* $genomicsService = new Google_Service_Genomics(...); * $readgroupsets = $genomicsService->readgroupsets; * */ class Google_Service_Genomics_Resource_Readgroupsets extends Google_Service_Resource { /** * 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 $optParams Optional parameters. * @return Google_Service_Genomics_GenomicsEmpty */ public function delete($readGroupSetId, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId); $params = array_merge($params, $optParams); return $this->call('delete', array($params), "Google_Service_Genomics_GenomicsEmpty"); } /** * Exports a read group set 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. See ImportReadGroupSets for * caveats. (readgroupsets.export) * * @param string $readGroupSetId Required. The ID of the read group set to * export. The caller must have READ access to this read group set. * @param Google_Service_Genomics_ExportReadGroupSetRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Operation */ public function export($readGroupSetId, Google_Service_Genomics_ExportReadGroupSetRequest $postBody, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('export', array($params), "Google_Service_Genomics_Operation"); } /** * Gets a read group set by ID. (readgroupsets.get) * * @param string $readGroupSetId The ID of the read group set. * @param array $optParams Optional parameters. * @return Google_Service_Genomics_ReadGroupSet */ public function get($readGroupSetId, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId); $params = array_merge($params, $optParams); return $this->call('get', array($params), "Google_Service_Genomics_ReadGroupSet"); } /** * Creates read group sets by asynchronously importing the provided information. * * The caller must have WRITE permissions to the dataset. * * ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import * * - Tags will be converted to strings - tag types are not preserved - Comments * (`@CO`) in the input file header will not be preserved - Original header * order of references (`@SQ`) will not be preserved - Any reverse stranded * unmapped reads will be reverse complemented, and their qualities (also the * "BQ" and "OQ" tags, if any) will be reversed - Unmapped reads will be * stripped of positional information (reference name and position) * (readgroupsets.import) * * @param Google_Service_Genomics_ImportReadGroupSetsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_Operation */ public function import(Google_Service_Genomics_ImportReadGroupSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('import', array($params), "Google_Service_Genomics_Operation"); } /** * Updates a read group set. * * This method supports patch semantics. (readgroupsets.patch) * * @param string $readGroupSetId The ID of the read group set to be updated. The * caller must have WRITE permissions to the dataset associated with this read * group set. * @param Google_Service_Genomics_ReadGroupSet $postBody * @param array $optParams Optional parameters. * * @opt_param string updateMask An optional mask specifying which fields to * update. Supported fields: * * * name. * referenceSetId. * * Leaving `updateMask` unset is equivalent to specifying all mutable fields. * @return Google_Service_Genomics_ReadGroupSet */ public function patch($readGroupSetId, Google_Service_Genomics_ReadGroupSet $postBody, $optParams = array()) { $params = array('readGroupSetId' => $readGroupSetId, 'postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('patch', array($params), "Google_Service_Genomics_ReadGroupSet"); } /** * Searches for read group sets matching the criteria. * * Implements [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/s * chemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135). * (readgroupsets.search) * * @param Google_Service_Genomics_SearchReadGroupSetsRequest $postBody * @param array $optParams Optional parameters. * @return Google_Service_Genomics_SearchReadGroupSetsResponse */ public function search(Google_Service_Genomics_SearchReadGroupSetsRequest $postBody, $optParams = array()) { $params = array('postBody' => $postBody); $params = array_merge($params, $optParams); return $this->call('search', array($params), "Google_Service_Genomics_SearchReadGroupSetsResponse"); } }