShards` with common divisors will
|
| - * share shard boundaries. For example, streaming `shard` 2 of 5 `totalShards`
|
| - * yields the same results as streaming `shard`s 4 and 5 of 10 `totalShards`.
|
| - * This property can be leveraged for adaptive retries.
|
| - */
|
| - core.int totalShards;
|
| -
|
| - StreamReadsRequest();
|
| -
|
| - StreamReadsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| - }
|
| - if (_json.containsKey("readGroupSetId")) {
|
| - readGroupSetId = _json["readGroupSetId"];
|
| - }
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| - }
|
| - if (_json.containsKey("shard")) {
|
| - shard = _json["shard"];
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| - }
|
| - if (_json.containsKey("totalShards")) {
|
| - totalShards = _json["totalShards"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| - }
|
| - if (readGroupSetId != null) {
|
| - _json["readGroupSetId"] = readGroupSetId;
|
| - }
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| - }
|
| - if (shard != null) {
|
| - _json["shard"] = shard;
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| - if (totalShards != null) {
|
| - _json["totalShards"] = totalShards;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class StreamReadsResponse {
|
| - core.List<Read> alignments;
|
| -
|
| - StreamReadsResponse();
|
| -
|
| - StreamReadsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("alignments")) {
|
| - alignments = _json["alignments"].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();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The stream variants request. */
|
| -class StreamVariantsRequest {
|
| - /**
|
| - * Only return variant calls which belong to call sets with these IDs. Leaving
|
| - * this blank returns all variant calls.
|
| - */
|
| - core.List<core.String> callSetIds;
|
| - /**
|
| - * The end of the window (0-based, exclusive) for which overlapping variants
|
| - * should be returned.
|
| - */
|
| - core.String end;
|
| - /**
|
| - * The Google Cloud project ID which will be billed for this access. The
|
| - * caller must have WRITE access to this project. Required.
|
| - */
|
| - core.String projectId;
|
| - /** Required. Only return variants in this reference sequence. */
|
| - core.String referenceName;
|
| - /**
|
| - * The beginning of the window (0-based, inclusive) for which overlapping
|
| - * variants should be returned.
|
| - */
|
| - core.String start;
|
| - /** The variant set ID from which to stream variants. */
|
| - core.String variantSetId;
|
| -
|
| - StreamVariantsRequest();
|
| -
|
| - StreamVariantsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("callSetIds")) {
|
| - callSetIds = _json["callSetIds"];
|
| - }
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| - }
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| - }
|
| - if (_json.containsKey("variantSetId")) {
|
| - variantSetId = _json["variantSetId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (callSetIds != null) {
|
| - _json["callSetIds"] = callSetIds;
|
| - }
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| - }
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| - if (variantSetId != null) {
|
| - _json["variantSetId"] = variantSetId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class StreamVariantsResponse {
|
| - core.List<Variant> variants;
|
| -
|
| - StreamVariantsResponse();
|
| -
|
| - StreamVariantsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("variants")) {
|
| - variants = _json["variants"].map((value) => new Variant.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (variants != null) {
|
| - _json["variants"] = variants.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| /** Request message for `TestIamPermissions` method. */
|
| class TestIamPermissionsRequest {
|
| /**
|
| - * REQUIRED: The set of permissions to check for the 'resource'. Permissions
|
| - * with wildcards (such as '*' or 'storage.*') are not allowed. Allowed
|
| - * permissions are: * `genomics.datasets.create` * `genomics.datasets.delete`
|
| - * * `genomics.datasets.get` * `genomics.datasets.list` *
|
| - * `genomics.datasets.update` * `genomics.datasets.getIamPolicy` *
|
| - * `genomics.datasets.setIamPolicy`
|
| + * REQUIRED: The set of permissions to check for the 'resource'.
|
| + * Permissions with wildcards (such as '*' or 'storage.*') are not allowed.
|
| + * Allowed permissions are:
|
| + *
|
| + * * `genomics.datasets.create`
|
| + * * `genomics.datasets.delete`
|
| + * * `genomics.datasets.get`
|
| + * * `genomics.datasets.list`
|
| + * * `genomics.datasets.update`
|
| + * * `genomics.datasets.getIamPolicy`
|
| + * * `genomics.datasets.setIamPolicy`
|
| */
|
| core.List<core.String> permissions;
|
|
|
| @@ -6847,25 +7017,34 @@ class Transcript {
|
| /**
|
| * The range of the coding sequence for this transcript, if any. To determine
|
| * the exact ranges of coding sequence, intersect this range with those of the
|
| - * exons, if any. If there are any exons, the codingSequence must start and
|
| - * end within them. Note that in some cases, the reference genome will not
|
| - * exactly match the observed mRNA transcript e.g. due to variance in the
|
| - * source genome from reference. In these cases, exon.frame will not
|
| - * necessarily match the expected reference reading frame and coding exon
|
| - * reference bases cannot necessarily be concatenated to produce the original
|
| - * transcript mRNA.
|
| + * exons, if any. If there are any
|
| + * exons, the
|
| + * codingSequence must start
|
| + * and end within them.
|
| + *
|
| + * Note that in some cases, the reference genome will not exactly match the
|
| + * observed mRNA transcript e.g. due to variance in the source genome from
|
| + * reference. In these cases,
|
| + * exon.frame will not necessarily
|
| + * match the expected reference reading frame and coding exon reference bases
|
| + * cannot necessarily be concatenated to produce the original transcript mRNA.
|
| */
|
| CodingSequence codingSequence;
|
| /**
|
| - * The exons that compose this transcript. This field should be unset for
|
| - * genomes where transcript splicing does not occur, for example prokaryotes.
|
| - * Introns are regions of the transcript that are not included in the spliced
|
| - * RNA product. Though not explicitly modeled here, intron ranges can be
|
| - * deduced; all regions of this transcript that are not exons are introns.
|
| - * Exonic sequences do not necessarily code for a translational product (amino
|
| - * acids). Only the regions of exons bounded by the codingSequence correspond
|
| - * to coding DNA sequence. Exons are ordered by start position and may not
|
| - * overlap.
|
| + * The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose
|
| + * this transcript. This field should be unset for genomes where transcript
|
| + * splicing does not occur, for example prokaryotes.
|
| + *
|
| + * Introns are regions of the transcript that are not included in the
|
| + * spliced RNA product. Though not explicitly modeled here, intron ranges can
|
| + * be deduced; all regions of this transcript that are not exons are introns.
|
| + *
|
| + * Exonic sequences do not necessarily code for a translational product
|
| + * (amino acids). Only the regions of exons bounded by the
|
| + * codingSequence correspond
|
| + * to coding DNA sequence.
|
| + *
|
| + * Exons are ordered by start position and may not overlap.
|
| */
|
| core.List<Exon> exons;
|
| /**
|
| @@ -6918,9 +7097,11 @@ class UndeleteDatasetRequest {
|
| /**
|
| * 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. For more genomics resource definitions, see
|
| - * [Fundamentals of Google
|
| + * Variants belong to a variant set.
|
| + *
|
| + * For more genomics resource definitions, see [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + *
|
| * 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
|
| @@ -6939,9 +7120,9 @@ class Variant {
|
| 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 - start). This is useful for variants that don't
|
| - * explicitly give alternate bases, for example large deletions.
|
| + * base after the last base in the reference allele. So, the length of
|
| + * the reference allele is (end - start). This is useful for variants
|
| + * that don't explicitly give alternate bases, for example large deletions.
|
| */
|
| core.String end;
|
| /**
|
| @@ -6952,8 +7133,8 @@ class Variant {
|
| /** The server-generated variant ID, unique across all variants. */
|
| core.String id;
|
| /**
|
| - * A map of additional variant information. This must be of the form map
|
| - * (string key mapping to a list of string values).
|
| + * A map of additional variant information. This must be of the form
|
| + * map<string, string[]> (string key mapping to a list of string values).
|
| *
|
| * The values for Object must be JSON objects. It can consist of `num`,
|
| * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| @@ -6962,19 +7143,23 @@ class Variant {
|
| /** Names for the variant, for example a RefSNP ID. */
|
| core.List<core.String> names;
|
| /**
|
| - * A measure of how likely this variant is to be real. A higher value is
|
| - * better.
|
| + * A measure of how likely this variant is to be real.
|
| + * A higher value is better.
|
| */
|
| core.double quality;
|
| /**
|
| - * The reference bases for this variant. They start at the given position.
|
| + * The reference bases for this variant. They start at the given
|
| + * position.
|
| */
|
| core.String referenceBases;
|
| - /** The reference on which this variant occurs. (such as `chr20` or `X`) */
|
| + /**
|
| + * The reference on which this variant occurs.
|
| + * (such as `chr20` or `X`)
|
| + */
|
| core.String referenceName;
|
| /**
|
| - * The position at which this variant occurs (0-based). This corresponds to
|
| - * the first base of the string of reference bases.
|
| + * The position at which this variant occurs (0-based).
|
| + * This corresponds to the first base of the string of reference bases.
|
| */
|
| core.String start;
|
| /** The ID of the variant set this variant belongs to. */
|
| @@ -7071,55 +7256,75 @@ class Variant {
|
|
|
| class VariantAnnotation {
|
| /**
|
| - * The alternate allele for this variant. If multiple alternate alleles exist
|
| - * at this location, create a separate variant for each one, as they may
|
| - * represent distinct conditions.
|
| + * The alternate allele for this variant. If multiple alternate alleles
|
| + * exist at this location, create a separate variant for each one, as they
|
| + * may represent distinct conditions.
|
| */
|
| core.String alternateBases;
|
| /**
|
| - * Describes the clinical significance of a variant. It is adapted from the
|
| - * ClinVar controlled vocabulary for clinical significance described at:
|
| + * Describes the clinical significance of a variant.
|
| + * It is adapted from the ClinVar controlled vocabulary for clinical
|
| + * significance described at:
|
| * http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
|
| * Possible string values are:
|
| - * - "CLINICAL_SIGNIFICANCE_UNSPECIFIED" : A
|
| - * CLINICAL_SIGNIFICANCE_UNSPECIFIED.
|
| - * - "CLINICAL_SIGNIFICANCE_OTHER" : A CLINICAL_SIGNIFICANCE_OTHER.
|
| - * - "UNCERTAIN" : A UNCERTAIN.
|
| - * - "BENIGN" : A BENIGN.
|
| - * - "LIKELY_BENIGN" : A LIKELY_BENIGN.
|
| - * - "LIKELY_PATHOGENIC" : A LIKELY_PATHOGENIC.
|
| - * - "PATHOGENIC" : A PATHOGENIC.
|
| - * - "DRUG_RESPONSE" : A DRUG_RESPONSE.
|
| - * - "HISTOCOMPATIBILITY" : A HISTOCOMPATIBILITY.
|
| - * - "CONFERS_SENSITIVITY" : A CONFERS_SENSITIVITY.
|
| - * - "RISK_FACTOR" : A RISK_FACTOR.
|
| - * - "ASSOCIATION" : A ASSOCIATION.
|
| - * - "PROTECTIVE" : A PROTECTIVE.
|
| - * - "MULTIPLE_REPORTED" : A MULTIPLE_REPORTED.
|
| + * - "CLINICAL_SIGNIFICANCE_UNSPECIFIED"
|
| + * - "CLINICAL_SIGNIFICANCE_OTHER" : `OTHER` should be used when no other
|
| + * clinical significance
|
| + * value will suffice.
|
| + * - "UNCERTAIN"
|
| + * - "BENIGN"
|
| + * - "LIKELY_BENIGN"
|
| + * - "LIKELY_PATHOGENIC"
|
| + * - "PATHOGENIC"
|
| + * - "DRUG_RESPONSE"
|
| + * - "HISTOCOMPATIBILITY"
|
| + * - "CONFERS_SENSITIVITY"
|
| + * - "RISK_FACTOR"
|
| + * - "ASSOCIATION"
|
| + * - "PROTECTIVE"
|
| + * - "MULTIPLE_REPORTED" : `MULTIPLE_REPORTED` should be used when multiple
|
| + * clinical
|
| + * signficances are reported for a variant. The original clinical
|
| + * significance values may be provided in the `info` field.
|
| */
|
| core.String clinicalSignificance;
|
| /**
|
| - * The set of conditions associated with this variant. A condition describes
|
| - * the way a variant influences human health.
|
| + * The set of conditions associated with this variant.
|
| + * A condition describes the way a variant influences human health.
|
| */
|
| core.List<ClinicalCondition> conditions;
|
| /**
|
| * Effect of the variant on the coding sequence.
|
| * Possible string values are:
|
| - * - "EFFECT_UNSPECIFIED" : A EFFECT_UNSPECIFIED.
|
| - * - "EFFECT_OTHER" : A EFFECT_OTHER.
|
| - * - "FRAMESHIFT" : A FRAMESHIFT.
|
| - * - "FRAME_PRESERVING_INDEL" : A FRAME_PRESERVING_INDEL.
|
| - * - "SYNONYMOUS_SNP" : A SYNONYMOUS_SNP.
|
| - * - "NONSYNONYMOUS_SNP" : A NONSYNONYMOUS_SNP.
|
| - * - "STOP_GAIN" : A STOP_GAIN.
|
| - * - "STOP_LOSS" : A STOP_LOSS.
|
| - * - "SPLICE_SITE_DISRUPTION" : A SPLICE_SITE_DISRUPTION.
|
| + * - "EFFECT_UNSPECIFIED"
|
| + * - "EFFECT_OTHER" : `EFFECT_OTHER` should be used when no other Effect
|
| + * will suffice.
|
| + * - "FRAMESHIFT" : `FRAMESHIFT` indicates a mutation in which the insertion
|
| + * or
|
| + * deletion of nucleotides resulted in a frameshift change.
|
| + * - "FRAME_PRESERVING_INDEL" : `FRAME_PRESERVING_INDEL` indicates a mutation
|
| + * in which a
|
| + * multiple of three nucleotides has been inserted or deleted, resulting
|
| + * in no change to the reading frame of the coding sequence.
|
| + * - "SYNONYMOUS_SNP" : `SYNONYMOUS_SNP` indicates a single nucleotide
|
| + * polymorphism
|
| + * mutation that results in no amino acid change.
|
| + * - "NONSYNONYMOUS_SNP" : `NONSYNONYMOUS_SNP` indicates a single nucleotide
|
| + * polymorphism mutation that results in an amino acid change.
|
| + * - "STOP_GAIN" : `STOP_GAIN` indicates a mutation that leads to the creation
|
| + * of a stop codon at the variant site. Frameshift mutations creating
|
| + * downstream stop codons do not count as `STOP_GAIN`.
|
| + * - "STOP_LOSS" : `STOP_LOSS` indicates a mutation that eliminates a
|
| + * stop codon at the variant site.
|
| + * - "SPLICE_SITE_DISRUPTION" : `SPLICE_SITE_DISRUPTION` indicates that this
|
| + * variant is
|
| + * found in a splice site for the associated transcript, and alters the
|
| + * normal splicing pattern.
|
| */
|
| core.String effect;
|
| /**
|
| - * Google annotation ID of the gene affected by this variant. This should be
|
| - * provided when the variant is created.
|
| + * Google annotation ID of the gene affected by this variant. This should
|
| + * be provided when the variant is created.
|
| */
|
| core.String geneId;
|
| /**
|
| @@ -7130,14 +7335,19 @@ class VariantAnnotation {
|
| /**
|
| * Type has been adapted from ClinVar's list of variant types.
|
| * Possible string values are:
|
| - * - "TYPE_UNSPECIFIED" : A TYPE_UNSPECIFIED.
|
| - * - "TYPE_OTHER" : A TYPE_OTHER.
|
| - * - "INSERTION" : A INSERTION.
|
| - * - "DELETION" : A DELETION.
|
| - * - "SUBSTITUTION" : A SUBSTITUTION.
|
| - * - "SNP" : A SNP.
|
| - * - "STRUCTURAL" : A STRUCTURAL.
|
| - * - "CNV" : A CNV.
|
| + * - "TYPE_UNSPECIFIED"
|
| + * - "TYPE_OTHER" : `TYPE_OTHER` should be used when no other Type will
|
| + * suffice.
|
| + * Further explanation of the variant type may be included in the
|
| + * info field.
|
| + * - "INSERTION" : `INSERTION` indicates an insertion.
|
| + * - "DELETION" : `DELETION` indicates a deletion.
|
| + * - "SUBSTITUTION" : `SUBSTITUTION` indicates a block substitution of
|
| + * two or more nucleotides.
|
| + * - "SNP" : `SNP` indicates a single nucleotide polymorphism.
|
| + * - "STRUCTURAL" : `STRUCTURAL` indicates a large structural variant,
|
| + * including chromosomal fusions, inversions, etc.
|
| + * - "CNV" : `CNV` indicates a variation in copy number.
|
| */
|
| core.String type;
|
|
|
| @@ -7197,8 +7407,8 @@ class VariantAnnotation {
|
| /**
|
| * 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 call set with the name NA12345.
|
| + * 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 VariantCall {
|
| /** The ID of the call set this variant call belongs to. */
|
| @@ -7207,38 +7417,42 @@ class VariantCall {
|
| 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` 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` is present. If a genotype is
|
| - * not called (that is, a `.` is present in the GT string) -1 is returned.
|
| + * of the `referenceBases` field or a 1-based index into
|
| + * `alternateBases`. If a 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` 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;
|
| /**
|
| - * The genotype likelihoods for this variant call. Each array entry represents
|
| - * how likely a specific genotype is for this call. The value ordering is
|
| - * defined by the GL tag in the VCF spec. If Phred-scaled genotype likelihood
|
| - * scores (PL) are available and log10(P) genotype likelihood scores (GL) are
|
| - * not, PL scores are converted to GL scores. If both are available, PL scores
|
| - * are stored in `info`.
|
| + * The genotype likelihoods for this variant call. Each array entry
|
| + * represents how likely a specific genotype is for this call. The value
|
| + * ordering is defined by the GL tag in the VCF spec.
|
| + * If Phred-scaled genotype likelihood scores (PL) are available and
|
| + * log10(P) genotype likelihood scores (GL) are not, PL scores are converted
|
| + * to GL scores. If both are available, PL scores are stored in `info`.
|
| */
|
| core.List<core.double> genotypeLikelihood;
|
| /**
|
| - * A map of additional variant call information. This must be of the form map
|
| - * (string key mapping to a list of string values).
|
| + * A map of additional variant call information. This must be of the form
|
| + * map<string, string[]> (string key mapping to a list of string values).
|
| *
|
| * The values for Object must be JSON objects. It can consist of `num`,
|
| * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| */
|
| core.Map<core.String, core.List<core.Object>> info;
|
| /**
|
| - * 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 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 `*`.
|
| + * 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 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;
|
|
|
| @@ -7291,8 +7505,9 @@ class VariantCall {
|
|
|
| /**
|
| * 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. For more
|
| - * genomics resource definitions, see [Fundamentals of Google
|
| + * statistics of those contents. A variant set belongs to a dataset.
|
| + *
|
| + * For more genomics resource definitions, see [Fundamentals of Google
|
| * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| */
|
| class VariantSet {
|
| @@ -7307,8 +7522,8 @@ class VariantSet {
|
| /** User-specified, mutable name. */
|
| core.String name;
|
| /**
|
| - * A list of all references used by the variants in a variant set with
|
| - * associated coordinate upper bounds for each one.
|
| + * 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;
|
| /**
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| @@ -7316,11 +7531,12 @@ class VariantSet {
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| * describes the alignment provenance of the variant set, while the
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| * `referenceBounds` describe the shape of the actual variant data. The
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| * reference set's reference names are a superset of those found in the
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| - * `referenceBounds`. For example, given a variant set that is mapped to the
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| - * GRCh38 reference set and contains a single variant on reference 'X',
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| - * `referenceBounds` would contain only an entry for 'X', while the associated
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| - * reference set enumerates all possible references: '1', '2', 'X', 'Y', 'MT',
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| - * etc.
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| + * `referenceBounds`.
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| + *
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| + * For example, given a variant set that is mapped to the GRCh38 reference set
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| + * and contains a single variant on reference 'X', `referenceBounds` would
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| + * contain only an entry for 'X', while the associated reference set
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| + * enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
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| */
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| core.String referenceSetId;
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|
|
| @@ -7378,22 +7594,23 @@ class VariantSet {
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| }
|
|
|
| /**
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| - * Metadata describes a single piece of variant call metadata. These data
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| - * include a top level key and either a single value string (value) or a list of
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| - * key-value pairs (info.) Value and info are mutually exclusive.
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| + * Metadata describes a single piece of variant call metadata.
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| + * These data include a top level key and either a single value string (value)
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| + * or a list of key-value pairs (info.)
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| + * Value and info are mutually exclusive.
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| */
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| class VariantSetMetadata {
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| /** A textual description of this metadata. */
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| core.String description;
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| /**
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| - * User-provided ID field, not enforced by this API. Two or more pieces of
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| - * structured metadata with identical id and key fields are considered
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| - * equivalent.
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| + * User-provided ID field, not enforced by this API.
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| + * Two or more pieces of structured metadata with identical
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| + * id and key fields are considered equivalent.
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| */
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| core.String id;
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| /**
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| - * Remaining structured metadata key-value pairs. This must be of the form map
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| - * (string key mapping to a list of string values).
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| + * Remaining structured metadata key-value pairs. This must be of the form
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| + * map<string, string[]> (string key mapping to a list of string values).
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| *
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| * The values for Object must be JSON objects. It can consist of `num`,
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| * `String`, `bool` and `null` as well as `Map` and `List` values.
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| @@ -7407,15 +7624,15 @@ class VariantSetMetadata {
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| */
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| core.String number;
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| /**
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| - * The type of data. Possible types include: Integer, Float, Flag, Character,
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| - * and String.
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| + * The type of data. Possible types include: Integer, Float,
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| + * Flag, Character, and String.
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| * Possible string values are:
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| - * - "TYPE_UNSPECIFIED" : A TYPE_UNSPECIFIED.
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| - * - "INTEGER" : A INTEGER.
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| - * - "FLOAT" : A FLOAT.
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| - * - "FLAG" : A FLAG.
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| - * - "CHARACTER" : A CHARACTER.
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| - * - "STRING" : A STRING.
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| + * - "TYPE_UNSPECIFIED"
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| + * - "INTEGER"
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| + * - "FLOAT"
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| + * - "FLAG"
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| + * - "CHARACTER"
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| + * - "STRING"
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| */
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| core.String type;
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| /** The value field for simple metadata */
|
|
|
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