* An API to store, process, explore, and share genomic data. It supports * reference-based alignments, genetic variants, and reference genomes. This API * provides an implementation of the Global Alliance for Genomics and Health * (GA4GH) v0.5.1 API as well as several extensions.

* *

* For more information about this service, see the API * Documentation *

* * @author Google, Inc. */ class Google_Service_Genomics extends Google_Service { /** View and manage your data in Google BigQuery. */ const BIGQUERY = "https://www.googleapis.com/auth/bigquery"; /** View and manage your data across Google Cloud Platform services. */ const CLOUD_PLATFORM = "https://www.googleapis.com/auth/cloud-platform"; /** Manage your data in Google Cloud Storage. */ const DEVSTORAGE_READ_WRITE = "https://www.googleapis.com/auth/devstorage.read_write"; /** View and manage Genomics data. */ const GENOMICS = "https://www.googleapis.com/auth/genomics"; /** View Genomics data. */ const GENOMICS_READONLY = "https://www.googleapis.com/auth/genomics.readonly"; public $callsets; public $datasets; public $operations; public $readgroupsets; public $readgroupsets_coveragebuckets; public $reads; public $references; public $references_bases; public $referencesets; public $variants; public $variantsets; /** * Constructs the internal representation of the Genomics service. * * @param Google_Client $client */ public function __construct(Google_Client $client) { parent::__construct($client); $this->rootUrl = 'https://genomics.googleapis.com/'; $this->servicePath = ''; $this->version = 'v1'; $this->serviceName = 'genomics'; $this->callsets = new Google_Service_Genomics_Callsets_Resource( $this, $this->serviceName, 'callsets', array( 'methods' => array( 'create' => array( 'path' => 'v1/callsets', 'httpMethod' => 'POST', 'parameters' => array(), ),'delete' => array( 'path' => 'v1/callsets/{callSetId}', 'httpMethod' => 'DELETE', 'parameters' => array( 'callSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'get' => array( 'path' => 'v1/callsets/{callSetId}', 'httpMethod' => 'GET', 'parameters' => array( 'callSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'patch' => array( 'path' => 'v1/callsets/{callSetId}', 'httpMethod' => 'PATCH', 'parameters' => array( 'callSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), 'updateMask' => array( 'location' => 'query', 'type' => 'string', ), ), ),'search' => array( 'path' => 'v1/callsets/search', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); $this->datasets = new Google_Service_Genomics_Datasets_Resource( $this, $this->serviceName, 'datasets', array( 'methods' => array( 'create' => array( 'path' => 'v1/datasets', 'httpMethod' => 'POST', 'parameters' => array(), ),'delete' => array( 'path' => 'v1/datasets/{datasetId}', 'httpMethod' => 'DELETE', 'parameters' => array( 'datasetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'get' => array( 'path' => 'v1/datasets/{datasetId}', 'httpMethod' => 'GET', 'parameters' => array( 'datasetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'getIamPolicy' => array( 'path' => 'v1/{+resource}:getIamPolicy', 'httpMethod' => 'POST', 'parameters' => array( 'resource' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'list' => array( 'path' => 'v1/datasets', 'httpMethod' => 'GET', 'parameters' => array( 'projectId' => array( 'location' => 'query', 'type' => 'string', ), 'pageSize' => array( 'location' => 'query', 'type' => 'integer', ), 'pageToken' => array( 'location' => 'query', 'type' => 'string', ), ), ),'patch' => array( 'path' => 'v1/datasets/{datasetId}', 'httpMethod' => 'PATCH', 'parameters' => array( 'datasetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), 'updateMask' => array( 'location' => 'query', 'type' => 'string', ), ), ),'setIamPolicy' => array( 'path' => 'v1/{+resource}:setIamPolicy', 'httpMethod' => 'POST', 'parameters' => array( 'resource' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'testIamPermissions' => array( 'path' => 'v1/{+resource}:testIamPermissions', 'httpMethod' => 'POST', 'parameters' => array( 'resource' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'undelete' => array( 'path' => 'v1/datasets/{datasetId}:undelete', 'httpMethod' => 'POST', 'parameters' => array( 'datasetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ), ) ) ); $this->operations = new Google_Service_Genomics_Operations_Resource( $this, $this->serviceName, 'operations', array( 'methods' => array( 'cancel' => array( 'path' => 'v1/{+name}:cancel', 'httpMethod' => 'POST', 'parameters' => array( 'name' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'get' => array( 'path' => 'v1/{+name}', 'httpMethod' => 'GET', 'parameters' => array( 'name' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'list' => array( 'path' => 'v1/{+name}', 'httpMethod' => 'GET', 'parameters' => array( 'name' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), 'filter' => array( 'location' => 'query', 'type' => 'string', ), 'pageSize' => array( 'location' => 'query', 'type' => 'integer', ), 'pageToken' => array( 'location' => 'query', 'type' => 'string', ), ), ), ) ) ); $this->readgroupsets = new Google_Service_Genomics_Readgroupsets_Resource( $this, $this->serviceName, 'readgroupsets', array( 'methods' => array( 'delete' => array( 'path' => 'v1/readgroupsets/{readGroupSetId}', 'httpMethod' => 'DELETE', 'parameters' => array( 'readGroupSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'export' => array( 'path' => 'v1/readgroupsets/{readGroupSetId}:export', 'httpMethod' => 'POST', 'parameters' => array( 'readGroupSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'get' => array( 'path' => 'v1/readgroupsets/{readGroupSetId}', 'httpMethod' => 'GET', 'parameters' => array( 'readGroupSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'import' => array( 'path' => 'v1/readgroupsets:import', 'httpMethod' => 'POST', 'parameters' => array(), ),'patch' => array( 'path' => 'v1/readgroupsets/{readGroupSetId}', 'httpMethod' => 'PATCH', 'parameters' => array( 'readGroupSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), 'updateMask' => array( 'location' => 'query', 'type' => 'string', ), ), ),'search' => array( 'path' => 'v1/readgroupsets/search', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); $this->readgroupsets_coveragebuckets = new Google_Service_Genomics_ReadgroupsetsCoveragebuckets_Resource( $this, $this->serviceName, 'coveragebuckets', array( 'methods' => array( 'list' => array( 'path' => 'v1/readgroupsets/{readGroupSetId}/coveragebuckets', 'httpMethod' => 'GET', 'parameters' => array( 'readGroupSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), 'referenceName' => array( 'location' => 'query', 'type' => 'string', ), 'start' => array( 'location' => 'query', 'type' => 'string', ), 'end' => array( 'location' => 'query', 'type' => 'string', ), 'targetBucketWidth' => array( 'location' => 'query', 'type' => 'string', ), 'pageToken' => array( 'location' => 'query', 'type' => 'string', ), 'pageSize' => array( 'location' => 'query', 'type' => 'integer', ), ), ), ) ) ); $this->reads = new Google_Service_Genomics_Reads_Resource( $this, $this->serviceName, 'reads', array( 'methods' => array( 'search' => array( 'path' => 'v1/reads/search', 'httpMethod' => 'POST', 'parameters' => array(), ),'stream' => array( 'path' => 'v1/reads:stream', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); $this->references = new Google_Service_Genomics_References_Resource( $this, $this->serviceName, 'references', array( 'methods' => array( 'get' => array( 'path' => 'v1/references/{referenceId}', 'httpMethod' => 'GET', 'parameters' => array( 'referenceId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'search' => array( 'path' => 'v1/references/search', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); $this->references_bases = new Google_Service_Genomics_ReferencesBases_Resource( $this, $this->serviceName, 'bases', array( 'methods' => array( 'list' => array( 'path' => 'v1/references/{referenceId}/bases', 'httpMethod' => 'GET', 'parameters' => array( 'referenceId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), 'start' => array( 'location' => 'query', 'type' => 'string', ), 'end' => array( 'location' => 'query', 'type' => 'string', ), 'pageToken' => array( 'location' => 'query', 'type' => 'string', ), 'pageSize' => array( 'location' => 'query', 'type' => 'integer', ), ), ), ) ) ); $this->referencesets = new Google_Service_Genomics_Referencesets_Resource( $this, $this->serviceName, 'referencesets', array( 'methods' => array( 'get' => array( 'path' => 'v1/referencesets/{referenceSetId}', 'httpMethod' => 'GET', 'parameters' => array( 'referenceSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'search' => array( 'path' => 'v1/referencesets/search', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); $this->variants = new Google_Service_Genomics_Variants_Resource( $this, $this->serviceName, 'variants', array( 'methods' => array( 'create' => array( 'path' => 'v1/variants', 'httpMethod' => 'POST', 'parameters' => array(), ),'delete' => array( 'path' => 'v1/variants/{variantId}', 'httpMethod' => 'DELETE', 'parameters' => array( 'variantId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'get' => array( 'path' => 'v1/variants/{variantId}', 'httpMethod' => 'GET', 'parameters' => array( 'variantId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'import' => array( 'path' => 'v1/variants:import', 'httpMethod' => 'POST', 'parameters' => array(), ),'patch' => array( 'path' => 'v1/variants/{variantId}', 'httpMethod' => 'PATCH', 'parameters' => array( 'variantId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), 'updateMask' => array( 'location' => 'query', 'type' => 'string', ), ), ),'search' => array( 'path' => 'v1/variants/search', 'httpMethod' => 'POST', 'parameters' => array(), ),'stream' => array( 'path' => 'v1/variants:stream', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); $this->variantsets = new Google_Service_Genomics_Variantsets_Resource( $this, $this->serviceName, 'variantsets', array( 'methods' => array( 'create' => array( 'path' => 'v1/variantsets', 'httpMethod' => 'POST', 'parameters' => array(), ),'delete' => array( 'path' => 'v1/variantsets/{variantSetId}', 'httpMethod' => 'DELETE', 'parameters' => array( 'variantSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'export' => array( 'path' => 'v1/variantsets/{variantSetId}:export', 'httpMethod' => 'POST', 'parameters' => array( 'variantSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'get' => array( 'path' => 'v1/variantsets/{variantSetId}', 'httpMethod' => 'GET', 'parameters' => array( 'variantSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'patch' => array( 'path' => 'v1/variantsets/{variantSetId}', 'httpMethod' => 'PATCH', 'parameters' => array( 'variantSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), 'updateMask' => array( 'location' => 'query', 'type' => 'string', ), ), ),'search' => array( 'path' => 'v1/variantsets/search', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); } } /** * The "callsets" collection of methods. * Typical usage is: * * $genomicsService = new Google_Service_Genomics(...); * $callsets = $genomicsService->callsets; * */ class Google_Service_Genomics_Callsets_Resource extends Google_Service_Resource { /** * 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) * (callsets.create) * * @param Google_CallSet $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_CallSet */ public function create(Google_Service_Genomics_CallSet $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('create', array($params), "Google_Service_Genomics_CallSet"); } /** * 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) * (callsets.delete) * * @param string $callSetId The ID of the call set to be deleted. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Empty */ public function delete($callSetId, $optParams = array()) { $params = array('callSetId' => $callSetId); $params = array_merge($params, $optParams); return $this->call('delete', array($params), "Google_Service_Genomics_Empty"); } /** * 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) * (callsets.get) * * @param string $callSetId The ID of the call set. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_CallSet */ public function get($callSetId, $optParams = array()) { $params = array('callSetId' => $callSetId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "Google_Service_Genomics_CallSet"); } /** * 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. (callsets.patch) * * @param string $callSetId The ID of the call set to be updated. * @param Google_CallSet $postBody * @param array $optParams Optional parameters. * * @opt_param string updateMask An optional mask specifying which fields to * update. At this time, the only mutable field is name. The only acceptable * value is "name". If unspecified, all mutable fields will be updated. * @return Google_Service_Genomics_CallSet */ public function patch($callSetId, Google_Service_Genomics_CallSet $postBody, $optParams = array()) { $params = array('callSetId' => $callSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('patch', array($params), "Google_Service_Genomics_CallSet"); } /** * 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/schema * s/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178). * (callsets.search) * * @param Google_SearchCallSetsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_SearchCallSetsResponse */ public function search(Google_Service_Genomics_SearchCallSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "Google_Service_Genomics_SearchCallSetsResponse"); } } /** * The "datasets" collection of methods. * Typical usage is: * * $genomicsService = new Google_Service_Genomics(...); * $datasets = $genomicsService->datasets; * */ class Google_Service_Genomics_Datasets_Resource extends Google_Service_Resource { /** * 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) * (datasets.create) * * @param Google_Dataset $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Dataset */ public function create(Google_Service_Genomics_Dataset $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('create', array($params), "Google_Service_Genomics_Dataset"); } /** * Deletes 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) * (datasets.delete) * * @param string $datasetId The ID of the dataset to be deleted. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Empty */ public function delete($datasetId, $optParams = array()) { $params = array('datasetId' => $datasetId); $params = array_merge($params, $optParams); return $this->call('delete', array($params), "Google_Service_Genomics_Empty"); } /** * 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) * (datasets.get) * * @param string $datasetId The ID of the dataset. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Dataset */ public function get($datasetId, $optParams = array()) { $params = array('datasetId' => $datasetId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "Google_Service_Genomics_Dataset"); } /** * 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 Genomics](https://cloud.google.com/genomics/fundamentals-of-google- * genomics) (datasets.getIamPolicy) * * @param string $resource REQUIRED: The resource for which policy is being * specified. Format is `datasets/`. * @param Google_GetIamPolicyRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Policy */ public function getIamPolicy($resource, Google_Service_Genomics_GetIamPolicyRequest $postBody, $optParams = array()) { $params = array('resource' => $resource, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('getIamPolicy', array($params), "Google_Service_Genomics_Policy"); } /** * 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) * (datasets.listDatasets) * * @param array $optParams Optional parameters. * * @opt_param string projectId Required. The project to list datasets for. * @opt_param int pageSize The maximum number of results to return in a single * page. If unspecified, defaults to 50. The maximum value is 1024. * @opt_param string pageToken The continuation token, which is used to page * through large result sets. To get the next page of results, set this * parameter to the value of `nextPageToken` from the previous response. * @return Google_Service_Genomics_ListDatasetsResponse */ public function listDatasets($optParams = array()) { $params = array(); $params = array_merge($params, $optParams); return $this->call('list', array($params), "Google_Service_Genomics_ListDatasetsResponse"); } /** * 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. (datasets.patch) * * @param string $datasetId The ID of the dataset to be updated. * @param Google_Dataset $postBody * @param array $optParams Optional parameters. * * @opt_param string updateMask An optional mask specifying which fields to * update. At this time, the only mutable field is name. The only acceptable * value is "name". If unspecified, all mutable fields will be updated. * @return Google_Service_Genomics_Dataset */ public function patch($datasetId, Google_Service_Genomics_Dataset $postBody, $optParams = array()) { $params = array('datasetId' => $datasetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('patch', array($params), "Google_Service_Genomics_Dataset"); } /** * 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 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) * See Setting a Policy for more information. (datasets.setIamPolicy) * * @param string $resource REQUIRED: The resource for which policy is being * specified. Format is `datasets/`. * @param Google_SetIamPolicyRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Policy */ public function setIamPolicy($resource, Google_Service_Genomics_SetIamPolicyRequest $postBody, $optParams = array()) { $params = array('resource' => $resource, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('setIamPolicy', array($params), "Google_Service_Genomics_Policy"); } /** * 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 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) * (datasets.testIamPermissions) * * @param string $resource REQUIRED: The resource for which policy is being * specified. Format is `datasets/`. * @param Google_TestIamPermissionsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_TestIamPermissionsResponse */ public function testIamPermissions($resource, Google_Service_Genomics_TestIamPermissionsRequest $postBody, $optParams = array()) { $params = array('resource' => $resource, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('testIamPermissions', array($params), "Google_Service_Genomics_TestIamPermissionsResponse"); } /** * 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. (datasets.undelete) * * @param string $datasetId The ID of the dataset to be undeleted. * @param Google_UndeleteDatasetRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Dataset */ public function undelete($datasetId, Google_Service_Genomics_UndeleteDatasetRequest $postBody, $optParams = array()) { $params = array('datasetId' => $datasetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('undelete', array($params), "Google_Service_Genomics_Dataset"); } } /** * The "operations" collection of methods. * Typical usage is: * * $genomicsService = new Google_Service_Genomics(...); * $operations = $genomicsService->operations; * */ class Google_Service_Genomics_Operations_Resource extends Google_Service_Resource { /** * Starts asynchronous cancellation on a long-running operation. The server * makes a best effort to cancel the operation, but success is not guaranteed. * Clients may use Operations.GetOperation or Operations.ListOperations to check * whether the cancellation succeeded or the operation completed despite * cancellation. (operations.cancel) * * @param string $name The name of the operation resource to be cancelled. * @param Google_CancelOperationRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Empty */ public function cancel($name, Google_Service_Genomics_CancelOperationRequest $postBody, $optParams = array()) { $params = array('name' => $name, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('cancel', array($params), "Google_Service_Genomics_Empty"); } /** * 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. (operations.get) * * @param string $name The name of the operation resource. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Operation */ public function get($name, $optParams = array()) { $params = array('name' => $name); $params = array_merge($params, $optParams); return $this->call('get', array($params), "Google_Service_Genomics_Operation"); } /** * Lists operations that match the specified filter in the request. * (operations.listOperations) * * @param string $name The name of the operation collection. * @param array $optParams Optional parameters. * * @opt_param string filter A string for filtering Operations. The following * filter fields are supported: * projectId: Required. Corresponds to * OperationMetadata.projectId. * createTime: The time this job was created, in * seconds from the [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use * `>=` and/or `= 1432140000` * `projectId = my-project AND createTime >= * 1432140000 AND createTime <= 1432150000 AND status = RUNNING` * @opt_param int pageSize The maximum number of results to return. If * unspecified, defaults to 256. The maximum value is 2048. * @opt_param string pageToken The standard list page token. * @return Google_Service_Genomics_ListOperationsResponse */ public function listOperations($name, $optParams = array()) { $params = array('name' => $name); $params = array_merge($params, $optParams); return $this->call('list', array($params), "Google_Service_Genomics_ListOperationsResponse"); } } /** * The "readgroupsets" collection of methods. * Typical usage is: * * $genomicsService = new Google_Service_Genomics(...); * $readgroupsets = $genomicsService->readgroupsets; * */ class Google_Service_Genomics_Readgroupsets_Resource extends Google_Service_Resource { /** * 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) * (readgroupsets.delete) * * @param string $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. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Empty */ public function delete($readGroupSetId, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId); $params = array_merge($params, $optParams); return $this->call('delete', array($params), "Google_Service_Genomics_Empty"); } /** * 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](google.genomics.v1.ReadServiceV1.ImportReadGroupSets) * for caveats. (readgroupsets.export) * * @param string $readGroupSetId Required. The ID of the read group set to * export. The caller must have READ access to this read group set. * @param Google_ExportReadGroupSetRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Operation */ public function export($readGroupSetId, Google_Service_Genomics_ExportReadGroupSetRequest $postBody, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('export', array($params), "Google_Service_Genomics_Operation"); } /** * 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) * (readgroupsets.get) * * @param string $readGroupSetId The ID of the read group set. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_ReadGroupSet */ public function get($readGroupSetId, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "Google_Service_Genomics_ReadGroupSet"); } /** * 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 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) (readgroupsets.import) * * @param Google_ImportReadGroupSetsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Operation */ public function import(Google_Service_Genomics_ImportReadGroupSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('import', array($params), "Google_Service_Genomics_Operation"); } /** * 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. (readgroupsets.patch) * * @param string $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. * @param Google_ReadGroupSet $postBody * @param array $optParams Optional parameters. * * @opt_param string updateMask An optional mask specifying which fields to * update. Supported fields: * name. * referenceSetId. Leaving `updateMask` * unset is equivalent to specifying all mutable fields. * @return Google_Service_Genomics_ReadGroupSet */ public function patch($readGroupSetId, Google_Service_Genomics_ReadGroupSet $postBody, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('patch', array($params), "Google_Service_Genomics_ReadGroupSet"); } /** * 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/s * chemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135). * (readgroupsets.search) * * @param Google_SearchReadGroupSetsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_SearchReadGroupSetsResponse */ public function search(Google_Service_Genomics_SearchReadGroupSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "Google_Service_Genomics_SearchReadGroupSetsResponse"); } } /** * The "coveragebuckets" collection of methods. * Typical usage is: * * $genomicsService = new Google_Service_Genomics(...); * $coveragebuckets = $genomicsService->coveragebuckets; * */ class Google_Service_Genomics_ReadgroupsetsCoveragebuckets_Resource extends Google_Service_Resource { /** * 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 * [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 levels'. The caller must have READ permissions for the * target read group set. (coveragebuckets.listReadgroupsetsCoveragebuckets) * * @param string $readGroupSetId Required. The ID of the read group set over * which coverage is requested. * @param array $optParams Optional parameters. * * @opt_param string referenceName The name of the reference to query, within * the reference set associated with this query. Optional. * @opt_param string start The start position of the range on the reference, * 0-based inclusive. If specified, `referenceName` must also be specified. * Defaults to 0. * @opt_param string end The end position of the range on the reference, 0-based * exclusive. If specified, `referenceName` must also be specified. If unset or * 0, defaults to the length of the reference. * @opt_param string targetBucketWidth The desired width of each reported * coverage bucket in base pairs. This will be rounded down to the nearest * precomputed bucket width; the value of which is returned as `bucketWidth` in * the response. Defaults to infinity (each bucket spans an entire reference * sequence) or the length of the target range, if specified. The smallest * precomputed `bucketWidth` is currently 2048 base pairs; this is subject to * change. * @opt_param string pageToken The continuation token, which is used to page * through large result sets. To get the next page of results, set this * parameter to the value of `nextPageToken` from the previous response. * @opt_param int pageSize The maximum number of results to return in a single * page. If unspecified, defaults to 1024. The maximum value is 2048. * @return Google_Service_Genomics_ListCoverageBucketsResponse */ public function listReadgroupsetsCoveragebuckets($readGroupSetId, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId); $params = array_merge($params, $optParams); return $this->call('list', array($params), "Google_Service_Genomics_ListCoverageBucketsResponse"); } } /** * The "reads" collection of methods. * Typical usage is: * * $genomicsService = new Google_Service_Genomics(...); * $reads = $genomicsService->reads; * */ class Google_Service_Genomics_Reads_Resource extends Google_Service_Resource { /** * 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 * [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/ * src/main/resources/avro/readmethods.avdl#L85). (reads.search) * * @param Google_SearchReadsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_SearchReadsResponse */ public function search(Google_Service_Genomics_SearchReadsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "Google_Service_Genomics_SearchReadsResponse"); } /** * Returns a stream of all the reads matching the search request, ordered by * reference name, position, and ID. (reads.stream) * * @param Google_StreamReadsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_StreamReadsResponse */ public function stream(Google_Service_Genomics_StreamReadsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('stream', array($params), "Google_Service_Genomics_StreamReadsResponse"); } } /** * The "references" collection of methods. * Typical usage is: * * $genomicsService = new Google_Service_Genomics(...); * $references = $genomicsService->references; * */ class Google_Service_Genomics_References_Resource extends Google_Service_Resource { /** * 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). * (references.get) * * @param string $referenceId The ID of the reference. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Reference */ public function get($referenceId, $optParams = array()) { $params = array('referenceId' => $referenceId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "Google_Service_Genomics_Reference"); } /** * 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/sche * mas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146). * (references.search) * * @param Google_SearchReferencesRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_SearchReferencesResponse */ public function search(Google_Service_Genomics_SearchReferencesRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "Google_Service_Genomics_SearchReferencesResponse"); } } /** * The "bases" collection of methods. * Typical usage is: * * $genomicsService = new Google_Service_Genomics(...); * $bases = $genomicsService->bases; * */ class Google_Service_Genomics_ReferencesBases_Resource extends Google_Service_Resource { /** * 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 * ). (bases.listReferencesBases) * * @param string $referenceId The ID of the reference. * @param array $optParams Optional parameters. * * @opt_param string start The start position (0-based) of this query. Defaults * to 0. * @opt_param string end The end position (0-based, exclusive) of this query. * Defaults to the length of this reference. * @opt_param string pageToken The continuation token, which is used to page * through large result sets. To get the next page of results, set this * parameter to the value of `nextPageToken` from the previous response. * @opt_param int pageSize The maximum number of bases to return in a single * page. If unspecified, defaults to 200Kbp (kilo base pairs). The maximum value * is 10Mbp (mega base pairs). * @return Google_Service_Genomics_ListBasesResponse */ public function listReferencesBases($referenceId, $optParams = array()) { $params = array('referenceId' => $referenceId); $params = array_merge($params, $optParams); return $this->call('list', array($params), "Google_Service_Genomics_ListBasesResponse"); } } /** * The "referencesets" collection of methods. * Typical usage is: * * $genomicsService = new Google_Service_Genomics(...); * $referencesets = $genomicsService->referencesets; * */ class Google_Service_Genomics_Referencesets_Resource extends Google_Service_Resource { /** * 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/schem * as/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83). * (referencesets.get) * * @param string $referenceSetId The ID of the reference set. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_ReferenceSet */ public function get($referenceSetId, $optParams = array()) { $params = array('referenceSetId' => $referenceSetId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "Google_Service_Genomics_ReferenceSet"); } /** * 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.c * om/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L7 * 1) (referencesets.search) * * @param Google_SearchReferenceSetsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_SearchReferenceSetsResponse */ public function search(Google_Service_Genomics_SearchReferenceSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "Google_Service_Genomics_SearchReferenceSetsResponse"); } } /** * The "variants" collection of methods. * Typical usage is: * * $genomicsService = new Google_Service_Genomics(...); * $variants = $genomicsService->variants; * */ class Google_Service_Genomics_Variants_Resource extends Google_Service_Resource { /** * 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) * (variants.create) * * @param Google_Variant $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Variant */ public function create(Google_Service_Genomics_Variant $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('create', array($params), "Google_Service_Genomics_Variant"); } /** * 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) * (variants.delete) * * @param string $variantId The ID of the variant to be deleted. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Empty */ public function delete($variantId, $optParams = array()) { $params = array('variantId' => $variantId); $params = array_merge($params, $optParams); return $this->call('delete', array($params), "Google_Service_Genomics_Empty"); } /** * 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) * (variants.get) * * @param string $variantId The ID of the variant. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Variant */ public function get($variantId, $optParams = array()) { $params = array('variantId' => $variantId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "Google_Service_Genomics_Variant"); } /** * 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 other fields (such as key/value * pairs) are discarded. In particular, this means for merged VCF variants that * have conflicting INFO fields, some data will be arbitrarily discarded. As a * special case, for single-sample VCF files, QUAL and FILTER fields will be * moved to the call level; these are sometimes interpreted in a call-specific * context. Imported VCF headers are appended to the metadata already in a * variant set. (variants.import) * * @param Google_ImportVariantsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Operation */ public function import(Google_Service_Genomics_ImportVariantsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('import', array($params), "Google_Service_Genomics_Operation"); } /** * 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. (variants.patch) * * @param string $variantId The ID of the variant to be updated. * @param Google_Variant $postBody * @param array $optParams Optional parameters. * * @opt_param string updateMask An optional mask specifying which fields to * update. At this time, mutable fields are names and info. Acceptable values * are "names" and "info". If unspecified, all mutable fields will be updated. * @return Google_Service_Genomics_Variant */ public function patch($variantId, Google_Service_Genomics_Variant $postBody, $optParams = array()) { $params = array('variantId' => $variantId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('patch', array($params), "Google_Service_Genomics_Variant"); } /** * 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/schema * s/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126). * (variants.search) * * @param Google_SearchVariantsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_SearchVariantsResponse */ public function search(Google_Service_Genomics_SearchVariantsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "Google_Service_Genomics_SearchVariantsResponse"); } /** * Returns a stream of all the variants matching the search request, ordered by * reference name, position, and ID. (variants.stream) * * @param Google_StreamVariantsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_StreamVariantsResponse */ public function stream(Google_Service_Genomics_StreamVariantsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('stream', array($params), "Google_Service_Genomics_StreamVariantsResponse"); } } /** * The "variantsets" collection of methods. * Typical usage is: * * $genomicsService = new Google_Service_Genomics(...); * $variantsets = $genomicsService->variantsets; * */ class Google_Service_Genomics_Variantsets_Resource extends Google_Service_Resource { /** * 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. (variantsets.create) * * @param Google_VariantSet $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_VariantSet */ public function create(Google_Service_Genomics_VariantSet $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('create', array($params), "Google_Service_Genomics_VariantSet"); } /** * Deletes the contents of a variant set. The variant set object is not deleted. * For the definitions of variant sets and other genomics resources, see * [Fundamentals of Google Genomics](https://cloud.google.com/genomics * /fundamentals-of-google-genomics) (variantsets.delete) * * @param string $variantSetId The ID of the variant set to be deleted. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Empty */ public function delete($variantSetId, $optParams = array()) { $params = array('variantSetId' => $variantSetId); $params = array_merge($params, $optParams); return $this->call('delete', array($params), "Google_Service_Genomics_Empty"); } /** * 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) * (variantsets.export) * * @param string $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. * @param Google_ExportVariantSetRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Operation */ public function export($variantSetId, Google_Service_Genomics_ExportVariantSetRequest $postBody, $optParams = array()) { $params = array('variantSetId' => $variantSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('export', array($params), "Google_Service_Genomics_Operation"); } /** * 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) * (variantsets.get) * * @param string $variantSetId Required. The ID of the variant set. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_VariantSet */ public function get($variantSetId, $optParams = array()) { $params = array('variantSetId' => $variantSetId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "Google_Service_Genomics_VariantSet"); } /** * 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) * (variantsets.patch) * * @param string $variantSetId The ID of the variant to be updated (must already * exist). * @param Google_VariantSet $postBody * @param array $optParams Optional parameters. * * @opt_param string updateMask An optional mask specifying which fields to * update. Supported fields: * metadata. Leaving `updateMask` unset is * equivalent to specifying all mutable fields. * @return Google_Service_Genomics_VariantSet */ public function patch($variantSetId, Google_Service_Genomics_VariantSet $postBody, $optParams = array()) { $params = array('variantSetId' => $variantSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('patch', array($params), "Google_Service_Genomics_VariantSet"); } /** * 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). * (variantsets.search) * * @param Google_SearchVariantSetsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_SearchVariantSetsResponse */ public function search(Google_Service_Genomics_SearchVariantSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "Google_Service_Genomics_SearchVariantSetsResponse"); } } class Google_Service_Genomics_Binding extends Google_Collection { protected $collection_key = 'members'; protected $internal_gapi_mappings = array( ); public $members; public $role; public function setMembers($members) { $this->members = $members; } public function getMembers() { return $this->members; } public function setRole($role) { $this->role = $role; } public function getRole() { return $this->role; } } class Google_Service_Genomics_CallSet extends Google_Collection { protected $collection_key = 'variantSetIds'; protected $internal_gapi_mappings = array( ); public $created; public $id; public $info; public $name; public $sampleId; public $variantSetIds; public function setCreated($created) { $this->created = $created; } public function getCreated() { return $this->created; } public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setInfo($info) { $this->info = $info; } public function getInfo() { return $this->info; } public function setName($name) { $this->name = $name; } public function getName() { return $this->name; } public function setSampleId($sampleId) { $this->sampleId = $sampleId; } public function getSampleId() { return $this->sampleId; } public function setVariantSetIds($variantSetIds) { $this->variantSetIds = $variantSetIds; } public function getVariantSetIds() { return $this->variantSetIds; } } class Google_Service_Genomics_CancelOperationRequest extends Google_Model { } class Google_Service_Genomics_CigarUnit extends Google_Model { protected $internal_gapi_mappings = array( ); public $operation; public $operationLength; public $referenceSequence; public function setOperation($operation) { $this->operation = $operation; } public function getOperation() { return $this->operation; } public function setOperationLength($operationLength) { $this->operationLength = $operationLength; } public function getOperationLength() { return $this->operationLength; } public function setReferenceSequence($referenceSequence) { $this->referenceSequence = $referenceSequence; } public function getReferenceSequence() { return $this->referenceSequence; } } class Google_Service_Genomics_CloudAuditOptions extends Google_Model { } class Google_Service_Genomics_Condition extends Google_Collection { protected $collection_key = 'values'; protected $internal_gapi_mappings = array( ); public $iam; public $op; public $svc; public $sys; public $value; public $values; public function setIam($iam) { $this->iam = $iam; } public function getIam() { return $this->iam; } public function setOp($op) { $this->op = $op; } public function getOp() { return $this->op; } public function setSvc($svc) { $this->svc = $svc; } public function getSvc() { return $this->svc; } public function setSys($sys) { $this->sys = $sys; } public function getSys() { return $this->sys; } public function setValue($value) { $this->value = $value; } public function getValue() { return $this->value; } public function setValues($values) { $this->values = $values; } public function getValues() { return $this->values; } } class Google_Service_Genomics_CounterOptions extends Google_Model { protected $internal_gapi_mappings = array( ); public $field; public $metric; public function setField($field) { $this->field = $field; } public function getField() { return $this->field; } public function setMetric($metric) { $this->metric = $metric; } public function getMetric() { return $this->metric; } } class Google_Service_Genomics_CoverageBucket extends Google_Model { protected $internal_gapi_mappings = array( ); public $meanCoverage; protected $rangeType = 'Google_Service_Genomics_Range'; protected $rangeDataType = ''; public function setMeanCoverage($meanCoverage) { $this->meanCoverage = $meanCoverage; } public function getMeanCoverage() { return $this->meanCoverage; } public function setRange(Google_Service_Genomics_Range $range) { $this->range = $range; } public function getRange() { return $this->range; } } class Google_Service_Genomics_DataAccessOptions extends Google_Model { } class Google_Service_Genomics_Dataset extends Google_Model { protected $internal_gapi_mappings = array( ); public $createTime; public $id; public $name; public $projectId; public function setCreateTime($createTime) { $this->createTime = $createTime; } public function getCreateTime() { return $this->createTime; } public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setName($name) { $this->name = $name; } public function getName() { return $this->name; } public function setProjectId($projectId) { $this->projectId = $projectId; } public function getProjectId() { return $this->projectId; } } class Google_Service_Genomics_Empty extends Google_Model { } class Google_Service_Genomics_Experiment extends Google_Model { protected $internal_gapi_mappings = array( ); public $instrumentModel; public $libraryId; public $platformUnit; public $sequencingCenter; public function setInstrumentModel($instrumentModel) { $this->instrumentModel = $instrumentModel; } public function getInstrumentModel() { return $this->instrumentModel; } public function setLibraryId($libraryId) { $this->libraryId = $libraryId; } public function getLibraryId() { return $this->libraryId; } public function setPlatformUnit($platformUnit) { $this->platformUnit = $platformUnit; } public function getPlatformUnit() { return $this->platformUnit; } public function setSequencingCenter($sequencingCenter) { $this->sequencingCenter = $sequencingCenter; } public function getSequencingCenter() { return $this->sequencingCenter; } } class Google_Service_Genomics_ExportReadGroupSetRequest extends Google_Collection { protected $collection_key = 'referenceNames'; protected $internal_gapi_mappings = array( ); public $exportUri; public $projectId; public $referenceNames; public function setExportUri($exportUri) { $this->exportUri = $exportUri; } public function getExportUri() { return $this->exportUri; } public function setProjectId($projectId) { $this->projectId = $projectId; } public function getProjectId() { return $this->projectId; } public function setReferenceNames($referenceNames) { $this->referenceNames = $referenceNames; } public function getReferenceNames() { return $this->referenceNames; } } class Google_Service_Genomics_ExportVariantSetRequest extends Google_Collection { protected $collection_key = 'callSetIds'; protected $internal_gapi_mappings = array( ); public $bigqueryDataset; public $bigqueryTable; public $callSetIds; public $format; public $projectId; public function setBigqueryDataset($bigqueryDataset) { $this->bigqueryDataset = $bigqueryDataset; } public function getBigqueryDataset() { return $this->bigqueryDataset; } public function setBigqueryTable($bigqueryTable) { $this->bigqueryTable = $bigqueryTable; } public function getBigqueryTable() { return $this->bigqueryTable; } public function setCallSetIds($callSetIds) { $this->callSetIds = $callSetIds; } public function getCallSetIds() { return $this->callSetIds; } public function setFormat($format) { $this->format = $format; } public function getFormat() { return $this->format; } public function setProjectId($projectId) { $this->projectId = $projectId; } public function getProjectId() { return $this->projectId; } } class Google_Service_Genomics_GetIamPolicyRequest extends Google_Model { } class Google_Service_Genomics_ImportReadGroupSetsRequest extends Google_Collection { protected $collection_key = 'sourceUris'; protected $internal_gapi_mappings = array( ); public $datasetId; public $partitionStrategy; public $referenceSetId; public $sourceUris; public function setDatasetId($datasetId) { $this->datasetId = $datasetId; } public function getDatasetId() { return $this->datasetId; } public function setPartitionStrategy($partitionStrategy) { $this->partitionStrategy = $partitionStrategy; } public function getPartitionStrategy() { return $this->partitionStrategy; } public function setReferenceSetId($referenceSetId) { $this->referenceSetId = $referenceSetId; } public function getReferenceSetId() { return $this->referenceSetId; } public function setSourceUris($sourceUris) { $this->sourceUris = $sourceUris; } public function getSourceUris() { return $this->sourceUris; } } class Google_Service_Genomics_ImportReadGroupSetsResponse extends Google_Collection { protected $collection_key = 'readGroupSetIds'; protected $internal_gapi_mappings = array( ); public $readGroupSetIds; public function setReadGroupSetIds($readGroupSetIds) { $this->readGroupSetIds = $readGroupSetIds; } public function getReadGroupSetIds() { return $this->readGroupSetIds; } } class Google_Service_Genomics_ImportVariantsRequest extends Google_Collection { protected $collection_key = 'sourceUris'; protected $internal_gapi_mappings = array( ); public $format; public $normalizeReferenceNames; public $sourceUris; public $variantSetId; public function setFormat($format) { $this->format = $format; } public function getFormat() { return $this->format; } public function setNormalizeReferenceNames($normalizeReferenceNames) { $this->normalizeReferenceNames = $normalizeReferenceNames; } public function getNormalizeReferenceNames() { return $this->normalizeReferenceNames; } public function setSourceUris($sourceUris) { $this->sourceUris = $sourceUris; } public function getSourceUris() { return $this->sourceUris; } public function setVariantSetId($variantSetId) { $this->variantSetId = $variantSetId; } public function getVariantSetId() { return $this->variantSetId; } } class Google_Service_Genomics_ImportVariantsResponse extends Google_Collection { protected $collection_key = 'callSetIds'; protected $internal_gapi_mappings = array( ); public $callSetIds; public function setCallSetIds($callSetIds) { $this->callSetIds = $callSetIds; } public function getCallSetIds() { return $this->callSetIds; } } class Google_Service_Genomics_LinearAlignment extends Google_Collection { protected $collection_key = 'cigar'; protected $internal_gapi_mappings = array( ); protected $cigarType = 'Google_Service_Genomics_CigarUnit'; protected $cigarDataType = 'array'; public $mappingQuality; protected $positionType = 'Google_Service_Genomics_Position'; protected $positionDataType = ''; public function setCigar($cigar) { $this->cigar = $cigar; } public function getCigar() { return $this->cigar; } public function setMappingQuality($mappingQuality) { $this->mappingQuality = $mappingQuality; } public function getMappingQuality() { return $this->mappingQuality; } public function setPosition(Google_Service_Genomics_Position $position) { $this->position = $position; } public function getPosition() { return $this->position; } } class Google_Service_Genomics_ListBasesResponse extends Google_Model { protected $internal_gapi_mappings = array( ); public $nextPageToken; public $offset; public $sequence; public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } public function setOffset($offset) { $this->offset = $offset; } public function getOffset() { return $this->offset; } public function setSequence($sequence) { $this->sequence = $sequence; } public function getSequence() { return $this->sequence; } } class Google_Service_Genomics_ListCoverageBucketsResponse extends Google_Collection { protected $collection_key = 'coverageBuckets'; protected $internal_gapi_mappings = array( ); public $bucketWidth; protected $coverageBucketsType = 'Google_Service_Genomics_CoverageBucket'; protected $coverageBucketsDataType = 'array'; public $nextPageToken; public function setBucketWidth($bucketWidth) { $this->bucketWidth = $bucketWidth; } public function getBucketWidth() { return $this->bucketWidth; } public function setCoverageBuckets($coverageBuckets) { $this->coverageBuckets = $coverageBuckets; } public function getCoverageBuckets() { return $this->coverageBuckets; } public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } } class Google_Service_Genomics_ListDatasetsResponse extends Google_Collection { protected $collection_key = 'datasets'; protected $internal_gapi_mappings = array( ); protected $datasetsType = 'Google_Service_Genomics_Dataset'; protected $datasetsDataType = 'array'; public $nextPageToken; public function setDatasets($datasets) { $this->datasets = $datasets; } public function getDatasets() { return $this->datasets; } public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } } class Google_Service_Genomics_ListOperationsResponse extends Google_Collection { protected $collection_key = 'operations'; protected $internal_gapi_mappings = array( ); public $nextPageToken; protected $operationsType = 'Google_Service_Genomics_Operation'; protected $operationsDataType = 'array'; public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } public function setOperations($operations) { $this->operations = $operations; } public function getOperations() { return $this->operations; } } class Google_Service_Genomics_LogConfig extends Google_Model { protected $internal_gapi_mappings = array( ); protected $cloudAuditType = 'Google_Service_Genomics_CloudAuditOptions'; protected $cloudAuditDataType = ''; protected $counterType = 'Google_Service_Genomics_CounterOptions'; protected $counterDataType = ''; protected $dataAccessType = 'Google_Service_Genomics_DataAccessOptions'; protected $dataAccessDataType = ''; public function setCloudAudit(Google_Service_Genomics_CloudAuditOptions $cloudAudit) { $this->cloudAudit = $cloudAudit; } public function getCloudAudit() { return $this->cloudAudit; } public function setCounter(Google_Service_Genomics_CounterOptions $counter) { $this->counter = $counter; } public function getCounter() { return $this->counter; } public function setDataAccess(Google_Service_Genomics_DataAccessOptions $dataAccess) { $this->dataAccess = $dataAccess; } public function getDataAccess() { return $this->dataAccess; } } class Google_Service_Genomics_Operation extends Google_Model { protected $internal_gapi_mappings = array( ); public $done; protected $errorType = 'Google_Service_Genomics_Status'; protected $errorDataType = ''; public $metadata; public $name; public $response; public function setDone($done) { $this->done = $done; } public function getDone() { return $this->done; } public function setError(Google_Service_Genomics_Status $error) { $this->error = $error; } public function getError() { return $this->error; } public function setMetadata($metadata) { $this->metadata = $metadata; } public function getMetadata() { return $this->metadata; } public function setName($name) { $this->name = $name; } public function getName() { return $this->name; } public function setResponse($response) { $this->response = $response; } public function getResponse() { return $this->response; } } class Google_Service_Genomics_OperationEvent extends Google_Model { protected $internal_gapi_mappings = array( ); public $description; public function setDescription($description) { $this->description = $description; } public function getDescription() { return $this->description; } } class Google_Service_Genomics_OperationMetadata extends Google_Collection { protected $collection_key = 'events'; protected $internal_gapi_mappings = array( ); public $createTime; protected $eventsType = 'Google_Service_Genomics_OperationEvent'; protected $eventsDataType = 'array'; public $projectId; public $request; public function setCreateTime($createTime) { $this->createTime = $createTime; } public function getCreateTime() { return $this->createTime; } public function setEvents($events) { $this->events = $events; } public function getEvents() { return $this->events; } public function setProjectId($projectId) { $this->projectId = $projectId; } public function getProjectId() { return $this->projectId; } public function setRequest($request) { $this->request = $request; } public function getRequest() { return $this->request; } } class Google_Service_Genomics_Policy extends Google_Collection { protected $collection_key = 'rules'; protected $internal_gapi_mappings = array( ); protected $bindingsType = 'Google_Service_Genomics_Binding'; protected $bindingsDataType = 'array'; public $etag; protected $rulesType = 'Google_Service_Genomics_Rule'; protected $rulesDataType = 'array'; public $version; public function setBindings($bindings) { $this->bindings = $bindings; } public function getBindings() { return $this->bindings; } public function setEtag($etag) { $this->etag = $etag; } public function getEtag() { return $this->etag; } public function setRules($rules) { $this->rules = $rules; } public function getRules() { return $this->rules; } public function setVersion($version) { $this->version = $version; } public function getVersion() { return $this->version; } } class Google_Service_Genomics_Position extends Google_Model { protected $internal_gapi_mappings = array( ); public $position; public $referenceName; public $reverseStrand; public function setPosition($position) { $this->position = $position; } public function getPosition() { return $this->position; } public function setReferenceName($referenceName) { $this->referenceName = $referenceName; } public function getReferenceName() { return $this->referenceName; } public function setReverseStrand($reverseStrand) { $this->reverseStrand = $reverseStrand; } public function getReverseStrand() { return $this->reverseStrand; } } class Google_Service_Genomics_Program extends Google_Model { protected $internal_gapi_mappings = array( ); public $commandLine; public $id; public $name; public $prevProgramId; public $version; public function setCommandLine($commandLine) { $this->commandLine = $commandLine; } public function getCommandLine() { return $this->commandLine; } public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setName($name) { $this->name = $name; } public function getName() { return $this->name; } public function setPrevProgramId($prevProgramId) { $this->prevProgramId = $prevProgramId; } public function getPrevProgramId() { return $this->prevProgramId; } public function setVersion($version) { $this->version = $version; } public function getVersion() { return $this->version; } } class Google_Service_Genomics_Range extends Google_Model { protected $internal_gapi_mappings = array( ); public $end; public $referenceName; public $start; public function setEnd($end) { $this->end = $end; } public function getEnd() { return $this->end; } public function setReferenceName($referenceName) { $this->referenceName = $referenceName; } public function getReferenceName() { return $this->referenceName; } public function setStart($start) { $this->start = $start; } public function getStart() { return $this->start; } } class Google_Service_Genomics_Read extends Google_Collection { protected $collection_key = 'alignedQuality'; protected $internal_gapi_mappings = array( ); public $alignedQuality; public $alignedSequence; protected $alignmentType = 'Google_Service_Genomics_LinearAlignment'; protected $alignmentDataType = ''; public $duplicateFragment; public $failedVendorQualityChecks; public $fragmentLength; public $fragmentName; public $id; public $info; protected $nextMatePositionType = 'Google_Service_Genomics_Position'; protected $nextMatePositionDataType = ''; public $numberReads; public $properPlacement; public $readGroupId; public $readGroupSetId; public $readNumber; public $secondaryAlignment; public $supplementaryAlignment; public function setAlignedQuality($alignedQuality) { $this->alignedQuality = $alignedQuality; } public function getAlignedQuality() { return $this->alignedQuality; } public function setAlignedSequence($alignedSequence) { $this->alignedSequence = $alignedSequence; } public function getAlignedSequence() { return $this->alignedSequence; } public function setAlignment(Google_Service_Genomics_LinearAlignment $alignment) { $this->alignment = $alignment; } public function getAlignment() { return $this->alignment; } public function setDuplicateFragment($duplicateFragment) { $this->duplicateFragment = $duplicateFragment; } public function getDuplicateFragment() { return $this->duplicateFragment; } public function setFailedVendorQualityChecks($failedVendorQualityChecks) { $this->failedVendorQualityChecks = $failedVendorQualityChecks; } public function getFailedVendorQualityChecks() { return $this->failedVendorQualityChecks; } public function setFragmentLength($fragmentLength) { $this->fragmentLength = $fragmentLength; } public function getFragmentLength() { return $this->fragmentLength; } public function setFragmentName($fragmentName) { $this->fragmentName = $fragmentName; } public function getFragmentName() { return $this->fragmentName; } public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setInfo($info) { $this->info = $info; } public function getInfo() { return $this->info; } public function setNextMatePosition(Google_Service_Genomics_Position $nextMatePosition) { $this->nextMatePosition = $nextMatePosition; } public function getNextMatePosition() { return $this->nextMatePosition; } public function setNumberReads($numberReads) { $this->numberReads = $numberReads; } public function getNumberReads() { return $this->numberReads; } public function setProperPlacement($properPlacement) { $this->properPlacement = $properPlacement; } public function getProperPlacement() { return $this->properPlacement; } public function setReadGroupId($readGroupId) { $this->readGroupId = $readGroupId; } public function getReadGroupId() { return $this->readGroupId; } public function setReadGroupSetId($readGroupSetId) { $this->readGroupSetId = $readGroupSetId; } public function getReadGroupSetId() { return $this->readGroupSetId; } public function setReadNumber($readNumber) { $this->readNumber = $readNumber; } public function getReadNumber() { return $this->readNumber; } public function setSecondaryAlignment($secondaryAlignment) { $this->secondaryAlignment = $secondaryAlignment; } public function getSecondaryAlignment() { return $this->secondaryAlignment; } public function setSupplementaryAlignment($supplementaryAlignment) { $this->supplementaryAlignment = $supplementaryAlignment; } public function getSupplementaryAlignment() { return $this->supplementaryAlignment; } } class Google_Service_Genomics_ReadGroup extends Google_Collection { protected $collection_key = 'programs'; protected $internal_gapi_mappings = array( ); public $datasetId; public $description; protected $experimentType = 'Google_Service_Genomics_Experiment'; protected $experimentDataType = ''; public $id; public $info; public $name; public $predictedInsertSize; protected $programsType = 'Google_Service_Genomics_Program'; protected $programsDataType = 'array'; public $referenceSetId; public $sampleId; public function setDatasetId($datasetId) { $this->datasetId = $datasetId; } public function getDatasetId() { return $this->datasetId; } public function setDescription($description) { $this->description = $description; } public function getDescription() { return $this->description; } public function setExperiment(Google_Service_Genomics_Experiment $experiment) { $this->experiment = $experiment; } public function getExperiment() { return $this->experiment; } public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setInfo($info) { $this->info = $info; } public function getInfo() { return $this->info; } public function setName($name) { $this->name = $name; } public function getName() { return $this->name; } public function setPredictedInsertSize($predictedInsertSize) { $this->predictedInsertSize = $predictedInsertSize; } public function getPredictedInsertSize() { return $this->predictedInsertSize; } public function setPrograms($programs) { $this->programs = $programs; } public function getPrograms() { return $this->programs; } public function setReferenceSetId($referenceSetId) { $this->referenceSetId = $referenceSetId; } public function getReferenceSetId() { return $this->referenceSetId; } public function setSampleId($sampleId) { $this->sampleId = $sampleId; } public function getSampleId() { return $this->sampleId; } } class Google_Service_Genomics_ReadGroupSet extends Google_Collection { protected $collection_key = 'readGroups'; protected $internal_gapi_mappings = array( ); public $datasetId; public $filename; public $id; public $info; public $name; protected $readGroupsType = 'Google_Service_Genomics_ReadGroup'; protected $readGroupsDataType = 'array'; public $referenceSetId; public function setDatasetId($datasetId) { $this->datasetId = $datasetId; } public function getDatasetId() { return $this->datasetId; } public function setFilename($filename) { $this->filename = $filename; } public function getFilename() { return $this->filename; } public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setInfo($info) { $this->info = $info; } public function getInfo() { return $this->info; } public function setName($name) { $this->name = $name; } public function getName() { return $this->name; } public function setReadGroups($readGroups) { $this->readGroups = $readGroups; } public function getReadGroups() { return $this->readGroups; } public function setReferenceSetId($referenceSetId) { $this->referenceSetId = $referenceSetId; } public function getReferenceSetId() { return $this->referenceSetId; } } class Google_Service_Genomics_Reference extends Google_Collection { protected $collection_key = 'sourceAccessions'; protected $internal_gapi_mappings = array( ); public $id; public $length; public $md5checksum; public $name; public $ncbiTaxonId; public $sourceAccessions; public $sourceUri; public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setLength($length) { $this->length = $length; } public function getLength() { return $this->length; } public function setMd5checksum($md5checksum) { $this->md5checksum = $md5checksum; } public function getMd5checksum() { return $this->md5checksum; } public function setName($name) { $this->name = $name; } public function getName() { return $this->name; } public function setNcbiTaxonId($ncbiTaxonId) { $this->ncbiTaxonId = $ncbiTaxonId; } public function getNcbiTaxonId() { return $this->ncbiTaxonId; } public function setSourceAccessions($sourceAccessions) { $this->sourceAccessions = $sourceAccessions; } public function getSourceAccessions() { return $this->sourceAccessions; } public function setSourceUri($sourceUri) { $this->sourceUri = $sourceUri; } public function getSourceUri() { return $this->sourceUri; } } class Google_Service_Genomics_ReferenceBound extends Google_Model { protected $internal_gapi_mappings = array( ); public $referenceName; public $upperBound; public function setReferenceName($referenceName) { $this->referenceName = $referenceName; } public function getReferenceName() { return $this->referenceName; } public function setUpperBound($upperBound) { $this->upperBound = $upperBound; } public function getUpperBound() { return $this->upperBound; } } class Google_Service_Genomics_ReferenceSet extends Google_Collection { protected $collection_key = 'sourceAccessions'; protected $internal_gapi_mappings = array( ); public $assemblyId; public $description; public $id; public $md5checksum; public $ncbiTaxonId; public $referenceIds; public $sourceAccessions; public $sourceUri; public function setAssemblyId($assemblyId) { $this->assemblyId = $assemblyId; } public function getAssemblyId() { return $this->assemblyId; } public function setDescription($description) { $this->description = $description; } public function getDescription() { return $this->description; } public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setMd5checksum($md5checksum) { $this->md5checksum = $md5checksum; } public function getMd5checksum() { return $this->md5checksum; } public function setNcbiTaxonId($ncbiTaxonId) { $this->ncbiTaxonId = $ncbiTaxonId; } public function getNcbiTaxonId() { return $this->ncbiTaxonId; } public function setReferenceIds($referenceIds) { $this->referenceIds = $referenceIds; } public function getReferenceIds() { return $this->referenceIds; } public function setSourceAccessions($sourceAccessions) { $this->sourceAccessions = $sourceAccessions; } public function getSourceAccessions() { return $this->sourceAccessions; } public function setSourceUri($sourceUri) { $this->sourceUri = $sourceUri; } public function getSourceUri() { return $this->sourceUri; } } class Google_Service_Genomics_Rule extends Google_Collection { protected $collection_key = 'permissions'; protected $internal_gapi_mappings = array( ); public $action; protected $conditionsType = 'Google_Service_Genomics_Condition'; protected $conditionsDataType = 'array'; public $description; public $in; protected $logConfigType = 'Google_Service_Genomics_LogConfig'; protected $logConfigDataType = 'array'; public $notIn; public $permissions; public function setAction($action) { $this->action = $action; } public function getAction() { return $this->action; } public function setConditions($conditions) { $this->conditions = $conditions; } public function getConditions() { return $this->conditions; } public function setDescription($description) { $this->description = $description; } public function getDescription() { return $this->description; } public function setIn($in) { $this->in = $in; } public function getIn() { return $this->in; } public function setLogConfig($logConfig) { $this->logConfig = $logConfig; } public function getLogConfig() { return $this->logConfig; } public function setNotIn($notIn) { $this->notIn = $notIn; } public function getNotIn() { return $this->notIn; } public function setPermissions($permissions) { $this->permissions = $permissions; } public function getPermissions() { return $this->permissions; } } class Google_Service_Genomics_SearchCallSetsRequest extends Google_Collection { protected $collection_key = 'variantSetIds'; protected $internal_gapi_mappings = array( ); public $name; public $pageSize; public $pageToken; public $variantSetIds; public function setName($name) { $this->name = $name; } public function getName() { return $this->name; } public function setPageSize($pageSize) { $this->pageSize = $pageSize; } public function getPageSize() { return $this->pageSize; } public function setPageToken($pageToken) { $this->pageToken = $pageToken; } public function getPageToken() { return $this->pageToken; } public function setVariantSetIds($variantSetIds) { $this->variantSetIds = $variantSetIds; } public function getVariantSetIds() { return $this->variantSetIds; } } class Google_Service_Genomics_SearchCallSetsResponse extends Google_Collection { protected $collection_key = 'callSets'; protected $internal_gapi_mappings = array( ); protected $callSetsType = 'Google_Service_Genomics_CallSet'; protected $callSetsDataType = 'array'; public $nextPageToken; public function setCallSets($callSets) { $this->callSets = $callSets; } public function getCallSets() { return $this->callSets; } public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } } class Google_Service_Genomics_SearchReadGroupSetsRequest extends Google_Collection { protected $collection_key = 'datasetIds'; protected $internal_gapi_mappings = array( ); public $datasetIds; public $name; public $pageSize; public $pageToken; public function setDatasetIds($datasetIds) { $this->datasetIds = $datasetIds; } public function getDatasetIds() { return $this->datasetIds; } public function setName($name) { $this->name = $name; } public function getName() { return $this->name; } public function setPageSize($pageSize) { $this->pageSize = $pageSize; } public function getPageSize() { return $this->pageSize; } public function setPageToken($pageToken) { $this->pageToken = $pageToken; } public function getPageToken() { return $this->pageToken; } } class Google_Service_Genomics_SearchReadGroupSetsResponse extends Google_Collection { protected $collection_key = 'readGroupSets'; protected $internal_gapi_mappings = array( ); public $nextPageToken; protected $readGroupSetsType = 'Google_Service_Genomics_ReadGroupSet'; protected $readGroupSetsDataType = 'array'; public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } public function setReadGroupSets($readGroupSets) { $this->readGroupSets = $readGroupSets; } public function getReadGroupSets() { return $this->readGroupSets; } } class Google_Service_Genomics_SearchReadsRequest extends Google_Collection { protected $collection_key = 'readGroupSetIds'; protected $internal_gapi_mappings = array( ); public $end; public $pageSize; public $pageToken; public $readGroupIds; public $readGroupSetIds; public $referenceName; public $start; public function setEnd($end) { $this->end = $end; } public function getEnd() { return $this->end; } public function setPageSize($pageSize) { $this->pageSize = $pageSize; } public function getPageSize() { return $this->pageSize; } public function setPageToken($pageToken) { $this->pageToken = $pageToken; } public function getPageToken() { return $this->pageToken; } public function setReadGroupIds($readGroupIds) { $this->readGroupIds = $readGroupIds; } public function getReadGroupIds() { return $this->readGroupIds; } public function setReadGroupSetIds($readGroupSetIds) { $this->readGroupSetIds = $readGroupSetIds; } public function getReadGroupSetIds() { return $this->readGroupSetIds; } public function setReferenceName($referenceName) { $this->referenceName = $referenceName; } public function getReferenceName() { return $this->referenceName; } public function setStart($start) { $this->start = $start; } public function getStart() { return $this->start; } } class Google_Service_Genomics_SearchReadsResponse extends Google_Collection { protected $collection_key = 'alignments'; protected $internal_gapi_mappings = array( ); protected $alignmentsType = 'Google_Service_Genomics_Read'; protected $alignmentsDataType = 'array'; public $nextPageToken; public function setAlignments($alignments) { $this->alignments = $alignments; } public function getAlignments() { return $this->alignments; } public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } } class Google_Service_Genomics_SearchReferenceSetsRequest extends Google_Collection { protected $collection_key = 'md5checksums'; protected $internal_gapi_mappings = array( ); public $accessions; public $assemblyId; public $md5checksums; public $pageSize; public $pageToken; public function setAccessions($accessions) { $this->accessions = $accessions; } public function getAccessions() { return $this->accessions; } public function setAssemblyId($assemblyId) { $this->assemblyId = $assemblyId; } public function getAssemblyId() { return $this->assemblyId; } public function setMd5checksums($md5checksums) { $this->md5checksums = $md5checksums; } public function getMd5checksums() { return $this->md5checksums; } public function setPageSize($pageSize) { $this->pageSize = $pageSize; } public function getPageSize() { return $this->pageSize; } public function setPageToken($pageToken) { $this->pageToken = $pageToken; } public function getPageToken() { return $this->pageToken; } } class Google_Service_Genomics_SearchReferenceSetsResponse extends Google_Collection { protected $collection_key = 'referenceSets'; protected $internal_gapi_mappings = array( ); public $nextPageToken; protected $referenceSetsType = 'Google_Service_Genomics_ReferenceSet'; protected $referenceSetsDataType = 'array'; public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } public function setReferenceSets($referenceSets) { $this->referenceSets = $referenceSets; } public function getReferenceSets() { return $this->referenceSets; } } class Google_Service_Genomics_SearchReferencesRequest extends Google_Collection { protected $collection_key = 'md5checksums'; protected $internal_gapi_mappings = array( ); public $accessions; public $md5checksums; public $pageSize; public $pageToken; public $referenceSetId; public function setAccessions($accessions) { $this->accessions = $accessions; } public function getAccessions() { return $this->accessions; } public function setMd5checksums($md5checksums) { $this->md5checksums = $md5checksums; } public function getMd5checksums() { return $this->md5checksums; } public function setPageSize($pageSize) { $this->pageSize = $pageSize; } public function getPageSize() { return $this->pageSize; } public function setPageToken($pageToken) { $this->pageToken = $pageToken; } public function getPageToken() { return $this->pageToken; } public function setReferenceSetId($referenceSetId) { $this->referenceSetId = $referenceSetId; } public function getReferenceSetId() { return $this->referenceSetId; } } class Google_Service_Genomics_SearchReferencesResponse extends Google_Collection { protected $collection_key = 'references'; protected $internal_gapi_mappings = array( ); public $nextPageToken; protected $referencesType = 'Google_Service_Genomics_Reference'; protected $referencesDataType = 'array'; public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } public function setReferences($references) { $this->references = $references; } public function getReferences() { return $this->references; } } class Google_Service_Genomics_SearchVariantSetsRequest extends Google_Collection { protected $collection_key = 'datasetIds'; protected $internal_gapi_mappings = array( ); public $datasetIds; public $pageSize; public $pageToken; public function setDatasetIds($datasetIds) { $this->datasetIds = $datasetIds; } public function getDatasetIds() { return $this->datasetIds; } public function setPageSize($pageSize) { $this->pageSize = $pageSize; } public function getPageSize() { return $this->pageSize; } public function setPageToken($pageToken) { $this->pageToken = $pageToken; } public function getPageToken() { return $this->pageToken; } } class Google_Service_Genomics_SearchVariantSetsResponse extends Google_Collection { protected $collection_key = 'variantSets'; protected $internal_gapi_mappings = array( ); public $nextPageToken; protected $variantSetsType = 'Google_Service_Genomics_VariantSet'; protected $variantSetsDataType = 'array'; public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } public function setVariantSets($variantSets) { $this->variantSets = $variantSets; } public function getVariantSets() { return $this->variantSets; } } class Google_Service_Genomics_SearchVariantsRequest extends Google_Collection { protected $collection_key = 'variantSetIds'; protected $internal_gapi_mappings = array( ); public $callSetIds; public $end; public $maxCalls; public $pageSize; public $pageToken; public $referenceName; public $start; public $variantName; public $variantSetIds; public function setCallSetIds($callSetIds) { $this->callSetIds = $callSetIds; } public function getCallSetIds() { return $this->callSetIds; } public function setEnd($end) { $this->end = $end; } public function getEnd() { return $this->end; } public function setMaxCalls($maxCalls) { $this->maxCalls = $maxCalls; } public function getMaxCalls() { return $this->maxCalls; } public function setPageSize($pageSize) { $this->pageSize = $pageSize; } public function getPageSize() { return $this->pageSize; } public function setPageToken($pageToken) { $this->pageToken = $pageToken; } public function getPageToken() { return $this->pageToken; } public function setReferenceName($referenceName) { $this->referenceName = $referenceName; } public function getReferenceName() { return $this->referenceName; } public function setStart($start) { $this->start = $start; } public function getStart() { return $this->start; } public function setVariantName($variantName) { $this->variantName = $variantName; } public function getVariantName() { return $this->variantName; } public function setVariantSetIds($variantSetIds) { $this->variantSetIds = $variantSetIds; } public function getVariantSetIds() { return $this->variantSetIds; } } class Google_Service_Genomics_SearchVariantsResponse extends Google_Collection { protected $collection_key = 'variants'; protected $internal_gapi_mappings = array( ); public $nextPageToken; protected $variantsType = 'Google_Service_Genomics_Variant'; protected $variantsDataType = 'array'; public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } public function setVariants($variants) { $this->variants = $variants; } public function getVariants() { return $this->variants; } } class Google_Service_Genomics_SetIamPolicyRequest extends Google_Model { protected $internal_gapi_mappings = array( ); protected $policyType = 'Google_Service_Genomics_Policy'; protected $policyDataType = ''; public function setPolicy(Google_Service_Genomics_Policy $policy) { $this->policy = $policy; } public function getPolicy() { return $this->policy; } } class Google_Service_Genomics_Status extends Google_Collection { protected $collection_key = 'details'; protected $internal_gapi_mappings = array( ); public $code; public $details; public $message; public function setCode($code) { $this->code = $code; } public function getCode() { return $this->code; } public function setDetails($details) { $this->details = $details; } public function getDetails() { return $this->details; } public function setMessage($message) { $this->message = $message; } public function getMessage() { return $this->message; } } class Google_Service_Genomics_StreamReadsRequest extends Google_Model { protected $internal_gapi_mappings = array( ); public $end; public $projectId; public $readGroupSetId; public $referenceName; public $start; public function setEnd($end) { $this->end = $end; } public function getEnd() { return $this->end; } public function setProjectId($projectId) { $this->projectId = $projectId; } public function getProjectId() { return $this->projectId; } public function setReadGroupSetId($readGroupSetId) { $this->readGroupSetId = $readGroupSetId; } public function getReadGroupSetId() { return $this->readGroupSetId; } public function setReferenceName($referenceName) { $this->referenceName = $referenceName; } public function getReferenceName() { return $this->referenceName; } public function setStart($start) { $this->start = $start; } public function getStart() { return $this->start; } } class Google_Service_Genomics_StreamReadsResponse extends Google_Collection { protected $collection_key = 'alignments'; protected $internal_gapi_mappings = array( ); protected $alignmentsType = 'Google_Service_Genomics_Read'; protected $alignmentsDataType = 'array'; public function setAlignments($alignments) { $this->alignments = $alignments; } public function getAlignments() { return $this->alignments; } } class Google_Service_Genomics_StreamVariantsRequest extends Google_Collection { protected $collection_key = 'callSetIds'; protected $internal_gapi_mappings = array( ); public $callSetIds; public $end; public $projectId; public $referenceName; public $start; public $variantSetId; public function setCallSetIds($callSetIds) { $this->callSetIds = $callSetIds; } public function getCallSetIds() { return $this->callSetIds; } public function setEnd($end) { $this->end = $end; } public function getEnd() { return $this->end; } public function setProjectId($projectId) { $this->projectId = $projectId; } public function getProjectId() { return $this->projectId; } public function setReferenceName($referenceName) { $this->referenceName = $referenceName; } public function getReferenceName() { return $this->referenceName; } public function setStart($start) { $this->start = $start; } public function getStart() { return $this->start; } public function setVariantSetId($variantSetId) { $this->variantSetId = $variantSetId; } public function getVariantSetId() { return $this->variantSetId; } } class Google_Service_Genomics_StreamVariantsResponse extends Google_Collection { protected $collection_key = 'variants'; protected $internal_gapi_mappings = array( ); protected $variantsType = 'Google_Service_Genomics_Variant'; protected $variantsDataType = 'array'; public function setVariants($variants) { $this->variants = $variants; } public function getVariants() { return $this->variants; } } class Google_Service_Genomics_TestIamPermissionsRequest extends Google_Collection { protected $collection_key = 'permissions'; protected $internal_gapi_mappings = array( ); public $permissions; public function setPermissions($permissions) { $this->permissions = $permissions; } public function getPermissions() { return $this->permissions; } } class Google_Service_Genomics_TestIamPermissionsResponse extends Google_Collection { protected $collection_key = 'permissions'; protected $internal_gapi_mappings = array( ); public $permissions; public function setPermissions($permissions) { $this->permissions = $permissions; } public function getPermissions() { return $this->permissions; } } class Google_Service_Genomics_UndeleteDatasetRequest extends Google_Model { } class Google_Service_Genomics_Variant extends Google_Collection { protected $collection_key = 'names'; protected $internal_gapi_mappings = array( ); public $alternateBases; protected $callsType = 'Google_Service_Genomics_VariantCall'; protected $callsDataType = 'array'; public $created; public $end; public $filter; public $id; public $info; public $names; public $quality; public $referenceBases; public $referenceName; public $start; public $variantSetId; public function setAlternateBases($alternateBases) { $this->alternateBases = $alternateBases; } public function getAlternateBases() { return $this->alternateBases; } public function setCalls($calls) { $this->calls = $calls; } public function getCalls() { return $this->calls; } public function setCreated($created) { $this->created = $created; } public function getCreated() { return $this->created; } public function setEnd($end) { $this->end = $end; } public function getEnd() { return $this->end; } public function setFilter($filter) { $this->filter = $filter; } public function getFilter() { return $this->filter; } public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setInfo($info) { $this->info = $info; } public function getInfo() { return $this->info; } public function setNames($names) { $this->names = $names; } public function getNames() { return $this->names; } public function setQuality($quality) { $this->quality = $quality; } public function getQuality() { return $this->quality; } public function setReferenceBases($referenceBases) { $this->referenceBases = $referenceBases; } public function getReferenceBases() { return $this->referenceBases; } public function setReferenceName($referenceName) { $this->referenceName = $referenceName; } public function getReferenceName() { return $this->referenceName; } public function setStart($start) { $this->start = $start; } public function getStart() { return $this->start; } public function setVariantSetId($variantSetId) { $this->variantSetId = $variantSetId; } public function getVariantSetId() { return $this->variantSetId; } } class Google_Service_Genomics_VariantCall extends Google_Collection { protected $collection_key = 'genotypeLikelihood'; protected $internal_gapi_mappings = array( ); public $callSetId; public $callSetName; public $genotype; public $genotypeLikelihood; public $info; public $phaseset; public function setCallSetId($callSetId) { $this->callSetId = $callSetId; } public function getCallSetId() { return $this->callSetId; } public function setCallSetName($callSetName) { $this->callSetName = $callSetName; } public function getCallSetName() { return $this->callSetName; } public function setGenotype($genotype) { $this->genotype = $genotype; } public function getGenotype() { return $this->genotype; } public function setGenotypeLikelihood($genotypeLikelihood) { $this->genotypeLikelihood = $genotypeLikelihood; } public function getGenotypeLikelihood() { return $this->genotypeLikelihood; } public function setInfo($info) { $this->info = $info; } public function getInfo() { return $this->info; } public function setPhaseset($phaseset) { $this->phaseset = $phaseset; } public function getPhaseset() { return $this->phaseset; } } class Google_Service_Genomics_VariantSet extends Google_Collection { protected $collection_key = 'referenceBounds'; protected $internal_gapi_mappings = array( ); public $datasetId; public $id; protected $metadataType = 'Google_Service_Genomics_VariantSetMetadata'; protected $metadataDataType = 'array'; protected $referenceBoundsType = 'Google_Service_Genomics_ReferenceBound'; protected $referenceBoundsDataType = 'array'; public $referenceSetId; public function setDatasetId($datasetId) { $this->datasetId = $datasetId; } public function getDatasetId() { return $this->datasetId; } public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setMetadata($metadata) { $this->metadata = $metadata; } public function getMetadata() { return $this->metadata; } public function setReferenceBounds($referenceBounds) { $this->referenceBounds = $referenceBounds; } public function getReferenceBounds() { return $this->referenceBounds; } public function setReferenceSetId($referenceSetId) { $this->referenceSetId = $referenceSetId; } public function getReferenceSetId() { return $this->referenceSetId; } } class Google_Service_Genomics_VariantSetMetadata extends Google_Model { protected $internal_gapi_mappings = array( ); public $description; public $id; public $info; public $key; public $number; public $type; public $value; public function setDescription($description) { $this->description = $description; } public function getDescription() { return $this->description; } public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setInfo($info) { $this->info = $info; } public function getInfo() { return $this->info; } public function setKey($key) { $this->key = $key; } public function getKey() { return $this->key; } public function setNumber($number) { $this->number = $number; } public function getNumber() { return $this->number; } public function setType($type) { $this->type = $type; } public function getType() { return $this->type; } public function setValue($value) { $this->value = $value; } public function getValue() { return $this->value; } }