* Provides access to Genomics data.

* *

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

* * @author Google, Inc. */ class GoogleGAL_Service_Genomics extends GoogleGAL_Service { /** View and manage your data in Google BigQuery. */ const BIGQUERY = "https://www.googleapis.com/auth/bigquery"; /** 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 $experimental_jobs; public $jobs; 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 GoogleGAL_Client $client */ public function __construct(GoogleGAL_Client $client) { parent::__construct($client); $this->servicePath = 'genomics/v1beta2/'; $this->version = 'v1beta2'; $this->serviceName = 'genomics'; $this->callsets = new GoogleGAL_Service_Genomics_Callsets_Resource( $this, $this->serviceName, 'callsets', array( 'methods' => array( 'create' => array( 'path' => 'callsets', 'httpMethod' => 'POST', 'parameters' => array(), ),'delete' => array( 'path' => 'callsets/{callSetId}', 'httpMethod' => 'DELETE', 'parameters' => array( 'callSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'get' => array( 'path' => 'callsets/{callSetId}', 'httpMethod' => 'GET', 'parameters' => array( 'callSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'patch' => array( 'path' => 'callsets/{callSetId}', 'httpMethod' => 'PATCH', 'parameters' => array( 'callSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'search' => array( 'path' => 'callsets/search', 'httpMethod' => 'POST', 'parameters' => array(), ),'update' => array( 'path' => 'callsets/{callSetId}', 'httpMethod' => 'PUT', 'parameters' => array( 'callSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ), ) ) ); $this->datasets = new GoogleGAL_Service_Genomics_Datasets_Resource( $this, $this->serviceName, 'datasets', array( 'methods' => array( 'create' => array( 'path' => 'datasets', 'httpMethod' => 'POST', 'parameters' => array(), ),'delete' => array( 'path' => 'datasets/{datasetId}', 'httpMethod' => 'DELETE', 'parameters' => array( 'datasetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'get' => array( 'path' => 'datasets/{datasetId}', 'httpMethod' => 'GET', 'parameters' => array( 'datasetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'list' => array( 'path' => 'datasets', 'httpMethod' => 'GET', 'parameters' => array( 'pageToken' => array( 'location' => 'query', 'type' => 'string', ), 'projectNumber' => array( 'location' => 'query', 'type' => 'string', ), 'pageSize' => array( 'location' => 'query', 'type' => 'integer', ), ), ),'patch' => array( 'path' => 'datasets/{datasetId}', 'httpMethod' => 'PATCH', 'parameters' => array( 'datasetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'undelete' => array( 'path' => 'datasets/{datasetId}/undelete', 'httpMethod' => 'POST', 'parameters' => array( 'datasetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'update' => array( 'path' => 'datasets/{datasetId}', 'httpMethod' => 'PUT', 'parameters' => array( 'datasetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ), ) ) ); $this->experimental_jobs = new GoogleGAL_Service_Genomics_ExperimentalJobs_Resource( $this, $this->serviceName, 'jobs', array( 'methods' => array( 'create' => array( 'path' => 'experimental/jobs/create', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); $this->jobs = new GoogleGAL_Service_Genomics_Jobs_Resource( $this, $this->serviceName, 'jobs', array( 'methods' => array( 'cancel' => array( 'path' => 'jobs/{jobId}/cancel', 'httpMethod' => 'POST', 'parameters' => array( 'jobId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'get' => array( 'path' => 'jobs/{jobId}', 'httpMethod' => 'GET', 'parameters' => array( 'jobId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'search' => array( 'path' => 'jobs/search', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); $this->readgroupsets = new GoogleGAL_Service_Genomics_Readgroupsets_Resource( $this, $this->serviceName, 'readgroupsets', array( 'methods' => array( 'align' => array( 'path' => 'readgroupsets/align', 'httpMethod' => 'POST', 'parameters' => array(), ),'call' => array( 'path' => 'readgroupsets/call', 'httpMethod' => 'POST', 'parameters' => array(), ),'delete' => array( 'path' => 'readgroupsets/{readGroupSetId}', 'httpMethod' => 'DELETE', 'parameters' => array( 'readGroupSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'export' => array( 'path' => 'readgroupsets/export', 'httpMethod' => 'POST', 'parameters' => array(), ),'get' => array( 'path' => 'readgroupsets/{readGroupSetId}', 'httpMethod' => 'GET', 'parameters' => array( 'readGroupSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'import' => array( 'path' => 'readgroupsets/import', 'httpMethod' => 'POST', 'parameters' => array(), ),'patch' => array( 'path' => 'readgroupsets/{readGroupSetId}', 'httpMethod' => 'PATCH', 'parameters' => array( 'readGroupSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'search' => array( 'path' => 'readgroupsets/search', 'httpMethod' => 'POST', 'parameters' => array(), ),'update' => array( 'path' => 'readgroupsets/{readGroupSetId}', 'httpMethod' => 'PUT', 'parameters' => array( 'readGroupSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ), ) ) ); $this->readgroupsets_coveragebuckets = new GoogleGAL_Service_Genomics_ReadgroupsetsCoveragebuckets_Resource( $this, $this->serviceName, 'coveragebuckets', array( 'methods' => array( 'list' => array( 'path' => 'readgroupsets/{readGroupSetId}/coveragebuckets', 'httpMethod' => 'GET', 'parameters' => array( 'readGroupSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), 'pageSize' => array( 'location' => 'query', 'type' => 'integer', ), 'range.start' => array( 'location' => 'query', 'type' => 'string', ), 'range.end' => array( 'location' => 'query', 'type' => 'string', ), 'range.referenceName' => array( 'location' => 'query', 'type' => 'string', ), 'pageToken' => array( 'location' => 'query', 'type' => 'string', ), 'targetBucketWidth' => array( 'location' => 'query', 'type' => 'string', ), ), ), ) ) ); $this->reads = new GoogleGAL_Service_Genomics_Reads_Resource( $this, $this->serviceName, 'reads', array( 'methods' => array( 'search' => array( 'path' => 'reads/search', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); $this->references = new GoogleGAL_Service_Genomics_References_Resource( $this, $this->serviceName, 'references', array( 'methods' => array( 'get' => array( 'path' => 'references/{referenceId}', 'httpMethod' => 'GET', 'parameters' => array( 'referenceId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'search' => array( 'path' => 'references/search', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); $this->references_bases = new GoogleGAL_Service_Genomics_ReferencesBases_Resource( $this, $this->serviceName, 'bases', array( 'methods' => array( 'list' => array( 'path' => 'references/{referenceId}/bases', 'httpMethod' => 'GET', 'parameters' => array( 'referenceId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), 'pageToken' => array( 'location' => 'query', 'type' => 'string', ), 'end' => array( 'location' => 'query', 'type' => 'string', ), 'pageSize' => array( 'location' => 'query', 'type' => 'integer', ), 'start' => array( 'location' => 'query', 'type' => 'string', ), ), ), ) ) ); $this->referencesets = new GoogleGAL_Service_Genomics_Referencesets_Resource( $this, $this->serviceName, 'referencesets', array( 'methods' => array( 'get' => array( 'path' => 'referencesets/{referenceSetId}', 'httpMethod' => 'GET', 'parameters' => array( 'referenceSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'search' => array( 'path' => 'referencesets/search', 'httpMethod' => 'POST', 'parameters' => array(), ), ) ) ); $this->variants = new GoogleGAL_Service_Genomics_Variants_Resource( $this, $this->serviceName, 'variants', array( 'methods' => array( 'create' => array( 'path' => 'variants', 'httpMethod' => 'POST', 'parameters' => array(), ),'delete' => array( 'path' => 'variants/{variantId}', 'httpMethod' => 'DELETE', 'parameters' => array( 'variantId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'get' => array( 'path' => 'variants/{variantId}', 'httpMethod' => 'GET', 'parameters' => array( 'variantId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'search' => array( 'path' => 'variants/search', 'httpMethod' => 'POST', 'parameters' => array(), ),'update' => array( 'path' => 'variants/{variantId}', 'httpMethod' => 'PUT', 'parameters' => array( 'variantId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ), ) ) ); $this->variantsets = new GoogleGAL_Service_Genomics_Variantsets_Resource( $this, $this->serviceName, 'variantsets', array( 'methods' => array( 'delete' => array( 'path' => 'variantsets/{variantSetId}', 'httpMethod' => 'DELETE', 'parameters' => array( 'variantSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'export' => array( 'path' => 'variantsets/{variantSetId}/export', 'httpMethod' => 'POST', 'parameters' => array( 'variantSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'get' => array( 'path' => 'variantsets/{variantSetId}', 'httpMethod' => 'GET', 'parameters' => array( 'variantSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'importVariants' => array( 'path' => 'variantsets/{variantSetId}/importVariants', 'httpMethod' => 'POST', 'parameters' => array( 'variantSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'mergeVariants' => array( 'path' => 'variantsets/{variantSetId}/mergeVariants', 'httpMethod' => 'POST', 'parameters' => array( 'variantSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'patch' => array( 'path' => 'variantsets/{variantSetId}', 'httpMethod' => 'PATCH', 'parameters' => array( 'variantSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ),'search' => array( 'path' => 'variantsets/search', 'httpMethod' => 'POST', 'parameters' => array(), ),'update' => array( 'path' => 'variantsets/{variantSetId}', 'httpMethod' => 'PUT', 'parameters' => array( 'variantSetId' => array( 'location' => 'path', 'type' => 'string', 'required' => true, ), ), ), ) ) ); } } /** * The "callsets" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $callsets = $genomicsService->callsets; * */ class GoogleGAL_Service_Genomics_Callsets_Resource extends GoogleGAL_Service_Resource { /** * Creates a new call set. (callsets.create) * * @param GoogleGAL_CallSet $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_CallSet */ public function create(GoogleGAL_Service_Genomics_CallSet $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('create', array($params), "GoogleGAL_Service_Genomics_CallSet"); } /** * Deletes a call set. (callsets.delete) * * @param string $callSetId The ID of the call set to be deleted. * @param array $optParams Optional parameters. */ public function delete($callSetId, $optParams = array()) { $params = array('callSetId' => $callSetId); $params = array_merge($params, $optParams); return $this->call('delete', array($params)); } /** * Gets a call set by ID. (callsets.get) * * @param string $callSetId The ID of the call set. * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_CallSet */ public function get($callSetId, $optParams = array()) { $params = array('callSetId' => $callSetId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "GoogleGAL_Service_Genomics_CallSet"); } /** * Updates a call set. This method supports patch semantics. (callsets.patch) * * @param string $callSetId The ID of the call set to be updated. * @param GoogleGAL_CallSet $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_CallSet */ public function patch($callSetId, GoogleGAL_Service_Genomics_CallSet $postBody, $optParams = array()) { $params = array('callSetId' => $callSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('patch', array($params), "GoogleGAL_Service_Genomics_CallSet"); } /** * Gets a list of call sets matching the criteria. * * Implements GlobalAllianceApi.searchCallSets. (callsets.search) * * @param GoogleGAL_SearchCallSetsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_SearchCallSetsResponse */ public function search(GoogleGAL_Service_Genomics_SearchCallSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "GoogleGAL_Service_Genomics_SearchCallSetsResponse"); } /** * Updates a call set. (callsets.update) * * @param string $callSetId The ID of the call set to be updated. * @param GoogleGAL_CallSet $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_CallSet */ public function update($callSetId, GoogleGAL_Service_Genomics_CallSet $postBody, $optParams = array()) { $params = array('callSetId' => $callSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('update', array($params), "GoogleGAL_Service_Genomics_CallSet"); } } /** * The "datasets" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $datasets = $genomicsService->datasets; * */ class GoogleGAL_Service_Genomics_Datasets_Resource extends GoogleGAL_Service_Resource { /** * Creates a new dataset. (datasets.create) * * @param GoogleGAL_Dataset $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_Dataset */ public function create(GoogleGAL_Service_Genomics_Dataset $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('create', array($params), "GoogleGAL_Service_Genomics_Dataset"); } /** * Deletes a dataset. (datasets.delete) * * @param string $datasetId The ID of the dataset to be deleted. * @param array $optParams Optional parameters. */ public function delete($datasetId, $optParams = array()) { $params = array('datasetId' => $datasetId); $params = array_merge($params, $optParams); return $this->call('delete', array($params)); } /** * Gets a dataset by ID. (datasets.get) * * @param string $datasetId The ID of the dataset. * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_Dataset */ public function get($datasetId, $optParams = array()) { $params = array('datasetId' => $datasetId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "GoogleGAL_Service_Genomics_Dataset"); } /** * Lists all datasets. (datasets.listDatasets) * * @param array $optParams Optional parameters. * * @opt_param string pageToken The continuation token, which is used to page * through large result sets. To get the next page of results, set this * parameter to the value of nextPageToken from the previous response. * @opt_param string projectNumber Only return datasets which belong to this * Google Developers Console project. Only accepts project numbers. Returns all * public projects if no project number is specified. * @opt_param int pageSize The maximum number of results returned by this * request. * @return GoogleGAL_Service_Genomics_ListDatasetsResponse */ public function listDatasets($optParams = array()) { $params = array(); $params = array_merge($params, $optParams); return $this->call('list', array($params), "GoogleGAL_Service_Genomics_ListDatasetsResponse"); } /** * Updates a dataset. This method supports patch semantics. (datasets.patch) * * @param string $datasetId The ID of the dataset to be updated. * @param GoogleGAL_Dataset $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_Dataset */ public function patch($datasetId, GoogleGAL_Service_Genomics_Dataset $postBody, $optParams = array()) { $params = array('datasetId' => $datasetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('patch', array($params), "GoogleGAL_Service_Genomics_Dataset"); } /** * Undeletes a dataset by restoring a dataset which was deleted via this API. * 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 array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_Dataset */ public function undelete($datasetId, $optParams = array()) { $params = array('datasetId' => $datasetId); $params = array_merge($params, $optParams); return $this->call('undelete', array($params), "GoogleGAL_Service_Genomics_Dataset"); } /** * Updates a dataset. (datasets.update) * * @param string $datasetId The ID of the dataset to be updated. * @param GoogleGAL_Dataset $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_Dataset */ public function update($datasetId, GoogleGAL_Service_Genomics_Dataset $postBody, $optParams = array()) { $params = array('datasetId' => $datasetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('update', array($params), "GoogleGAL_Service_Genomics_Dataset"); } } /** * The "experimental" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $experimental = $genomicsService->experimental; * */ class GoogleGAL_Service_Genomics_Experimental_Resource extends GoogleGAL_Service_Resource { } /** * The "jobs" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $jobs = $genomicsService->jobs; * */ class GoogleGAL_Service_Genomics_ExperimentalJobs_Resource extends GoogleGAL_Service_Resource { /** * Creates and asynchronously runs an ad-hoc job. This is an experimental call * and may be removed or changed at any time. (jobs.create) * * @param GoogleGAL_ExperimentalCreateJobRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_ExperimentalCreateJobResponse */ public function create(GoogleGAL_Service_Genomics_ExperimentalCreateJobRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('create', array($params), "GoogleGAL_Service_Genomics_ExperimentalCreateJobResponse"); } } /** * The "jobs" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $jobs = $genomicsService->jobs; * */ class GoogleGAL_Service_Genomics_Jobs_Resource extends GoogleGAL_Service_Resource { /** * Cancels a job by ID. Note that it is possible for partial results to be * generated and stored for cancelled jobs. (jobs.cancel) * * @param string $jobId Required. The ID of the job. * @param array $optParams Optional parameters. */ public function cancel($jobId, $optParams = array()) { $params = array('jobId' => $jobId); $params = array_merge($params, $optParams); return $this->call('cancel', array($params)); } /** * Gets a job by ID. (jobs.get) * * @param string $jobId Required. The ID of the job. * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_Job */ public function get($jobId, $optParams = array()) { $params = array('jobId' => $jobId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "GoogleGAL_Service_Genomics_Job"); } /** * Gets a list of jobs matching the criteria. (jobs.search) * * @param GoogleGAL_SearchJobsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_SearchJobsResponse */ public function search(GoogleGAL_Service_Genomics_SearchJobsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "GoogleGAL_Service_Genomics_SearchJobsResponse"); } } /** * The "readgroupsets" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $readgroupsets = $genomicsService->readgroupsets; * */ class GoogleGAL_Service_Genomics_Readgroupsets_Resource extends GoogleGAL_Service_Resource { /** * Aligns read data from existing read group sets or files from Google Cloud * Storage. See the alignment and variant calling documentation for more * details. (readgroupsets.align) * * @param GoogleGAL_AlignReadGroupSetsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_AlignReadGroupSetsResponse */ public function align(GoogleGAL_Service_Genomics_AlignReadGroupSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('align', array($params), "GoogleGAL_Service_Genomics_AlignReadGroupSetsResponse"); } /** * Calls variants on read data from existing read group sets or files from * Google Cloud Storage. See the alignment and variant calling documentation * for more details. (readgroupsets.callReadgroupsets) * * @param GoogleGAL_CallReadGroupSetsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_CallReadGroupSetsResponse */ public function callReadgroupsets(GoogleGAL_Service_Genomics_CallReadGroupSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('call', array($params), "GoogleGAL_Service_Genomics_CallReadGroupSetsResponse"); } /** * Deletes a read group set. (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 $optParams Optional parameters. */ public function delete($readGroupSetId, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId); $params = array_merge($params, $optParams); return $this->call('delete', array($params)); } /** * Exports read group sets to a BAM file in Google Cloud Storage. * * Note that currently there may be some differences between exported BAM files * and the original BAM file at the time of import. In particular, comments in * the input file header will not be preserved, and some custom tags will be * converted to strings. (readgroupsets.export) * * @param GoogleGAL_ExportReadGroupSetsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_ExportReadGroupSetsResponse */ public function export(GoogleGAL_Service_Genomics_ExportReadGroupSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('export', array($params), "GoogleGAL_Service_Genomics_ExportReadGroupSetsResponse"); } /** * Gets a read group set by ID. (readgroupsets.get) * * @param string $readGroupSetId The ID of the read group set. * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_ReadGroupSet */ public function get($readGroupSetId, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "GoogleGAL_Service_Genomics_ReadGroupSet"); } /** * Creates read group sets by asynchronously importing the provided information. * * Note that currently comments in the input file header are not imported and * some custom tags will be converted to strings, rather than preserving tag * types. The caller must have WRITE permissions to the dataset. * (readgroupsets.import) * * @param GoogleGAL_ImportReadGroupSetsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_ImportReadGroupSetsResponse */ public function import(GoogleGAL_Service_Genomics_ImportReadGroupSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('import', array($params), "GoogleGAL_Service_Genomics_ImportReadGroupSetsResponse"); } /** * Updates a read group set. 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 GoogleGAL_ReadGroupSet $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_ReadGroupSet */ public function patch($readGroupSetId, GoogleGAL_Service_Genomics_ReadGroupSet $postBody, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('patch', array($params), "GoogleGAL_Service_Genomics_ReadGroupSet"); } /** * Searches for read group sets matching the criteria. * * Implements GlobalAllianceApi.searchReadGroupSets. (readgroupsets.search) * * @param GoogleGAL_SearchReadGroupSetsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_SearchReadGroupSetsResponse */ public function search(GoogleGAL_Service_Genomics_SearchReadGroupSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "GoogleGAL_Service_Genomics_SearchReadGroupSetsResponse"); } /** * Updates a read group set. (readgroupsets.update) * * @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 GoogleGAL_ReadGroupSet $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_ReadGroupSet */ public function update($readGroupSetId, GoogleGAL_Service_Genomics_ReadGroupSet $postBody, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('update', array($params), "GoogleGAL_Service_Genomics_ReadGroupSet"); } } /** * The "coveragebuckets" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $coveragebuckets = $genomicsService->coveragebuckets; * */ class GoogleGAL_Service_Genomics_ReadgroupsetsCoveragebuckets_Resource extends GoogleGAL_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. * * 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 $optParams Optional parameters. * * @opt_param int pageSize The maximum number of results to return in a single * page. If unspecified, defaults to 1024. The maximum value is 2048. * @opt_param string range.start The start position of the range on the * reference, 0-based inclusive. If specified, referenceName must also be * specified. * @opt_param string range.end The end position of the range on the reference, * 0-based exclusive. If specified, referenceName must also be specified. * @opt_param string range.referenceName The reference sequence name, for * example chr1, 1, or chrX. * @opt_param string pageToken The continuation token, which is used to page * through large result sets. To get the next page of results, set this * parameter to the value of nextPageToken from the previous response. * @opt_param string targetBucketWidth The desired width of each reported * coverage bucket in base pairs. This will be rounded down to the nearest * precomputed bucket width; the value of which is returned as bucketWidth in * the response. Defaults to infinity (each bucket spans an entire reference * sequence) or the length of the target range, if specified. The smallest * precomputed bucketWidth is currently 2048 base pairs; this is subject to * change. * @return GoogleGAL_Service_Genomics_ListCoverageBucketsResponse */ public function listReadgroupsetsCoveragebuckets($readGroupSetId, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId); $params = array_merge($params, $optParams); return $this->call('list', array($params), "GoogleGAL_Service_Genomics_ListCoverageBucketsResponse"); } } /** * The "reads" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $reads = $genomicsService->reads; * */ class GoogleGAL_Service_Genomics_Reads_Resource extends GoogleGAL_Service_Resource { /** * Gets a list of reads for one or more read group sets. Reads search operates * over a genomic coordinate space of reference sequence & position defined over * the reference sequences to which the requested read group sets are aligned. * * If a target positional range is specified, search returns all reads whose * alignment to the reference genome overlap the range. A query which specifies * only read group set IDs yields all reads in those read group sets, including * unmapped reads. * * All reads returned (including reads on subsequent pages) are ordered by * genomic coordinate (reference sequence & position). Reads with equivalent * genomic coordinates are returned in a deterministic order. * * Implements GlobalAllianceApi.searchReads. (reads.search) * * @param GoogleGAL_SearchReadsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_SearchReadsResponse */ public function search(GoogleGAL_Service_Genomics_SearchReadsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "GoogleGAL_Service_Genomics_SearchReadsResponse"); } } /** * The "references" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $references = $genomicsService->references; * */ class GoogleGAL_Service_Genomics_References_Resource extends GoogleGAL_Service_Resource { /** * Gets a reference. * * Implements GlobalAllianceApi.getReference. (references.get) * * @param string $referenceId The ID of the reference. * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_Reference */ public function get($referenceId, $optParams = array()) { $params = array('referenceId' => $referenceId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "GoogleGAL_Service_Genomics_Reference"); } /** * Searches for references which match the given criteria. * * Implements GlobalAllianceApi.searchReferences. (references.search) * * @param GoogleGAL_SearchReferencesRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_SearchReferencesResponse */ public function search(GoogleGAL_Service_Genomics_SearchReferencesRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "GoogleGAL_Service_Genomics_SearchReferencesResponse"); } } /** * The "bases" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $bases = $genomicsService->bases; * */ class GoogleGAL_Service_Genomics_ReferencesBases_Resource extends GoogleGAL_Service_Resource { /** * Lists the bases in a reference, optionally restricted to a range. * * Implements GlobalAllianceApi.getReferenceBases. (bases.listReferencesBases) * * @param string $referenceId The ID of the reference. * @param array $optParams Optional parameters. * * @opt_param string pageToken The continuation token, which is used to page * through large result sets. To get the next page of results, set this * parameter to the value of nextPageToken from the previous response. * @opt_param string end The end position (0-based, exclusive) of this query. * Defaults to the length of this reference. * @opt_param int pageSize Specifies the maximum number of bases to return in a * single page. * @opt_param string start The start position (0-based) of this query. Defaults * to 0. * @return GoogleGAL_Service_Genomics_ListBasesResponse */ public function listReferencesBases($referenceId, $optParams = array()) { $params = array('referenceId' => $referenceId); $params = array_merge($params, $optParams); return $this->call('list', array($params), "GoogleGAL_Service_Genomics_ListBasesResponse"); } } /** * The "referencesets" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $referencesets = $genomicsService->referencesets; * */ class GoogleGAL_Service_Genomics_Referencesets_Resource extends GoogleGAL_Service_Resource { /** * Gets a reference set. * * Implements GlobalAllianceApi.getReferenceSet. (referencesets.get) * * @param string $referenceSetId The ID of the reference set. * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_ReferenceSet */ public function get($referenceSetId, $optParams = array()) { $params = array('referenceSetId' => $referenceSetId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "GoogleGAL_Service_Genomics_ReferenceSet"); } /** * Searches for reference sets which match the given criteria. * * Implements GlobalAllianceApi.searchReferenceSets. (referencesets.search) * * @param GoogleGAL_SearchReferenceSetsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_SearchReferenceSetsResponse */ public function search(GoogleGAL_Service_Genomics_SearchReferenceSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "GoogleGAL_Service_Genomics_SearchReferenceSetsResponse"); } } /** * The "variants" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $variants = $genomicsService->variants; * */ class GoogleGAL_Service_Genomics_Variants_Resource extends GoogleGAL_Service_Resource { /** * Creates a new variant. (variants.create) * * @param GoogleGAL_Variant $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_Variant */ public function create(GoogleGAL_Service_Genomics_Variant $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('create', array($params), "GoogleGAL_Service_Genomics_Variant"); } /** * Deletes a variant. (variants.delete) * * @param string $variantId The ID of the variant to be deleted. * @param array $optParams Optional parameters. */ public function delete($variantId, $optParams = array()) { $params = array('variantId' => $variantId); $params = array_merge($params, $optParams); return $this->call('delete', array($params)); } /** * Gets a variant by ID. (variants.get) * * @param string $variantId The ID of the variant. * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_Variant */ public function get($variantId, $optParams = array()) { $params = array('variantId' => $variantId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "GoogleGAL_Service_Genomics_Variant"); } /** * Gets a list of variants matching the criteria. * * Implements GlobalAllianceApi.searchVariants. (variants.search) * * @param GoogleGAL_SearchVariantsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_SearchVariantsResponse */ public function search(GoogleGAL_Service_Genomics_SearchVariantsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "GoogleGAL_Service_Genomics_SearchVariantsResponse"); } /** * Updates a variant's names and info fields. All other modifications are * silently ignored. Returns the modified variant without its calls. * (variants.update) * * @param string $variantId The ID of the variant to be updated. * @param GoogleGAL_Variant $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_Variant */ public function update($variantId, GoogleGAL_Service_Genomics_Variant $postBody, $optParams = array()) { $params = array('variantId' => $variantId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('update', array($params), "GoogleGAL_Service_Genomics_Variant"); } } /** * The "variantsets" collection of methods. * Typical usage is: * * $genomicsService = new GoogleGAL_Service_Genomics(...); * $variantsets = $genomicsService->variantsets; * */ class GoogleGAL_Service_Genomics_Variantsets_Resource extends GoogleGAL_Service_Resource { /** * Deletes the contents of a variant set. The variant set object is not deleted. * (variantsets.delete) * * @param string $variantSetId The ID of the variant set to be deleted. * @param array $optParams Optional parameters. */ public function delete($variantSetId, $optParams = array()) { $params = array('variantSetId' => $variantSetId); $params = array_merge($params, $optParams); return $this->call('delete', array($params)); } /** * Exports variant set data to an external destination. (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 GoogleGAL_ExportVariantSetRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_ExportVariantSetResponse */ public function export($variantSetId, GoogleGAL_Service_Genomics_ExportVariantSetRequest $postBody, $optParams = array()) { $params = array('variantSetId' => $variantSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('export', array($params), "GoogleGAL_Service_Genomics_ExportVariantSetResponse"); } /** * Gets a variant set by ID. (variantsets.get) * * @param string $variantSetId Required. The ID of the variant set. * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_VariantSet */ public function get($variantSetId, $optParams = array()) { $params = array('variantSetId' => $variantSetId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "GoogleGAL_Service_Genomics_VariantSet"); } /** * Creates variant data by asynchronously importing the provided information. * * The variants for import will be merged with any existing data and each other * according to the behavior of mergeVariants. In particular, this means for * merged VCF variants that have conflicting INFO fields, some data will be * arbitrarily discarded. As a special case, for single-sample VCF files, QUAL * and FILTER fields will be moved to the call level; these are sometimes * interpreted in a call-specific context. Imported VCF headers are appended to * the metadata already in a variant set. (variantsets.importVariants) * * @param string $variantSetId Required. The variant set to which variant data * should be imported. * @param GoogleGAL_ImportVariantsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_ImportVariantsResponse */ public function importVariants($variantSetId, GoogleGAL_Service_Genomics_ImportVariantsRequest $postBody, $optParams = array()) { $params = array('variantSetId' => $variantSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('importVariants', array($params), "GoogleGAL_Service_Genomics_ImportVariantsResponse"); } /** * Merges the given variants with existing variants. Each variant will be merged * with an existing variant that matches its reference sequence, start, end, * reference bases, and alternative bases. If no such variant exists, a new one * will be created. * * When variants are merged, the call information from the new variant is added * to the existing variant, and other fields (such as key/value pairs) are * discarded. (variantsets.mergeVariants) * * @param string $variantSetId The destination variant set. * @param GoogleGAL_MergeVariantsRequest $postBody * @param array $optParams Optional parameters. */ public function mergeVariants($variantSetId, GoogleGAL_Service_Genomics_MergeVariantsRequest $postBody, $optParams = array()) { $params = array('variantSetId' => $variantSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('mergeVariants', array($params)); } /** * Updates a variant set's metadata. All other modifications are silently * ignored. This method supports patch semantics. (variantsets.patch) * * @param string $variantSetId The ID of the variant to be updated. * @param GoogleGAL_VariantSet $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_VariantSet */ public function patch($variantSetId, GoogleGAL_Service_Genomics_VariantSet $postBody, $optParams = array()) { $params = array('variantSetId' => $variantSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('patch', array($params), "GoogleGAL_Service_Genomics_VariantSet"); } /** * Returns a list of all variant sets matching search criteria. * * Implements GlobalAllianceApi.searchVariantSets. (variantsets.search) * * @param GoogleGAL_SearchVariantSetsRequest $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_SearchVariantSetsResponse */ public function search(GoogleGAL_Service_Genomics_SearchVariantSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "GoogleGAL_Service_Genomics_SearchVariantSetsResponse"); } /** * Updates a variant set's metadata. All other modifications are silently * ignored. (variantsets.update) * * @param string $variantSetId The ID of the variant to be updated. * @param GoogleGAL_VariantSet $postBody * @param array $optParams Optional parameters. * @return GoogleGAL_Service_Genomics_VariantSet */ public function update($variantSetId, GoogleGAL_Service_Genomics_VariantSet $postBody, $optParams = array()) { $params = array('variantSetId' => $variantSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('update', array($params), "GoogleGAL_Service_Genomics_VariantSet"); } } class GoogleGAL_Service_Genomics_AlignReadGroupSetsRequest extends GoogleGAL_Collection { protected $collection_key = 'readGroupSetIds'; protected $internal_gapi_mappings = array( ); public $bamSourceUris; public $datasetId; protected $interleavedFastqSourceType = 'GoogleGAL_Service_Genomics_InterleavedFastqSource'; protected $interleavedFastqSourceDataType = ''; protected $pairedFastqSourceType = 'GoogleGAL_Service_Genomics_PairedFastqSource'; protected $pairedFastqSourceDataType = ''; public $readGroupSetIds; public function setBamSourceUris($bamSourceUris) { $this->bamSourceUris = $bamSourceUris; } public function getBamSourceUris() { return $this->bamSourceUris; } public function setDatasetId($datasetId) { $this->datasetId = $datasetId; } public function getDatasetId() { return $this->datasetId; } public function setInterleavedFastqSource(GoogleGAL_Service_Genomics_InterleavedFastqSource $interleavedFastqSource) { $this->interleavedFastqSource = $interleavedFastqSource; } public function getInterleavedFastqSource() { return $this->interleavedFastqSource; } public function setPairedFastqSource(GoogleGAL_Service_Genomics_PairedFastqSource $pairedFastqSource) { $this->pairedFastqSource = $pairedFastqSource; } public function getPairedFastqSource() { return $this->pairedFastqSource; } public function setReadGroupSetIds($readGroupSetIds) { $this->readGroupSetIds = $readGroupSetIds; } public function getReadGroupSetIds() { return $this->readGroupSetIds; } } class GoogleGAL_Service_Genomics_AlignReadGroupSetsResponse extends GoogleGAL_Model { protected $internal_gapi_mappings = array( ); public $jobId; public function setJobId($jobId) { $this->jobId = $jobId; } public function getJobId() { return $this->jobId; } } class GoogleGAL_Service_Genomics_CallReadGroupSetsRequest extends GoogleGAL_Collection { protected $collection_key = 'sourceUris'; protected $internal_gapi_mappings = array( ); public $datasetId; public $readGroupSetIds; public $sourceUris; public function setDatasetId($datasetId) { $this->datasetId = $datasetId; } public function getDatasetId() { return $this->datasetId; } public function setReadGroupSetIds($readGroupSetIds) { $this->readGroupSetIds = $readGroupSetIds; } public function getReadGroupSetIds() { return $this->readGroupSetIds; } public function setSourceUris($sourceUris) { $this->sourceUris = $sourceUris; } public function getSourceUris() { return $this->sourceUris; } } class GoogleGAL_Service_Genomics_CallReadGroupSetsResponse extends GoogleGAL_Model { protected $internal_gapi_mappings = array( ); public $jobId; public function setJobId($jobId) { $this->jobId = $jobId; } public function getJobId() { return $this->jobId; } } class GoogleGAL_Service_Genomics_CallSet extends GoogleGAL_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 GoogleGAL_Service_Genomics_CallSetInfo extends GoogleGAL_Model { } class GoogleGAL_Service_Genomics_CigarUnit extends GoogleGAL_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 GoogleGAL_Service_Genomics_CoverageBucket extends GoogleGAL_Model { protected $internal_gapi_mappings = array( ); public $meanCoverage; protected $rangeType = 'GoogleGAL_Service_Genomics_Range'; protected $rangeDataType = ''; public function setMeanCoverage($meanCoverage) { $this->meanCoverage = $meanCoverage; } public function getMeanCoverage() { return $this->meanCoverage; } public function setRange(GoogleGAL_Service_Genomics_Range $range) { $this->range = $range; } public function getRange() { return $this->range; } } class GoogleGAL_Service_Genomics_Dataset extends GoogleGAL_Model { protected $internal_gapi_mappings = array( ); public $id; public $isPublic; public $name; public $projectNumber; public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setIsPublic($isPublic) { $this->isPublic = $isPublic; } public function getIsPublic() { return $this->isPublic; } public function setName($name) { $this->name = $name; } public function getName() { return $this->name; } public function setProjectNumber($projectNumber) { $this->projectNumber = $projectNumber; } public function getProjectNumber() { return $this->projectNumber; } } class GoogleGAL_Service_Genomics_ExperimentalCreateJobRequest extends GoogleGAL_Collection { protected $collection_key = 'sourceUris'; protected $internal_gapi_mappings = array( ); public $align; public $callVariants; public $gcsOutputPath; public $pairedSourceUris; public $projectNumber; public $sourceUris; public function setAlign($align) { $this->align = $align; } public function getAlign() { return $this->align; } public function setCallVariants($callVariants) { $this->callVariants = $callVariants; } public function getCallVariants() { return $this->callVariants; } public function setGcsOutputPath($gcsOutputPath) { $this->gcsOutputPath = $gcsOutputPath; } public function getGcsOutputPath() { return $this->gcsOutputPath; } public function setPairedSourceUris($pairedSourceUris) { $this->pairedSourceUris = $pairedSourceUris; } public function getPairedSourceUris() { return $this->pairedSourceUris; } public function setProjectNumber($projectNumber) { $this->projectNumber = $projectNumber; } public function getProjectNumber() { return $this->projectNumber; } public function setSourceUris($sourceUris) { $this->sourceUris = $sourceUris; } public function getSourceUris() { return $this->sourceUris; } } class GoogleGAL_Service_Genomics_ExperimentalCreateJobResponse extends GoogleGAL_Model { protected $internal_gapi_mappings = array( ); public $jobId; public function setJobId($jobId) { $this->jobId = $jobId; } public function getJobId() { return $this->jobId; } } class GoogleGAL_Service_Genomics_ExportReadGroupSetsRequest extends GoogleGAL_Collection { protected $collection_key = 'referenceNames'; protected $internal_gapi_mappings = array( ); public $exportUri; public $projectNumber; public $readGroupSetIds; public $referenceNames; public function setExportUri($exportUri) { $this->exportUri = $exportUri; } public function getExportUri() { return $this->exportUri; } public function setProjectNumber($projectNumber) { $this->projectNumber = $projectNumber; } public function getProjectNumber() { return $this->projectNumber; } public function setReadGroupSetIds($readGroupSetIds) { $this->readGroupSetIds = $readGroupSetIds; } public function getReadGroupSetIds() { return $this->readGroupSetIds; } public function setReferenceNames($referenceNames) { $this->referenceNames = $referenceNames; } public function getReferenceNames() { return $this->referenceNames; } } class GoogleGAL_Service_Genomics_ExportReadGroupSetsResponse extends GoogleGAL_Model { protected $internal_gapi_mappings = array( ); public $jobId; public function setJobId($jobId) { $this->jobId = $jobId; } public function getJobId() { return $this->jobId; } } class GoogleGAL_Service_Genomics_ExportVariantSetRequest extends GoogleGAL_Collection { protected $collection_key = 'callSetIds'; protected $internal_gapi_mappings = array( ); public $bigqueryDataset; public $bigqueryTable; public $callSetIds; public $format; public $projectNumber; public function setBigqueryDataset($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 $this->format; } public function setProjectNumber($projectNumber) { $this->projectNumber = $projectNumber; } public function getProjectNumber() { return $this->projectNumber; } } class GoogleGAL_Service_Genomics_ExportVariantSetResponse extends GoogleGAL_Model { protected $internal_gapi_mappings = array( ); public $jobId; public function setJobId($jobId) { $this->jobId = $jobId; } public function getJobId() { return $this->jobId; } } class GoogleGAL_Service_Genomics_FastqMetadata extends GoogleGAL_Model { protected $internal_gapi_mappings = array( ); public $libraryName; public $platformName; public $platformUnit; public $readGroupName; public $sampleName; public function setLibraryName($libraryName) { $this->libraryName = $libraryName; } public function getLibraryName() { return $this->libraryName; } public function setPlatformName($platformName) { $this->platformName = $platformName; } public function getPlatformName() { return $this->platformName; } public function setPlatformUnit($platformUnit) { $this->platformUnit = $platformUnit; } public function getPlatformUnit() { return $this->platformUnit; } public function setReadGroupName($readGroupName) { $this->readGroupName = $readGroupName; } public function getReadGroupName() { return $this->readGroupName; } public function setSampleName($sampleName) { $this->sampleName = $sampleName; } public function getSampleName() { return $this->sampleName; } } class GoogleGAL_Service_Genomics_GenomicsCall extends GoogleGAL_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 GoogleGAL_Service_Genomics_GenomicsCallInfo extends GoogleGAL_Model { } class GoogleGAL_Service_Genomics_ImportReadGroupSetsRequest extends GoogleGAL_Collection { protected $collection_key = 'sourceUris'; protected $internal_gapi_mappings = array( ); public $datasetId; public $referenceSetId; public $sourceUris; public function setDatasetId($datasetId) { $this->datasetId = $datasetId; } public function getDatasetId() { return $this->datasetId; } public function setReferenceSetId($referenceSetId) { $this->referenceSetId = $referenceSetId; } public function getReferenceSetId() { return $this->referenceSetId; } public function setSourceUris($sourceUris) { $this->sourceUris = $sourceUris; } public function getSourceUris() { return $this->sourceUris; } } class GoogleGAL_Service_Genomics_ImportReadGroupSetsResponse extends GoogleGAL_Model { protected $internal_gapi_mappings = array( ); public $jobId; public function setJobId($jobId) { $this->jobId = $jobId; } public function getJobId() { return $this->jobId; } } class GoogleGAL_Service_Genomics_ImportVariantsRequest extends GoogleGAL_Collection { protected $collection_key = 'sourceUris'; protected $internal_gapi_mappings = array( ); public $format; public $sourceUris; public function setFormat($format) { $this->format = $format; } public function getFormat() { return $this->format; } public function setSourceUris($sourceUris) { $this->sourceUris = $sourceUris; } public function getSourceUris() { return $this->sourceUris; } } class GoogleGAL_Service_Genomics_ImportVariantsResponse extends GoogleGAL_Model { protected $internal_gapi_mappings = array( ); public $jobId; public function setJobId($jobId) { $this->jobId = $jobId; } public function getJobId() { return $this->jobId; } } class GoogleGAL_Service_Genomics_InterleavedFastqSource extends GoogleGAL_Collection { protected $collection_key = 'sourceUris'; protected $internal_gapi_mappings = array( ); protected $metadataType = 'GoogleGAL_Service_Genomics_FastqMetadata'; protected $metadataDataType = ''; public $sourceUris; public function setMetadata(GoogleGAL_Service_Genomics_FastqMetadata $metadata) { $this->metadata = $metadata; } public function getMetadata() { return $this->metadata; } public function setSourceUris($sourceUris) { $this->sourceUris = $sourceUris; } public function getSourceUris() { return $this->sourceUris; } } class GoogleGAL_Service_Genomics_Job extends GoogleGAL_Collection { protected $collection_key = 'warnings'; protected $internal_gapi_mappings = array( ); public $created; public $detailedStatus; public $errors; public $id; public $importedIds; public $projectNumber; protected $requestType = 'GoogleGAL_Service_Genomics_JobRequest'; protected $requestDataType = ''; public $status; public $warnings; public function setCreated($created) { $this->created = $created; } public function getCreated() { return $this->created; } public function setDetailedStatus($detailedStatus) { $this->detailedStatus = $detailedStatus; } public function getDetailedStatus() { return $this->detailedStatus; } public function setErrors($errors) { $this->errors = $errors; } public function getErrors() { return $this->errors; } public function setId($id) { $this->id = $id; } public function getId() { return $this->id; } public function setImportedIds($importedIds) { $this->importedIds = $importedIds; } public function getImportedIds() { return $this->importedIds; } public function setProjectNumber($projectNumber) { $this->projectNumber = $projectNumber; } public function getProjectNumber() { return $this->projectNumber; } public function setRequest(GoogleGAL_Service_Genomics_JobRequest $request) { $this->request = $request; } public function getRequest() { return $this->request; } public function setStatus($status) { $this->status = $status; } public function getStatus() { return $this->status; } public function setWarnings($warnings) { $this->warnings = $warnings; } public function getWarnings() { return $this->warnings; } } class GoogleGAL_Service_Genomics_JobRequest extends GoogleGAL_Collection { protected $collection_key = 'source'; protected $internal_gapi_mappings = array( ); public $destination; public $source; public $type; public function setDestination($destination) { $this->destination = $destination; } public function getDestination() { return $this->destination; } public function setSource($source) { $this->source = $source; } public function getSource() { return $this->source; } public function setType($type) { $this->type = $type; } public function getType() { return $this->type; } } class GoogleGAL_Service_Genomics_LinearAlignment extends GoogleGAL_Collection { protected $collection_key = 'cigar'; protected $internal_gapi_mappings = array( ); protected $cigarType = 'GoogleGAL_Service_Genomics_CigarUnit'; protected $cigarDataType = 'array'; public $mappingQuality; protected $positionType = 'GoogleGAL_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(GoogleGAL_Service_Genomics_Position $position) { $this->position = $position; } public function getPosition() { return $this->position; } } class GoogleGAL_Service_Genomics_ListBasesResponse extends GoogleGAL_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 GoogleGAL_Service_Genomics_ListCoverageBucketsResponse extends GoogleGAL_Collection { protected $collection_key = 'coverageBuckets'; protected $internal_gapi_mappings = array( ); public $bucketWidth; protected $coverageBucketsType = 'GoogleGAL_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 GoogleGAL_Service_Genomics_ListDatasetsResponse extends GoogleGAL_Collection { protected $collection_key = 'datasets'; protected $internal_gapi_mappings = array( ); protected $datasetsType = 'GoogleGAL_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 GoogleGAL_Service_Genomics_MergeVariantsRequest extends GoogleGAL_Collection { protected $collection_key = 'variants'; protected $internal_gapi_mappings = array( ); protected $variantsType = 'GoogleGAL_Service_Genomics_Variant'; protected $variantsDataType = 'array'; public function setVariants($variants) { $this->variants = $variants; } public function getVariants() { return $this->variants; } } class GoogleGAL_Service_Genomics_Metadata extends GoogleGAL_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; } } class GoogleGAL_Service_Genomics_MetadataInfo extends GoogleGAL_Model { } class GoogleGAL_Service_Genomics_PairedFastqSource extends GoogleGAL_Collection { protected $collection_key = 'secondSourceUris'; protected $internal_gapi_mappings = array( ); public $firstSourceUris; protected $metadataType = 'GoogleGAL_Service_Genomics_FastqMetadata'; protected $metadataDataType = ''; public $secondSourceUris; public function setFirstSourceUris($firstSourceUris) { $this->firstSourceUris = $firstSourceUris; } public function getFirstSourceUris() { return $this->firstSourceUris; } public function setMetadata(GoogleGAL_Service_Genomics_FastqMetadata $metadata) { $this->metadata = $metadata; } public function getMetadata() { return $this->metadata; } public function setSecondSourceUris($secondSourceUris) { $this->secondSourceUris = $secondSourceUris; } public function getSecondSourceUris() { return $this->secondSourceUris; } } class GoogleGAL_Service_Genomics_Position extends GoogleGAL_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 GoogleGAL_Service_Genomics_Range extends GoogleGAL_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 GoogleGAL_Service_Genomics_Read extends GoogleGAL_Collection { protected $collection_key = 'alignedQuality'; protected $internal_gapi_mappings = array( ); public $alignedQuality; public $alignedSequence; protected $alignmentType = 'GoogleGAL_Service_Genomics_LinearAlignment'; protected $alignmentDataType = ''; public $duplicateFragment; public $failedVendorQualityChecks; public $fragmentLength; public $fragmentName; public $id; public $info; protected $nextMatePositionType = 'GoogleGAL_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(GoogleGAL_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(GoogleGAL_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 GoogleGAL_Service_Genomics_ReadGroup extends GoogleGAL_Collection { protected $collection_key = 'programs'; protected $internal_gapi_mappings = array( ); public $datasetId; public $description; protected $experimentType = 'GoogleGAL_Service_Genomics_ReadGroupExperiment'; protected $experimentDataType = ''; public $id; public $info; public $name; public $predictedInsertSize; protected $programsType = 'GoogleGAL_Service_Genomics_ReadGroupProgram'; 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(GoogleGAL_Service_Genomics_ReadGroupExperiment $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 GoogleGAL_Service_Genomics_ReadGroupExperiment extends GoogleGAL_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 GoogleGAL_Service_Genomics_ReadGroupInfo extends GoogleGAL_Model { } class GoogleGAL_Service_Genomics_ReadGroupProgram extends GoogleGAL_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 GoogleGAL_Service_Genomics_ReadGroupSet extends GoogleGAL_Collection { protected $collection_key = 'readGroups'; protected $internal_gapi_mappings = array( ); public $datasetId; public $filename; public $id; public $name; protected $readGroupsType = 'GoogleGAL_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 $this->id; } public function setName($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 GoogleGAL_Service_Genomics_ReadInfo extends GoogleGAL_Model { } class GoogleGAL_Service_Genomics_Reference extends GoogleGAL_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 GoogleGAL_Service_Genomics_ReferenceBound extends GoogleGAL_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 GoogleGAL_Service_Genomics_ReferenceSet extends GoogleGAL_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 GoogleGAL_Service_Genomics_SearchCallSetsRequest extends GoogleGAL_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 GoogleGAL_Service_Genomics_SearchCallSetsResponse extends GoogleGAL_Collection { protected $collection_key = 'callSets'; protected $internal_gapi_mappings = array( ); protected $callSetsType = 'GoogleGAL_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 GoogleGAL_Service_Genomics_SearchJobsRequest extends GoogleGAL_Collection { protected $collection_key = 'status'; protected $internal_gapi_mappings = array( ); public $createdAfter; public $createdBefore; public $pageSize; public $pageToken; public $projectNumber; public $status; public function setCreatedAfter($createdAfter) { $this->createdAfter = $createdAfter; } public function getCreatedAfter() { return $this->createdAfter; } public function setCreatedBefore($createdBefore) { $this->createdBefore = $createdBefore; } public function getCreatedBefore() { return $this->createdBefore; } public function setPageSize($pageSize) { $this->pageSize = $pageSize; } public function getPageSize() { return $this->pageSize; } public function setPageToken($pageToken) { $this->pageToken = $pageToken; } public function getPageToken() { return $this->pageToken; } public function setProjectNumber($projectNumber) { $this->projectNumber = $projectNumber; } public function getProjectNumber() { return $this->projectNumber; } public function setStatus($status) { $this->status = $status; } public function getStatus() { return $this->status; } } class GoogleGAL_Service_Genomics_SearchJobsResponse extends GoogleGAL_Collection { protected $collection_key = 'jobs'; protected $internal_gapi_mappings = array( ); protected $jobsType = 'GoogleGAL_Service_Genomics_Job'; protected $jobsDataType = 'array'; public $nextPageToken; public function setJobs($jobs) { $this->jobs = $jobs; } public function getJobs() { return $this->jobs; } public function setNextPageToken($nextPageToken) { $this->nextPageToken = $nextPageToken; } public function getNextPageToken() { return $this->nextPageToken; } } class GoogleGAL_Service_Genomics_SearchReadGroupSetsRequest extends GoogleGAL_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 GoogleGAL_Service_Genomics_SearchReadGroupSetsResponse extends GoogleGAL_Collection { protected $collection_key = 'readGroupSets'; protected $internal_gapi_mappings = array( ); public $nextPageToken; protected $readGroupSetsType = 'GoogleGAL_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 GoogleGAL_Service_Genomics_SearchReadsRequest extends GoogleGAL_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 GoogleGAL_Service_Genomics_SearchReadsResponse extends GoogleGAL_Collection { protected $collection_key = 'alignments'; protected $internal_gapi_mappings = array( ); protected $alignmentsType = 'GoogleGAL_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 GoogleGAL_Service_Genomics_SearchReferenceSetsRequest extends GoogleGAL_Collection { protected $collection_key = 'md5checksums'; protected $internal_gapi_mappings = array( ); public $accessions; public $md5checksums; public $pageSize; public $pageToken; public function setAccessions($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; } } class GoogleGAL_Service_Genomics_SearchReferenceSetsResponse extends GoogleGAL_Collection { protected $collection_key = 'referenceSets'; protected $internal_gapi_mappings = array( ); public $nextPageToken; protected $referenceSetsType = 'GoogleGAL_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 GoogleGAL_Service_Genomics_SearchReferencesRequest extends GoogleGAL_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 GoogleGAL_Service_Genomics_SearchReferencesResponse extends GoogleGAL_Collection { protected $collection_key = 'references'; protected $internal_gapi_mappings = array( ); public $nextPageToken; protected $referencesType = 'GoogleGAL_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 GoogleGAL_Service_Genomics_SearchVariantSetsRequest extends GoogleGAL_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 GoogleGAL_Service_Genomics_SearchVariantSetsResponse extends GoogleGAL_Collection { protected $collection_key = 'variantSets'; protected $internal_gapi_mappings = array( ); public $nextPageToken; protected $variantSetsType = 'GoogleGAL_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 GoogleGAL_Service_Genomics_SearchVariantsRequest extends GoogleGAL_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 GoogleGAL_Service_Genomics_SearchVariantsResponse extends GoogleGAL_Collection { protected $collection_key = 'variants'; protected $internal_gapi_mappings = array( ); public $nextPageToken; protected $variantsType = 'GoogleGAL_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 GoogleGAL_Service_Genomics_Variant extends GoogleGAL_Collection { protected $collection_key = 'names'; protected $internal_gapi_mappings = array( ); public $alternateBases; protected $callsType = 'GoogleGAL_Service_Genomics_GenomicsCall'; 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 GoogleGAL_Service_Genomics_VariantInfo extends GoogleGAL_Model { } class GoogleGAL_Service_Genomics_VariantSet extends GoogleGAL_Collection { protected $collection_key = 'referenceBounds'; protected $internal_gapi_mappings = array( ); public $datasetId; public $id; protected $metadataType = 'GoogleGAL_Service_Genomics_Metadata'; protected $metadataDataType = 'array'; protected $referenceBoundsType = 'GoogleGAL_Service_Genomics_ReferenceBound'; protected $referenceBoundsDataType = 'array'; public function setDatasetId($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; } }