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<?php
/*
* Copyright 2010 Google Inc.
*
* Licensed under the Apache License, Version 2.0 (the "License"); you may not
* use this file except in compliance with the License. You may obtain a copy of
* the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
* WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
* License for the specific language governing permissions and limitations under
* the License.
*/
/**
* Service definition for Genomics (v1beta2).
*
* <p>
* Provides access to Genomics data.
* </p>
*
* <p>
* For more information about this service, see the API
* <a href="https://developers.google.com/genomics/v1beta2/reference" target="_blank">Documentation</a>
* </p>
*
* @author Google, Inc.
*/
class Google_Service_Genomics extends Google_Service
{
/** View and manage your data in Google BigQuery. */
const BIGQUERY = "https://www.googleapis.com/auth/bigquery";
/** 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 Google_Client $client
*/
public function __construct(Google_Client $client)
{
parent::__construct($client);
$this->servicePath = 'genomics/v1beta2/';
$this->version = 'v1beta2';
$this->serviceName = 'genomics';
$this->callsets = new Google_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 Google_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 Google_Service_Genomics_ExperimentalJobs_Resource(
$this,
$this->serviceName,
'jobs',
array(
'methods' => array(
'create' => array(
'path' => 'experimental/jobs/create',
'httpMethod' => 'POST',
'parameters' => array(),
),
)
)
);
$this->jobs = new Google_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 Google_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 Google_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 Google_Service_Genomics_Reads_Resource(
$this,
$this->serviceName,
'reads',
array(
'methods' => array(
'search' => array(
'path' => 'reads/search',
'httpMethod' => 'POST',
'parameters' => array(),
),
)
)
);
$this->references = new Google_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 Google_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 Google_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 Google_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 Google_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:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $callsets = $genomicsService->callsets;
* </code>
*/
class Google_Service_Genomics_Callsets_Resource extends Google_Service_Resource
{
/**
* Creates a new call set. (callsets.create)
*
* @param Google_CallSet $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_CallSet
*/
public function create(Google_Service_Genomics_CallSet $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('create', array($params), "Google_Service_Genomics_CallSet");
}
/**
* Deletes a call set. (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 $optParams Optional parameters.
* @return Google_Service_Genomics_CallSet
*/
public function get($callSetId, $optParams = array())
{
$params = array('callSetId' => $callSetId);
$params = array_merge($params, $optParams);
return $this->call('get', array($params), "Google_Service_Genomics_CallSet");
}
/**
* Updates a call set. This method supports patch semantics. (callsets.patch)
*
* @param string $callSetId
* The ID of the call set to be updated.
* @param Google_CallSet $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_CallSet
*/
public function patch($callSetId, Google_Service_Genomics_CallSet $postBody, $optParams = array())
{
$params = array('callSetId' => $callSetId, 'postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('patch', array($params), "Google_Service_Genomics_CallSet");
}
/**
* Gets a list of call sets matching the criteria.
*
* Implements GlobalAllianceApi.searchCallSets. (callsets.search)
*
* @param Google_SearchCallSetsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_SearchCallSetsResponse
*/
public function search(Google_Service_Genomics_SearchCallSetsRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('search', array($params), "Google_Service_Genomics_SearchCallSetsResponse");
}
/**
* Updates a call set. (callsets.update)
*
* @param string $callSetId
* The ID of the call set to be updated.
* @param Google_CallSet $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_CallSet
*/
public function update($callSetId, Google_Service_Genomics_CallSet $postBody, $optParams = array())
{
$params = array('callSetId' => $callSetId, 'postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('update', array($params), "Google_Service_Genomics_CallSet");
}
}
/**
* The "datasets" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $datasets = $genomicsService->datasets;
* </code>
*/
class Google_Service_Genomics_Datasets_Resource extends Google_Service_Resource
{
/**
* Creates a new dataset. (datasets.create)
*
* @param Google_Dataset $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_Dataset
*/
public function create(Google_Service_Genomics_Dataset $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('create', array($params), "Google_Service_Genomics_Dataset");
}
/**
* Deletes a dataset. (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 $optParams Optional parameters.
* @return Google_Service_Genomics_Dataset
*/
public function get($datasetId, $optParams = array())
{
$params = array('datasetId' => $datasetId);
$params = array_merge($params, $optParams);
return $this->call('get', array($params), "Google_Service_Genomics_Dataset");
}
/**
* Lists all datasets. (datasets.listDatasets)
*
* @param array $optParams Optional parameters.
*
* @opt_param string pageToken
* The continuation token, which is used to page through large result sets. To get the next page of
* results, set this parameter to the value of nextPageToken from the previous response.
* @opt_param string projectNumber
* Only return datasets which belong to this Google Developers Console project. Only accepts
* project numbers. Returns all public projects if no project number is specified.
* @opt_param int pageSize
* The maximum number of results returned by this request.
* @return Google_Service_Genomics_ListDatasetsResponse
*/
public function listDatasets($optParams = array())
{
$params = array();
$params = array_merge($params, $optParams);
return $this->call('list', array($params), "Google_Service_Genomics_ListDatasetsResponse");
}
/**
* Updates a dataset. This method supports patch semantics. (datasets.patch)
*
* @param string $datasetId
* The ID of the dataset to be updated.
* @param Google_Dataset $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_Dataset
*/
public function patch($datasetId, Google_Service_Genomics_Dataset $postBody, $optParams = array())
{
$params = array('datasetId' => $datasetId, 'postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('patch', array($params), "Google_Service_Genomics_Dataset");
}
/**
* 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 $optParams Optional parameters.
* @return Google_Service_Genomics_Dataset
*/
public function undelete($datasetId, $optParams = array())
{
$params = array('datasetId' => $datasetId);
$params = array_merge($params, $optParams);
return $this->call('undelete', array($params), "Google_Service_Genomics_Dataset");
}
/**
* Updates a dataset. (datasets.update)
*
* @param string $datasetId
* The ID of the dataset to be updated.
* @param Google_Dataset $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_Dataset
*/
public function update($datasetId, Google_Service_Genomics_Dataset $postBody, $optParams = array())
{
$params = array('datasetId' => $datasetId, 'postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('update', array($params), "Google_Service_Genomics_Dataset");
}
}
/**
* The "experimental" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $experimental = $genomicsService->experimental;
* </code>
*/
class Google_Service_Genomics_Experimental_Resource extends Google_Service_Resource
{
}
/**
* The "jobs" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $jobs = $genomicsService->jobs;
* </code>
*/
class Google_Service_Genomics_ExperimentalJobs_Resource extends Google_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 Google_ExperimentalCreateJobRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_ExperimentalCreateJobResponse
*/
public function create(Google_Service_Genomics_ExperimentalCreateJobRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('create', array($params), "Google_Service_Genomics_ExperimentalCreateJobResponse");
}
}
/**
* The "jobs" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $jobs = $genomicsService->jobs;
* </code>
*/
class Google_Service_Genomics_Jobs_Resource extends Google_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 $optParams Optional parameters.
* @return Google_Service_Genomics_Job
*/
public function get($jobId, $optParams = array())
{
$params = array('jobId' => $jobId);
$params = array_merge($params, $optParams);
return $this->call('get', array($params), "Google_Service_Genomics_Job");
}
/**
* Gets a list of jobs matching the criteria. (jobs.search)
*
* @param Google_SearchJobsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_SearchJobsResponse
*/
public function search(Google_Service_Genomics_SearchJobsRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('search', array($params), "Google_Service_Genomics_SearchJobsResponse");
}
}
/**
* The "readgroupsets" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $readgroupsets = $genomicsService->readgroupsets;
* </code>
*/
class Google_Service_Genomics_Readgroupsets_Resource extends Google_Service_Resource
{
/**
* Aligns read data from existing read group sets or files from Google Cloud
* Storage. See Alignment for more details. (readgroupsets.align)
*
* @param Google_AlignReadGroupSetsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_AlignReadGroupSetsResponse
*/
public function align(Google_Service_Genomics_AlignReadGroupSetsRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('align', array($params), "Google_Service_Genomics_AlignReadGroupSetsResponse");
}
/**
* Calls variants on read data from existing read group sets or files from
* Google Cloud Storage. See Variant Calling for more details.
* (readgroupsets.call)
*
* @param Google_CallReadGroupSetsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_CallReadGroupSetsResponse
*/
public function call(Google_Service_Genomics_CallReadGroupSetsRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('call', array($params), "Google_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 Google_ExportReadGroupSetsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_ExportReadGroupSetsResponse
*/
public function export(Google_Service_Genomics_ExportReadGroupSetsRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('export', array($params), "Google_Service_Genomics_ExportReadGroupSetsResponse");
}
/**
* Gets a read group set by ID. (readgroupsets.get)
*
* @param string $readGroupSetId
* The ID of the read group set.
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_ReadGroupSet
*/
public function get($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.
*
* 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 Google_ImportReadGroupSetsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_ImportReadGroupSetsResponse
*/
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_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 Google_ReadGroupSet $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_ReadGroupSet
*/
public function patch($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. (readgroupsets.search)
*
* @param Google_SearchReadGroupSetsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_SearchReadGroupSetsResponse
*/
public function search(Google_Service_Genomics_SearchReadGroupSetsRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('search', array($params), "Google_Service_Genomics_SearchReadGroupSetsResponse");
}
/**
* 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 Google_ReadGroupSet $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_ReadGroupSet
*/
public function update($readGroupSetId, Google_Service_Genomics_ReadGroupSet $postBody, $optParams = array())
{
$params = array('readGroupSetId' => $readGroupSetId, 'postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('update', array($params), "Google_Service_Genomics_ReadGroupSet");
}
}
/**
* The "coveragebuckets" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $coveragebuckets = $genomicsService->coveragebuckets;
* </code>
*/
class Google_Service_Genomics_ReadgroupsetsCoveragebuckets_Resource extends Google_Service_Resource
{
/**
* Lists fixed width coverage buckets for a read group set, each of which
* correspond to a range of a reference sequence. Each bucket summarizes
* coverage information across its corresponding genomic range.
*
* 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 $optParams Optional parameters.
*
* @opt_param int pageSize
* The maximum number of results to return in a single page. If unspecified, defaults to 1024. The
* maximum value is 2048.
* @opt_param string range.start
* The start position of the range on the reference, 0-based inclusive. If specified, referenceName
* must also be specified.
* @opt_param string range.end
* The end position of the range on the reference, 0-based exclusive. If specified, referenceName
* must also be specified.
* @opt_param string range.referenceName
* The reference sequence name, for example chr1, 1, or chrX.
* @opt_param string pageToken
* The continuation token, which is used to page through large result sets. To get the next page of
* results, set this parameter to the value of nextPageToken from the previous response.
* @opt_param string targetBucketWidth
* The desired width of each reported coverage bucket in base pairs. This will be rounded down to
* the nearest precomputed bucket width; the value of which is returned as bucketWidth in the
* response. Defaults to infinity (each bucket spans an entire reference sequence) or the length of
* the target range, if specified. The smallest precomputed bucketWidth is currently 2048 base
* pairs; this is subject to change.
* @return Google_Service_Genomics_ListCoverageBucketsResponse
*/
public function listReadgroupsetsCoveragebuckets($readGroupSetId, $optParams = array())
{
$params = array('readGroupSetId' => $readGroupSetId);
$params = array_merge($params, $optParams);
return $this->call('list', array($params), "Google_Service_Genomics_ListCoverageBucketsResponse");
}
}
/**
* The "reads" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $reads = $genomicsService->reads;
* </code>
*/
class Google_Service_Genomics_Reads_Resource extends Google_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 Google_SearchReadsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_SearchReadsResponse
*/
public function search(Google_Service_Genomics_SearchReadsRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('search', array($params), "Google_Service_Genomics_SearchReadsResponse");
}
}
/**
* The "references" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $references = $genomicsService->references;
* </code>
*/
class Google_Service_Genomics_References_Resource extends Google_Service_Resource
{
/**
* Gets a reference.
*
* Implements GlobalAllianceApi.getReference. (references.get)
*
* @param string $referenceId
* The ID of the reference.
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_Reference
*/
public function get($referenceId, $optParams = array())
{
$params = array('referenceId' => $referenceId);
$params = array_merge($params, $optParams);
return $this->call('get', array($params), "Google_Service_Genomics_Reference");
}
/**
* Searches for references which match the given criteria.
*
* Implements GlobalAllianceApi.searchReferences. (references.search)
*
* @param Google_SearchReferencesRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_SearchReferencesResponse
*/
public function search(Google_Service_Genomics_SearchReferencesRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('search', array($params), "Google_Service_Genomics_SearchReferencesResponse");
}
}
/**
* The "bases" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $bases = $genomicsService->bases;
* </code>
*/
class Google_Service_Genomics_ReferencesBases_Resource extends Google_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 $optParams Optional parameters.
*
* @opt_param string pageToken
* The continuation token, which is used to page through large result sets. To get the next page of
* results, set this parameter to the value of nextPageToken from the previous response.
* @opt_param string end
* The end position (0-based, exclusive) of this query. Defaults to the length of this reference.
* @opt_param int pageSize
* Specifies the maximum number of bases to return in a single page.
* @opt_param string start
* The start position (0-based) of this query. Defaults to 0.
* @return Google_Service_Genomics_ListBasesResponse
*/
public function listReferencesBases($referenceId, $optParams = array())
{
$params = array('referenceId' => $referenceId);
$params = array_merge($params, $optParams);
return $this->call('list', array($params), "Google_Service_Genomics_ListBasesResponse");
}
}
/**
* The "referencesets" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $referencesets = $genomicsService->referencesets;
* </code>
*/
class Google_Service_Genomics_Referencesets_Resource extends Google_Service_Resource
{
/**
* Gets a reference set.
*
* Implements GlobalAllianceApi.getReferenceSet. (referencesets.get)
*
* @param string $referenceSetId
* The ID of the reference set.
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_ReferenceSet
*/
public function get($referenceSetId, $optParams = array())
{
$params = array('referenceSetId' => $referenceSetId);
$params = array_merge($params, $optParams);
return $this->call('get', array($params), "Google_Service_Genomics_ReferenceSet");
}
/**
* Searches for reference sets which match the given criteria.
*
* Implements GlobalAllianceApi.searchReferenceSets. (referencesets.search)
*
* @param Google_SearchReferenceSetsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_SearchReferenceSetsResponse
*/
public function search(Google_Service_Genomics_SearchReferenceSetsRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('search', array($params), "Google_Service_Genomics_SearchReferenceSetsResponse");
}
}
/**
* The "variants" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $variants = $genomicsService->variants;
* </code>
*/
class Google_Service_Genomics_Variants_Resource extends Google_Service_Resource
{
/**
* Creates a new variant. (variants.create)
*
* @param Google_Variant $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_Variant
*/
public function create(Google_Service_Genomics_Variant $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('create', array($params), "Google_Service_Genomics_Variant");
}
/**
* Deletes a variant. (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 $optParams Optional parameters.
* @return Google_Service_Genomics_Variant
*/
public function get($variantId, $optParams = array())
{
$params = array('variantId' => $variantId);
$params = array_merge($params, $optParams);
return $this->call('get', array($params), "Google_Service_Genomics_Variant");
}
/**
* Gets a list of variants matching the criteria.
*
* Implements GlobalAllianceApi.searchVariants. (variants.search)
*
* @param Google_SearchVariantsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_SearchVariantsResponse
*/
public function search(Google_Service_Genomics_SearchVariantsRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('search', array($params), "Google_Service_Genomics_SearchVariantsResponse");
}
/**
* 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 Google_Variant $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_Variant
*/
public function update($variantId, Google_Service_Genomics_Variant $postBody, $optParams = array())
{
$params = array('variantId' => $variantId, 'postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('update', array($params), "Google_Service_Genomics_Variant");
}
}
/**
* The "variantsets" collection of methods.
* Typical usage is:
* <code>
* $genomicsService = new Google_Service_Genomics(...);
* $variantsets = $genomicsService->variantsets;
* </code>
*/
class Google_Service_Genomics_Variantsets_Resource extends Google_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 Google_ExportVariantSetRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_ExportVariantSetResponse
*/
public function export($variantSetId, Google_Service_Genomics_ExportVariantSetRequest $postBody, $optParams = array())
{
$params = array('variantSetId' => $variantSetId, 'postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('export', array($params), "Google_Service_Genomics_ExportVariantSetResponse");
}
/**
* Gets a variant set by ID. (variantsets.get)
*
* @param string $variantSetId
* Required. The ID of the variant set.
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_VariantSet
*/
public function get($variantSetId, $optParams = array())
{
$params = array('variantSetId' => $variantSetId);
$params = array_merge($params, $optParams);
return $this->call('get', array($params), "Google_Service_Genomics_VariantSet");
}
/**
* 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 Google_ImportVariantsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_ImportVariantsResponse
*/
public function importVariants($variantSetId, Google_Service_Genomics_ImportVariantsRequest $postBody, $optParams = array())
{
$params = array('variantSetId' => $variantSetId, 'postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('importVariants', array($params), "Google_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 Google_MergeVariantsRequest $postBody
* @param array $optParams Optional parameters.
*/
public function mergeVariants($variantSetId, Google_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 Google_VariantSet $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_VariantSet
*/
public function patch($variantSetId, Google_Service_Genomics_VariantSet $postBody, $optParams = array())
{
$params = array('variantSetId' => $variantSetId, 'postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('patch', array($params), "Google_Service_Genomics_VariantSet");
}
/**
* Returns a list of all variant sets matching search criteria.
*
* Implements GlobalAllianceApi.searchVariantSets. (variantsets.search)
*
* @param Google_SearchVariantSetsRequest $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_SearchVariantSetsResponse
*/
public function search(Google_Service_Genomics_SearchVariantSetsRequest $postBody, $optParams = array())
{
$params = array('postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('search', array($params), "Google_Service_Genomics_SearchVariantSetsResponse");
}
/**
* 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 Google_VariantSet $postBody
* @param array $optParams Optional parameters.
* @return Google_Service_Genomics_VariantSet
*/
public function update($variantSetId, Google_Service_Genomics_VariantSet $postBody, $optParams = array())
{
$params = array('variantSetId' => $variantSetId, 'postBody' => $postBody);
$params = array_merge($params, $optParams);
return $this->call('update', array($params), "Google_Service_Genomics_VariantSet");
}
}
class Google_Service_Genomics_AlignReadGroupSetsRequest extends Google_Collection
{
protected $collection_key = 'readGroupSetIds';
protected $internal_gapi_mappings = array(
);
public $bamSourceUris;
public $datasetId;
protected $interleavedFastqSourceType = 'Google_Service_Genomics_InterleavedFastqSource';
protected $interleavedFastqSourceDataType = '';
protected $pairedFastqSourceType = 'Google_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(Google_Service_Genomics_InterleavedFastqSource $interleavedFastqSource)
{
$this->interleavedFastqSource = $interleavedFastqSource;
}
public function getInterleavedFastqSource()
{
return $this->interleavedFastqSource;
}
public function setPairedFastqSource(Google_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 Google_Service_Genomics_AlignReadGroupSetsResponse extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $jobId;
public function setJobId($jobId)
{
$this->jobId = $jobId;
}
public function getJobId()
{
return $this->jobId;
}
}
class Google_Service_Genomics_Call extends Google_Collection
{
protected $collection_key = 'genotypeLikelihood';
protected $internal_gapi_mappings = array(
);
public $callSetId;
public $callSetName;
public $genotype;
public $genotypeLikelihood;
public $info;
public $phaseset;
public function setCallSetId($callSetId)
{
$this->callSetId = $callSetId;
}
public function getCallSetId()
{
return $this->callSetId;
}
public function setCallSetName($callSetName)
{
$this->callSetName = $callSetName;
}
public function getCallSetName()
{
return $this->callSetName;
}
public function setGenotype($genotype)
{
$this->genotype = $genotype;
}
public function getGenotype()
{
return $this->genotype;
}
public function setGenotypeLikelihood($genotypeLikelihood)
{
$this->genotypeLikelihood = $genotypeLikelihood;
}
public function getGenotypeLikelihood()
{
return $this->genotypeLikelihood;
}
public function setInfo($info)
{
$this->info = $info;
}
public function getInfo()
{
return $this->info;
}
public function setPhaseset($phaseset)
{
$this->phaseset = $phaseset;
}
public function getPhaseset()
{
return $this->phaseset;
}
}
class Google_Service_Genomics_CallInfo extends Google_Model
{
protected $internal_gapi_mappings = array(
);
}
class Google_Service_Genomics_CallReadGroupSetsRequest extends Google_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 Google_Service_Genomics_CallReadGroupSetsResponse extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $jobId;
public function setJobId($jobId)
{
$this->jobId = $jobId;
}
public function getJobId()
{
return $this->jobId;
}
}
class Google_Service_Genomics_CallSet extends Google_Collection
{
protected $collection_key = 'variantSetIds';
protected $internal_gapi_mappings = array(
);
public $created;
public $id;
public $info;
public $name;
public $sampleId;
public $variantSetIds;
public function setCreated($created)
{
$this->created = $created;
}
public function getCreated()
{
return $this->created;
}
public function setId($id)
{
$this->id = $id;
}
public function getId()
{
return $this->id;
}
public function setInfo($info)
{
$this->info = $info;
}
public function getInfo()
{
return $this->info;
}
public function setName($name)
{
$this->name = $name;
}
public function getName()
{
return $this->name;
}
public function setSampleId($sampleId)
{
$this->sampleId = $sampleId;
}
public function getSampleId()
{
return $this->sampleId;
}
public function setVariantSetIds($variantSetIds)
{
$this->variantSetIds = $variantSetIds;
}
public function getVariantSetIds()
{
return $this->variantSetIds;
}
}
class Google_Service_Genomics_CallSetInfo extends Google_Model
{
protected $internal_gapi_mappings = array(
);
}
class Google_Service_Genomics_CigarUnit extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $operation;
public $operationLength;
public $referenceSequence;
public function setOperation($operation)
{
$this->operation = $operation;
}
public function getOperation()
{
return $this->operation;
}
public function setOperationLength($operationLength)
{
$this->operationLength = $operationLength;
}
public function getOperationLength()
{
return $this->operationLength;
}
public function setReferenceSequence($referenceSequence)
{
$this->referenceSequence = $referenceSequence;
}
public function getReferenceSequence()
{
return $this->referenceSequence;
}
}
class Google_Service_Genomics_CoverageBucket extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $meanCoverage;
protected $rangeType = 'Google_Service_Genomics_Range';
protected $rangeDataType = '';
public function setMeanCoverage($meanCoverage)
{
$this->meanCoverage = $meanCoverage;
}
public function getMeanCoverage()
{
return $this->meanCoverage;
}
public function setRange(Google_Service_Genomics_Range $range)
{
$this->range = $range;
}
public function getRange()
{
return $this->range;
}
}
class Google_Service_Genomics_Dataset extends Google_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 Google_Service_Genomics_ExperimentalCreateJobRequest extends Google_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 Google_Service_Genomics_ExperimentalCreateJobResponse extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $jobId;
public function setJobId($jobId)
{
$this->jobId = $jobId;
}
public function getJobId()
{
return $this->jobId;
}
}
class Google_Service_Genomics_ExportReadGroupSetsRequest extends Google_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 Google_Service_Genomics_ExportReadGroupSetsResponse extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $jobId;
public function setJobId($jobId)
{
$this->jobId = $jobId;
}
public function getJobId()
{
return $this->jobId;
}
}
class Google_Service_Genomics_ExportVariantSetRequest extends Google_Collection
{
protected $collection_key = 'callSetIds';
protected $internal_gapi_mappings = array(
);
public $bigqueryDataset;
public $bigqueryTable;
public $callSetIds;
public $format;
public $projectNumber;
public function setBigqueryDataset($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 Google_Service_Genomics_ExportVariantSetResponse extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $jobId;
public function setJobId($jobId)
{
$this->jobId = $jobId;
}
public function getJobId()
{
return $this->jobId;
}
}
class Google_Service_Genomics_FastqMetadata extends Google_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 Google_Service_Genomics_ImportReadGroupSetsRequest extends Google_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 Google_Service_Genomics_ImportReadGroupSetsResponse extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $jobId;
public function setJobId($jobId)
{
$this->jobId = $jobId;
}
public function getJobId()
{
return $this->jobId;
}
}
class Google_Service_Genomics_ImportVariantsRequest extends Google_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 Google_Service_Genomics_ImportVariantsResponse extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $jobId;
public function setJobId($jobId)
{
$this->jobId = $jobId;
}
public function getJobId()
{
return $this->jobId;
}
}
class Google_Service_Genomics_InterleavedFastqSource extends Google_Collection
{
protected $collection_key = 'sourceUris';
protected $internal_gapi_mappings = array(
);
protected $metadataType = 'Google_Service_Genomics_FastqMetadata';
protected $metadataDataType = '';
public $sourceUris;
public function setMetadata(Google_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 Google_Service_Genomics_Job extends Google_Collection
{
protected $collection_key = 'warnings';
protected $internal_gapi_mappings = array(
);
public $created;
public $detailedStatus;
public $errors;
public $id;
public $importedIds;
public $projectNumber;
protected $requestType = 'Google_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(Google_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 Google_Service_Genomics_JobRequest extends Google_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 Google_Service_Genomics_LinearAlignment extends Google_Collection
{
protected $collection_key = 'cigar';
protected $internal_gapi_mappings = array(
);
protected $cigarType = 'Google_Service_Genomics_CigarUnit';
protected $cigarDataType = 'array';
public $mappingQuality;
protected $positionType = 'Google_Service_Genomics_Position';
protected $positionDataType = '';
public function setCigar($cigar)
{
$this->cigar = $cigar;
}
public function getCigar()
{
return $this->cigar;
}
public function setMappingQuality($mappingQuality)
{
$this->mappingQuality = $mappingQuality;
}
public function getMappingQuality()
{
return $this->mappingQuality;
}
public function setPosition(Google_Service_Genomics_Position $position)
{
$this->position = $position;
}
public function getPosition()
{
return $this->position;
}
}
class Google_Service_Genomics_ListBasesResponse extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $nextPageToken;
public $offset;
public $sequence;
public function setNextPageToken($nextPageToken)
{
$this->nextPageToken = $nextPageToken;
}
public function getNextPageToken()
{
return $this->nextPageToken;
}
public function setOffset($offset)
{
$this->offset = $offset;
}
public function getOffset()
{
return $this->offset;
}
public function setSequence($sequence)
{
$this->sequence = $sequence;
}
public function getSequence()
{
return $this->sequence;
}
}
class Google_Service_Genomics_ListCoverageBucketsResponse extends Google_Collection
{
protected $collection_key = 'coverageBuckets';
protected $internal_gapi_mappings = array(
);
public $bucketWidth;
protected $coverageBucketsType = 'Google_Service_Genomics_CoverageBucket';
protected $coverageBucketsDataType = 'array';
public $nextPageToken;
public function setBucketWidth($bucketWidth)
{
$this->bucketWidth = $bucketWidth;
}
public function getBucketWidth()
{
return $this->bucketWidth;
}
public function setCoverageBuckets($coverageBuckets)
{
$this->coverageBuckets = $coverageBuckets;
}
public function getCoverageBuckets()
{
return $this->coverageBuckets;
}
public function setNextPageToken($nextPageToken)
{
$this->nextPageToken = $nextPageToken;
}
public function getNextPageToken()
{
return $this->nextPageToken;
}
}
class Google_Service_Genomics_ListDatasetsResponse extends Google_Collection
{
protected $collection_key = 'datasets';
protected $internal_gapi_mappings = array(
);
protected $datasetsType = 'Google_Service_Genomics_Dataset';
protected $datasetsDataType = 'array';
public $nextPageToken;
public function setDatasets($datasets)
{
$this->datasets = $datasets;
}
public function getDatasets()
{
return $this->datasets;
}
public function setNextPageToken($nextPageToken)
{
$this->nextPageToken = $nextPageToken;
}
public function getNextPageToken()
{
return $this->nextPageToken;
}
}
class Google_Service_Genomics_MergeVariantsRequest extends Google_Collection
{
protected $collection_key = 'variants';
protected $internal_gapi_mappings = array(
);
protected $variantsType = 'Google_Service_Genomics_Variant';
protected $variantsDataType = 'array';
public function setVariants($variants)
{
$this->variants = $variants;
}
public function getVariants()
{
return $this->variants;
}
}
class Google_Service_Genomics_Metadata extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $description;
public $id;
public $info;
public $key;
public $number;
public $type;
public $value;
public function setDescription($description)
{
$this->description = $description;
}
public function getDescription()
{
return $this->description;
}
public function setId($id)
{
$this->id = $id;
}
public function getId()
{
return $this->id;
}
public function setInfo($info)
{
$this->info = $info;
}
public function getInfo()
{
return $this->info;
}
public function setKey($key)
{
$this->key = $key;
}
public function getKey()
{
return $this->key;
}
public function setNumber($number)
{
$this->number = $number;
}
public function getNumber()
{
return $this->number;
}
public function setType($type)
{
$this->type = $type;
}
public function getType()
{
return $this->type;
}
public function setValue($value)
{
$this->value = $value;
}
public function getValue()
{
return $this->value;
}
}
class Google_Service_Genomics_MetadataInfo extends Google_Model
{
protected $internal_gapi_mappings = array(
);
}
class Google_Service_Genomics_PairedFastqSource extends Google_Collection
{
protected $collection_key = 'secondSourceUris';
protected $internal_gapi_mappings = array(
);
public $firstSourceUris;
protected $metadataType = 'Google_Service_Genomics_FastqMetadata';
protected $metadataDataType = '';
public $secondSourceUris;
public function setFirstSourceUris($firstSourceUris)
{
$this->firstSourceUris = $firstSourceUris;
}
public function getFirstSourceUris()
{
return $this->firstSourceUris;
}
public function setMetadata(Google_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 Google_Service_Genomics_Position extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $position;
public $referenceName;
public $reverseStrand;
public function setPosition($position)
{
$this->position = $position;
}
public function getPosition()
{
return $this->position;
}
public function setReferenceName($referenceName)
{
$this->referenceName = $referenceName;
}
public function getReferenceName()
{
return $this->referenceName;
}
public function setReverseStrand($reverseStrand)
{
$this->reverseStrand = $reverseStrand;
}
public function getReverseStrand()
{
return $this->reverseStrand;
}
}
class Google_Service_Genomics_Range extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $end;
public $referenceName;
public $start;
public function setEnd($end)
{
$this->end = $end;
}
public function getEnd()
{
return $this->end;
}
public function setReferenceName($referenceName)
{
$this->referenceName = $referenceName;
}
public function getReferenceName()
{
return $this->referenceName;
}
public function setStart($start)
{
$this->start = $start;
}
public function getStart()
{
return $this->start;
}
}
class Google_Service_Genomics_Read extends Google_Collection
{
protected $collection_key = 'alignedQuality';
protected $internal_gapi_mappings = array(
);
public $alignedQuality;
public $alignedSequence;
protected $alignmentType = 'Google_Service_Genomics_LinearAlignment';
protected $alignmentDataType = '';
public $duplicateFragment;
public $failedVendorQualityChecks;
public $fragmentLength;
public $fragmentName;
public $id;
public $info;
protected $nextMatePositionType = 'Google_Service_Genomics_Position';
protected $nextMatePositionDataType = '';
public $numberReads;
public $properPlacement;
public $readGroupId;
public $readGroupSetId;
public $readNumber;
public $secondaryAlignment;
public $supplementaryAlignment;
public function setAlignedQuality($alignedQuality)
{
$this->alignedQuality = $alignedQuality;
}
public function getAlignedQuality()
{
return $this->alignedQuality;
}
public function setAlignedSequence($alignedSequence)
{
$this->alignedSequence = $alignedSequence;
}
public function getAlignedSequence()
{
return $this->alignedSequence;
}
public function setAlignment(Google_Service_Genomics_LinearAlignment $alignment)
{
$this->alignment = $alignment;
}
public function getAlignment()
{
return $this->alignment;
}
public function setDuplicateFragment($duplicateFragment)
{
$this->duplicateFragment = $duplicateFragment;
}
public function getDuplicateFragment()
{
return $this->duplicateFragment;
}
public function setFailedVendorQualityChecks($failedVendorQualityChecks)
{
$this->failedVendorQualityChecks = $failedVendorQualityChecks;
}
public function getFailedVendorQualityChecks()
{
return $this->failedVendorQualityChecks;
}
public function setFragmentLength($fragmentLength)
{
$this->fragmentLength = $fragmentLength;
}
public function getFragmentLength()
{
return $this->fragmentLength;
}
public function setFragmentName($fragmentName)
{
$this->fragmentName = $fragmentName;
}
public function getFragmentName()
{
return $this->fragmentName;
}
public function setId($id)
{
$this->id = $id;
}
public function getId()
{
return $this->id;
}
public function setInfo($info)
{
$this->info = $info;
}
public function getInfo()
{
return $this->info;
}
public function setNextMatePosition(Google_Service_Genomics_Position $nextMatePosition)
{
$this->nextMatePosition = $nextMatePosition;
}
public function getNextMatePosition()
{
return $this->nextMatePosition;
}
public function setNumberReads($numberReads)
{
$this->numberReads = $numberReads;
}
public function getNumberReads()
{
return $this->numberReads;
}
public function setProperPlacement($properPlacement)
{
$this->properPlacement = $properPlacement;
}
public function getProperPlacement()
{
return $this->properPlacement;
}
public function setReadGroupId($readGroupId)
{
$this->readGroupId = $readGroupId;
}
public function getReadGroupId()
{
return $this->readGroupId;
}
public function setReadGroupSetId($readGroupSetId)
{
$this->readGroupSetId = $readGroupSetId;
}
public function getReadGroupSetId()
{
return $this->readGroupSetId;
}
public function setReadNumber($readNumber)
{
$this->readNumber = $readNumber;
}
public function getReadNumber()
{
return $this->readNumber;
}
public function setSecondaryAlignment($secondaryAlignment)
{
$this->secondaryAlignment = $secondaryAlignment;
}
public function getSecondaryAlignment()
{
return $this->secondaryAlignment;
}
public function setSupplementaryAlignment($supplementaryAlignment)
{
$this->supplementaryAlignment = $supplementaryAlignment;
}
public function getSupplementaryAlignment()
{
return $this->supplementaryAlignment;
}
}
class Google_Service_Genomics_ReadGroup extends Google_Collection
{
protected $collection_key = 'programs';
protected $internal_gapi_mappings = array(
);
public $datasetId;
public $description;
protected $experimentType = 'Google_Service_Genomics_ReadGroupExperiment';
protected $experimentDataType = '';
public $id;
public $info;
public $name;
public $predictedInsertSize;
protected $programsType = 'Google_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(Google_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 Google_Service_Genomics_ReadGroupExperiment extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $instrumentModel;
public $libraryId;
public $platformUnit;
public $sequencingCenter;
public function setInstrumentModel($instrumentModel)
{
$this->instrumentModel = $instrumentModel;
}
public function getInstrumentModel()
{
return $this->instrumentModel;
}
public function setLibraryId($libraryId)
{
$this->libraryId = $libraryId;
}
public function getLibraryId()
{
return $this->libraryId;
}
public function setPlatformUnit($platformUnit)
{
$this->platformUnit = $platformUnit;
}
public function getPlatformUnit()
{
return $this->platformUnit;
}
public function setSequencingCenter($sequencingCenter)
{
$this->sequencingCenter = $sequencingCenter;
}
public function getSequencingCenter()
{
return $this->sequencingCenter;
}
}
class Google_Service_Genomics_ReadGroupInfo extends Google_Model
{
protected $internal_gapi_mappings = array(
);
}
class Google_Service_Genomics_ReadGroupProgram extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $commandLine;
public $id;
public $name;
public $prevProgramId;
public $version;
public function setCommandLine($commandLine)
{
$this->commandLine = $commandLine;
}
public function getCommandLine()
{
return $this->commandLine;
}
public function setId($id)
{
$this->id = $id;
}
public function getId()
{
return $this->id;
}
public function setName($name)
{
$this->name = $name;
}
public function getName()
{
return $this->name;
}
public function setPrevProgramId($prevProgramId)
{
$this->prevProgramId = $prevProgramId;
}
public function getPrevProgramId()
{
return $this->prevProgramId;
}
public function setVersion($version)
{
$this->version = $version;
}
public function getVersion()
{
return $this->version;
}
}
class Google_Service_Genomics_ReadGroupSet extends Google_Collection
{
protected $collection_key = 'readGroups';
protected $internal_gapi_mappings = array(
);
public $datasetId;
public $filename;
public $id;
public $name;
protected $readGroupsType = 'Google_Service_Genomics_ReadGroup';
protected $readGroupsDataType = 'array';
public $referenceSetId;
public function setDatasetId($datasetId)
{
$this->datasetId = $datasetId;
}
public function getDatasetId()
{
return $this->datasetId;
}
public function setFilename($filename)
{
$this->filename = $filename;
}
public function getFilename()
{
return $this->filename;
}
public function setId($id)
{
$this->id = $id;
}
public function getId()
{
return $this->id;
}
public function setName($name)
{
$this->name = $name;
}
public function getName()
{
return $this->name;
}
public function setReadGroups($readGroups)
{
$this->readGroups = $readGroups;
}
public function getReadGroups()
{
return $this->readGroups;
}
public function setReferenceSetId($referenceSetId)
{
$this->referenceSetId = $referenceSetId;
}
public function getReferenceSetId()
{
return $this->referenceSetId;
}
}
class Google_Service_Genomics_ReadInfo extends Google_Model
{
protected $internal_gapi_mappings = array(
);
}
class Google_Service_Genomics_Reference extends Google_Collection
{
protected $collection_key = 'sourceAccessions';
protected $internal_gapi_mappings = array(
);
public $id;
public $length;
public $md5checksum;
public $name;
public $ncbiTaxonId;
public $sourceAccessions;
public $sourceURI;
public function setId($id)
{
$this->id = $id;
}
public function getId()
{
return $this->id;
}
public function setLength($length)
{
$this->length = $length;
}
public function getLength()
{
return $this->length;
}
public function setMd5checksum($md5checksum)
{
$this->md5checksum = $md5checksum;
}
public function getMd5checksum()
{
return $this->md5checksum;
}
public function setName($name)
{
$this->name = $name;
}
public function getName()
{
return $this->name;
}
public function setNcbiTaxonId($ncbiTaxonId)
{
$this->ncbiTaxonId = $ncbiTaxonId;
}
public function getNcbiTaxonId()
{
return $this->ncbiTaxonId;
}
public function setSourceAccessions($sourceAccessions)
{
$this->sourceAccessions = $sourceAccessions;
}
public function getSourceAccessions()
{
return $this->sourceAccessions;
}
public function setSourceURI($sourceURI)
{
$this->sourceURI = $sourceURI;
}
public function getSourceURI()
{
return $this->sourceURI;
}
}
class Google_Service_Genomics_ReferenceBound extends Google_Model
{
protected $internal_gapi_mappings = array(
);
public $referenceName;
public $upperBound;
public function setReferenceName($referenceName)
{
$this->referenceName = $referenceName;
}
public function getReferenceName()
{
return $this->referenceName;
}
public function setUpperBound($upperBound)
{
$this->upperBound = $upperBound;
}
public function getUpperBound()
{
return $this->upperBound;
}
}
class Google_Service_Genomics_ReferenceSet extends Google_Collection
{
protected $collection_key = 'sourceAccessions';
protected $internal_gapi_mappings = array(
);
public $assemblyId;
public $description;
public $id;
public $md5checksum;
public $ncbiTaxonId;
public $referenceIds;
public $sourceAccessions;
public $sourceURI;
public function setAssemblyId($assemblyId)
{
$this->assemblyId = $assemblyId;
}
public function getAssemblyId()
{
return $this->assemblyId;
}
public function setDescription($description)
{
$this->description = $description;
}
public function getDescription()
{
return $this->description;
}
public function setId($id)
{
$this->id = $id;
}
public function getId()
{
return $this->id;
}
public function setMd5checksum($md5checksum)
{
$this->md5checksum = $md5checksum;
}
public function getMd5checksum()
{
return $this->md5checksum;
}
public function setNcbiTaxonId($ncbiTaxonId)
{
$this->ncbiTaxonId = $ncbiTaxonId;
}
public function getNcbiTaxonId()
{
return $this->ncbiTaxonId;
}
public function setReferenceIds($referenceIds)
{
$this->referenceIds = $referenceIds;
}
public function getReferenceIds()
{
return $this->referenceIds;
}
public function setSourceAccessions($sourceAccessions)
{
$this->sourceAccessions = $sourceAccessions;
}
public function getSourceAccessions()
{
return $this->sourceAccessions;
}
public function setSourceURI($sourceURI)
{
$this->sourceURI = $sourceURI;
}
public function getSourceURI()
{
return $this->sourceURI;
}
}
class Google_Service_Genomics_SearchCallSetsRequest extends Google_Collection
{
protected $collection_key = 'variantSetIds';
protected $internal_gapi_mappings = array(
);
public $name;
public $pageSize;
public $pageToken;
public $variantSetIds;
public function setName($name)
{
$this->name = $name;
}
public function getName()
{
return $this->name;
}
public function setPageSize($pageSize)
{
$this->pageSize = $pageSize;
}
public function getPageSize()
{
return $this->pageSize;
}
public function setPageToken($pageToken)
{
$this->pageToken = $pageToken;
}
public function getPageToken()
{
return $this->pageToken;
}
public function setVariantSetIds($variantSetIds)
{
$this->variantSetIds = $variantSetIds;
}
public function getVariantSetIds()
{
return $this->variantSetIds;
}
}
class Google_Service_Genomics_SearchCallSetsResponse extends Google_Collection
{
protected $collection_key = 'callSets';
protected $internal_gapi_mappings = array(
);
protected $callSetsType = 'Google_Service_Genomics_CallSet';
protected $callSetsDataType = 'array';
public $nextPageToken;
public function setCallSets($callSets)
{
$this->callSets = $callSets;
}
public function getCallSets()
{
return $this->callSets;
}
public function setNextPageToken($nextPageToken)
{
$this->nextPageToken = $nextPageToken;
}
public function getNextPageToken()
{
return $this->nextPageToken;
}
}
class Google_Service_Genomics_SearchJobsRequest extends Google_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 Google_Service_Genomics_SearchJobsResponse extends Google_Collection
{
protected $collection_key = 'jobs';
protected $internal_gapi_mappings = array(
);
protected $jobsType = 'Google_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 Google_Service_Genomics_SearchReadGroupSetsRequest extends Google_Collection
{
protected $collection_key = 'datasetIds';
protected $internal_gapi_mappings = array(
);
public $datasetIds;
public $name;
public $pageSize;
public $pageToken;
public function setDatasetIds($datasetIds)
{
$this->datasetIds = $datasetIds;
}
public function getDatasetIds()
{
return $this->datasetIds;
}
public function setName($name)
{
$this->name = $name;
}
public function getName()
{
return $this->name;
}
public function setPageSize($pageSize)
{
$this->pageSize = $pageSize;
}
public function getPageSize()
{
return $this->pageSize;
}
public function setPageToken($pageToken)
{
$this->pageToken = $pageToken;
}
public function getPageToken()
{
return $this->pageToken;
}
}
class Google_Service_Genomics_SearchReadGroupSetsResponse extends Google_Collection
{
protected $collection_key = 'readGroupSets';
protected $internal_gapi_mappings = array(
);
public $nextPageToken;
protected $readGroupSetsType = 'Google_Service_Genomics_ReadGroupSet';
protected $readGroupSetsDataType = 'array';
public function setNextPageToken($nextPageToken)
{
$this->nextPageToken = $nextPageToken;
}
public function getNextPageToken()
{
return $this->nextPageToken;
}
public function setReadGroupSets($readGroupSets)
{
$this->readGroupSets = $readGroupSets;
}
public function getReadGroupSets()
{
return $this->readGroupSets;
}
}
class Google_Service_Genomics_SearchReadsRequest extends Google_Collection
{
protected $collection_key = 'readGroupSetIds';
protected $internal_gapi_mappings = array(
);
public $end;
public $pageSize;
public $pageToken;
public $readGroupIds;
public $readGroupSetIds;
public $referenceName;
public $start;
public function setEnd($end)
{
$this->end = $end;
}
public function getEnd()
{
return $this->end;
}
public function setPageSize($pageSize)
{
$this->pageSize = $pageSize;
}
public function getPageSize()
{
return $this->pageSize;
}
public function setPageToken($pageToken)
{
$this->pageToken = $pageToken;
}
public function getPageToken()
{
return $this->pageToken;
}
public function setReadGroupIds($readGroupIds)
{
$this->readGroupIds = $readGroupIds;
}
public function getReadGroupIds()
{
return $this->readGroupIds;
}
public function setReadGroupSetIds($readGroupSetIds)
{
$this->readGroupSetIds = $readGroupSetIds;
}
public function getReadGroupSetIds()
{
return $this->readGroupSetIds;
}
public function setReferenceName($referenceName)
{
$this->referenceName = $referenceName;
}
public function getReferenceName()
{
return $this->referenceName;
}
public function setStart($start)
{
$this->start = $start;
}
public function getStart()
{
return $this->start;
}
}
class Google_Service_Genomics_SearchReadsResponse extends Google_Collection
{
protected $collection_key = 'alignments';
protected $internal_gapi_mappings = array(
);
protected $alignmentsType = 'Google_Service_Genomics_Read';
protected $alignmentsDataType = 'array';
public $nextPageToken;
public function setAlignments($alignments)
{
$this->alignments = $alignments;
}
public function getAlignments()
{
return $this->alignments;
}
public function setNextPageToken($nextPageToken)
{
$this->nextPageToken = $nextPageToken;
}
public function getNextPageToken()
{
return $this->nextPageToken;
}
}
class Google_Service_Genomics_SearchReferenceSetsRequest extends Google_Collection
{
protected $collection_key = 'md5checksums';
protected $internal_gapi_mappings = array(
);
public $accessions;
public $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 Google_Service_Genomics_SearchReferenceSetsResponse extends Google_Collection
{
protected $collection_key = 'referenceSets';
protected $internal_gapi_mappings = array(
);
public $nextPageToken;
protected $referenceSetsType = 'Google_Service_Genomics_ReferenceSet';
protected $referenceSetsDataType = 'array';
public function setNextPageToken($nextPageToken)
{
$this->nextPageToken = $nextPageToken;
}
public function getNextPageToken()
{
return $this->nextPageToken;
}
public function setReferenceSets($referenceSets)
{
$this->referenceSets = $referenceSets;
}
public function getReferenceSets()
{
return $this->referenceSets;
}
}
class Google_Service_Genomics_SearchReferencesRequest extends Google_Collection
{
protected $collection_key = 'md5checksums';
protected $internal_gapi_mappings = array(
);
public $accessions;
public $md5checksums;
public $pageSize;
public $pageToken;
public $referenceSetId;
public function setAccessions($accessions)
{
$this->accessions = $accessions;
}
public function getAccessions()
{
return $this->accessions;
}
public function setMd5checksums($md5checksums)
{
$this->md5checksums = $md5checksums;
}
public function getMd5checksums()
{
return $this->md5checksums;
}
public function setPageSize($pageSize)
{
$this->pageSize = $pageSize;
}
public function getPageSize()
{
return $this->pageSize;
}
public function setPageToken($pageToken)
{
$this->pageToken = $pageToken;
}
public function getPageToken()
{
return $this->pageToken;
}
public function setReferenceSetId($referenceSetId)
{
$this->referenceSetId = $referenceSetId;
}
public function getReferenceSetId()
{
return $this->referenceSetId;
}
}
class Google_Service_Genomics_SearchReferencesResponse extends Google_Collection
{
protected $collection_key = 'references';
protected $internal_gapi_mappings = array(
);
public $nextPageToken;
protected $referencesType = 'Google_Service_Genomics_Reference';
protected $referencesDataType = 'array';
public function setNextPageToken($nextPageToken)
{
$this->nextPageToken = $nextPageToken;
}
public function getNextPageToken()
{
return $this->nextPageToken;
}
public function setReferences($references)
{
$this->references = $references;
}
public function getReferences()
{
return $this->references;
}
}
class Google_Service_Genomics_SearchVariantSetsRequest extends Google_Collection
{
protected $collection_key = 'datasetIds';
protected $internal_gapi_mappings = array(
);
public $datasetIds;
public $pageSize;
public $pageToken;
public function setDatasetIds($datasetIds)
{
$this->datasetIds = $datasetIds;
}
public function getDatasetIds()
{
return $this->datasetIds;
}
public function setPageSize($pageSize)
{
$this->pageSize = $pageSize;
}
public function getPageSize()
{
return $this->pageSize;
}
public function setPageToken($pageToken)
{
$this->pageToken = $pageToken;
}
public function getPageToken()
{
return $this->pageToken;
}
}
class Google_Service_Genomics_SearchVariantSetsResponse extends Google_Collection
{
protected $collection_key = 'variantSets';
protected $internal_gapi_mappings = array(
);
public $nextPageToken;
protected $variantSetsType = 'Google_Service_Genomics_VariantSet';
protected $variantSetsDataType = 'array';
public function setNextPageToken($nextPageToken)
{
$this->nextPageToken = $nextPageToken;
}
public function getNextPageToken()
{
return $this->nextPageToken;
}
public function setVariantSets($variantSets)
{
$this->variantSets = $variantSets;
}
public function getVariantSets()
{
return $this->variantSets;
}
}
class Google_Service_Genomics_SearchVariantsRequest extends Google_Collection
{
protected $collection_key = 'variantSetIds';
protected $internal_gapi_mappings = array(
);
public $callSetIds;
public $end;
public $maxCalls;
public $pageSize;
public $pageToken;
public $referenceName;
public $start;
public $variantName;
public $variantSetIds;
public function setCallSetIds($callSetIds)
{
$this->callSetIds = $callSetIds;
}
public function getCallSetIds()
{
return $this->callSetIds;
}
public function setEnd($end)
{
$this->end = $end;
}
public function getEnd()
{
return $this->end;
}
public function setMaxCalls($maxCalls)
{
$this->maxCalls = $maxCalls;
}
public function getMaxCalls()
{
return $this->maxCalls;
}
public function setPageSize($pageSize)
{
$this->pageSize = $pageSize;
}
public function getPageSize()
{
return $this->pageSize;
}
public function setPageToken($pageToken)
{
$this->pageToken = $pageToken;
}
public function getPageToken()
{
return $this->pageToken;
}
public function setReferenceName($referenceName)
{
$this->referenceName = $referenceName;
}
public function getReferenceName()
{
return $this->referenceName;
}
public function setStart($start)
{
$this->start = $start;
}
public function getStart()
{
return $this->start;
}
public function setVariantName($variantName)
{
$this->variantName = $variantName;
}
public function getVariantName()
{
return $this->variantName;
}
public function setVariantSetIds($variantSetIds)
{
$this->variantSetIds = $variantSetIds;
}
public function getVariantSetIds()
{
return $this->variantSetIds;
}
}
class Google_Service_Genomics_SearchVariantsResponse extends Google_Collection
{
protected $collection_key = 'variants';
protected $internal_gapi_mappings = array(
);
public $nextPageToken;
protected $variantsType = 'Google_Service_Genomics_Variant';
protected $variantsDataType = 'array';
public function setNextPageToken($nextPageToken)
{
$this->nextPageToken = $nextPageToken;
}
public function getNextPageToken()
{
return $this->nextPageToken;
}
public function setVariants($variants)
{
$this->variants = $variants;
}
public function getVariants()
{
return $this->variants;
}
}
class Google_Service_Genomics_Variant extends Google_Collection
{
protected $collection_key = 'names';
protected $internal_gapi_mappings = array(
);
public $alternateBases;
protected $callsType = 'Google_Service_Genomics_Call';
protected $callsDataType = 'array';
public $created;
public $end;
public $filter;
public $id;
public $info;
public $names;
public $quality;
public $referenceBases;
public $referenceName;
public $start;
public $variantSetId;
public function setAlternateBases($alternateBases)
{
$this->alternateBases = $alternateBases;
}
public function getAlternateBases()
{
return $this->alternateBases;
}
public function setCalls($calls)
{
$this->calls = $calls;
}
public function getCalls()
{
return $this->calls;
}
public function setCreated($created)
{
$this->created = $created;
}
public function getCreated()
{
return $this->created;
}
public function setEnd($end)
{
$this->end = $end;
}
public function getEnd()
{
return $this->end;
}
public function setFilter($filter)
{
$this->filter = $filter;
}
public function getFilter()
{
return $this->filter;
}
public function setId($id)
{
$this->id = $id;
}
public function getId()
{
return $this->id;
}
public function setInfo($info)
{
$this->info = $info;
}
public function getInfo()
{
return $this->info;
}
public function setNames($names)
{
$this->names = $names;
}
public function getNames()
{
return $this->names;
}
public function setQuality($quality)
{
$this->quality = $quality;
}
public function getQuality()
{
return $this->quality;
}
public function setReferenceBases($referenceBases)
{
$this->referenceBases = $referenceBases;
}
public function getReferenceBases()
{
return $this->referenceBases;
}
public function setReferenceName($referenceName)
{
$this->referenceName = $referenceName;
}
public function getReferenceName()
{
return $this->referenceName;
}
public function setStart($start)
{
$this->start = $start;
}
public function getStart()
{
return $this->start;
}
public function setVariantSetId($variantSetId)
{
$this->variantSetId = $variantSetId;
}
public function getVariantSetId()
{
return $this->variantSetId;
}
}
class Google_Service_Genomics_VariantInfo extends Google_Model
{
protected $internal_gapi_mappings = array(
);
}
class Google_Service_Genomics_VariantSet extends Google_Collection
{
protected $collection_key = 'referenceBounds';
protected $internal_gapi_mappings = array(
);
public $datasetId;
public $id;
protected $metadataType = 'Google_Service_Genomics_Metadata';
protected $metadataDataType = 'array';
protected $referenceBoundsType = 'Google_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;
}
}