3247 lines
74 KiB
PHP
3247 lines
74 KiB
PHP
<?php
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/*
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* Copyright 2010 Google Inc.
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*
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* Licensed under the Apache License, Version 2.0 (the "License"); you may not
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* use this file except in compliance with the License. You may obtain a copy of
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* the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
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* WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
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* License for the specific language governing permissions and limitations under
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* the License.
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*/
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/**
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* Service definition for Genomics (v1beta).
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*
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* <p>
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* Provides access to Genomics data.
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* </p>
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*
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* <p>
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* For more information about this service, see the API
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* <a href="https://developers.google.com/genomics/v1beta/reference" target="_blank">Documentation</a>
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* </p>
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*
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* @author Google, Inc.
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*/
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class Google_Service_Genomics extends Google_Service
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{
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/** View and manage your data in Google BigQuery. */
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const BIGQUERY = "https://www.googleapis.com/auth/bigquery";
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/** Manage your data in Google Cloud Storage. */
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const DEVSTORAGE_READ_WRITE = "https://www.googleapis.com/auth/devstorage.read_write";
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/** View and manage Genomics data. */
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const GENOMICS = "https://www.googleapis.com/auth/genomics";
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/** View Genomics data. */
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const GENOMICS_READONLY = "https://www.googleapis.com/auth/genomics.readonly";
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public $beacons;
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public $callsets;
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public $datasets;
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public $experimental_jobs;
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public $jobs;
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public $reads;
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public $readsets;
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public $readsets_coveragebuckets;
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public $variants;
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/**
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* Constructs the internal representation of the Genomics service.
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*
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* @param Google_Client $client
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*/
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public function __construct(Google_Client $client)
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{
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parent::__construct($client);
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$this->servicePath = 'genomics/v1beta/';
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$this->version = 'v1beta';
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$this->serviceName = 'genomics';
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$this->beacons = new Google_Service_Genomics_Beacons_Resource(
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$this,
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$this->serviceName,
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'beacons',
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array(
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'methods' => array(
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'get' => array(
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'path' => 'beacons/{datasetId}',
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'httpMethod' => 'GET',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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'allele' => array(
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'location' => 'query',
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'type' => 'string',
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),
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'contig' => array(
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'location' => 'query',
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'type' => 'string',
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),
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'position' => array(
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'location' => 'query',
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'type' => 'string',
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),
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),
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),
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)
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)
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);
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$this->callsets = new Google_Service_Genomics_Callsets_Resource(
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$this,
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$this->serviceName,
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'callsets',
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array(
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'methods' => array(
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'create' => array(
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'path' => 'callsets',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'delete' => array(
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'path' => 'callsets/{callsetId}',
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'httpMethod' => 'DELETE',
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'parameters' => array(
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'callsetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'get' => array(
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'path' => 'callsets/{callsetId}',
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'httpMethod' => 'GET',
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'parameters' => array(
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'callsetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'patch' => array(
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'path' => 'callsets/{callsetId}',
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'httpMethod' => 'PATCH',
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'parameters' => array(
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'callsetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'search' => array(
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'path' => 'callsets/search',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'update' => array(
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'path' => 'callsets/{callsetId}',
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'httpMethod' => 'PUT',
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'parameters' => array(
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'callsetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),
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)
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)
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);
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$this->datasets = new Google_Service_Genomics_Datasets_Resource(
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$this,
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$this->serviceName,
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'datasets',
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array(
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'methods' => array(
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'create' => array(
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'path' => 'datasets',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'delete' => array(
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'path' => 'datasets/{datasetId}',
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'httpMethod' => 'DELETE',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'get' => array(
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'path' => 'datasets/{datasetId}',
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'httpMethod' => 'GET',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'list' => array(
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'path' => 'datasets',
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'httpMethod' => 'GET',
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'parameters' => array(
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'pageToken' => array(
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'location' => 'query',
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'type' => 'string',
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),
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'maxResults' => array(
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'location' => 'query',
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'type' => 'string',
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),
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'projectId' => array(
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'location' => 'query',
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'type' => 'string',
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),
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),
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),'patch' => array(
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'path' => 'datasets/{datasetId}',
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'httpMethod' => 'PATCH',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'undelete' => array(
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'path' => 'datasets/{datasetId}/undelete',
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'httpMethod' => 'POST',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'update' => array(
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'path' => 'datasets/{datasetId}',
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'httpMethod' => 'PUT',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),
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)
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)
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);
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$this->experimental_jobs = new Google_Service_Genomics_ExperimentalJobs_Resource(
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$this,
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$this->serviceName,
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'jobs',
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array(
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'methods' => array(
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'create' => array(
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'path' => 'experimental/jobs/create',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),
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)
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)
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);
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$this->jobs = new Google_Service_Genomics_Jobs_Resource(
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$this,
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$this->serviceName,
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'jobs',
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array(
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'methods' => array(
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'cancel' => array(
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'path' => 'jobs/{jobId}/cancel',
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'httpMethod' => 'POST',
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'parameters' => array(
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'jobId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'get' => array(
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'path' => 'jobs/{jobId}',
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'httpMethod' => 'GET',
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'parameters' => array(
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'jobId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'search' => array(
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'path' => 'jobs/search',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),
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)
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)
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);
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$this->reads = new Google_Service_Genomics_Reads_Resource(
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$this,
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$this->serviceName,
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'reads',
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array(
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'methods' => array(
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'search' => array(
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'path' => 'reads/search',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),
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)
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)
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);
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$this->readsets = new Google_Service_Genomics_Readsets_Resource(
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$this,
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$this->serviceName,
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'readsets',
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array(
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'methods' => array(
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'delete' => array(
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'path' => 'readsets/{readsetId}',
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'httpMethod' => 'DELETE',
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'parameters' => array(
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'readsetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'export' => array(
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'path' => 'readsets/export',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'get' => array(
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'path' => 'readsets/{readsetId}',
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'httpMethod' => 'GET',
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'parameters' => array(
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'readsetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'import' => array(
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'path' => 'readsets/import',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'patch' => array(
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'path' => 'readsets/{readsetId}',
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'httpMethod' => 'PATCH',
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'parameters' => array(
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'readsetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'search' => array(
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'path' => 'readsets/search',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'update' => array(
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'path' => 'readsets/{readsetId}',
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'httpMethod' => 'PUT',
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'parameters' => array(
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'readsetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),
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)
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)
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);
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$this->readsets_coveragebuckets = new Google_Service_Genomics_ReadsetsCoveragebuckets_Resource(
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$this,
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$this->serviceName,
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'coveragebuckets',
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array(
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'methods' => array(
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'list' => array(
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'path' => 'readsets/{readsetId}/coveragebuckets',
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'httpMethod' => 'GET',
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'parameters' => array(
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'readsetId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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'range.sequenceStart' => array(
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'location' => 'query',
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'type' => 'string',
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),
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'maxResults' => array(
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'location' => 'query',
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'type' => 'string',
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),
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'range.sequenceName' => array(
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'location' => 'query',
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'type' => 'string',
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),
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'pageToken' => array(
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'location' => 'query',
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'type' => 'string',
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),
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'targetBucketWidth' => array(
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'location' => 'query',
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'type' => 'string',
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),
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'range.sequenceEnd' => array(
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'location' => 'query',
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'type' => 'string',
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),
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),
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),
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)
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)
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);
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$this->variants = new Google_Service_Genomics_Variants_Resource(
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$this,
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$this->serviceName,
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'variants',
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array(
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'methods' => array(
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'create' => array(
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'path' => 'variants',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'delete' => array(
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'path' => 'variants/{variantId}',
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'httpMethod' => 'DELETE',
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'parameters' => array(
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'variantId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'export' => array(
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'path' => 'variants/export',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'get' => array(
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'path' => 'variants/{variantId}',
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'httpMethod' => 'GET',
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'parameters' => array(
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'variantId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'getSummary' => array(
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'path' => 'variants/summary',
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'httpMethod' => 'GET',
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'parameters' => array(
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'datasetId' => array(
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'location' => 'query',
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'type' => 'string',
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),
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),
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),'import' => array(
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'path' => 'variants/import',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'patch' => array(
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'path' => 'variants/{variantId}',
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'httpMethod' => 'PATCH',
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'parameters' => array(
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'variantId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),'search' => array(
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'path' => 'variants/search',
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'httpMethod' => 'POST',
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'parameters' => array(),
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),'update' => array(
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'path' => 'variants/{variantId}',
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'httpMethod' => 'PUT',
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'parameters' => array(
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'variantId' => array(
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'location' => 'path',
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'type' => 'string',
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'required' => true,
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),
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),
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),
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)
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)
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);
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}
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}
|
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|
|
|
|
/**
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* The "beacons" collection of methods.
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* Typical usage is:
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* <code>
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* $genomicsService = new Google_Service_Genomics(...);
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* $beacons = $genomicsService->beacons;
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* </code>
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*/
|
|
class Google_Service_Genomics_Beacons_Resource extends Google_Service_Resource
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{
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|
|
/**
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* This is an experimental API that provides a Global Alliance for Genomics and
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* Health Beacon. It may change at any time. (beacons.get)
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|
*
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* @param string $datasetId
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* The ID of the dataset to query over. It must be public. Private datasets will return an
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* unauthorized exception.
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|
* @param array $optParams Optional parameters.
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|
*
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* @opt_param string allele
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* Required. The allele to look for ('A', 'C', 'G' or 'T').
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|
* @opt_param string contig
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* Required. The contig to query over.
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* @opt_param string position
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* Required. The 1-based position to query at.
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* @return Google_Service_Genomics_Beacon
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*/
|
|
public function get($datasetId, $optParams = array())
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{
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$params = array('datasetId' => $datasetId);
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$params = array_merge($params, $optParams);
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return $this->call('get', array($params), "Google_Service_Genomics_Beacon");
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}
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}
|
|
|
|
/**
|
|
* The "callsets" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
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* $callsets = $genomicsService->callsets;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Callsets_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Creates a new callset. (callsets.create)
|
|
*
|
|
* @param Google_Callset $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Callset
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*/
|
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public function create(Google_Service_Genomics_Callset $postBody, $optParams = array())
|
|
{
|
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$params = array('postBody' => $postBody);
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$params = array_merge($params, $optParams);
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return $this->call('create', array($params), "Google_Service_Genomics_Callset");
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}
|
|
/**
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|
* Deletes a callset. (callsets.delete)
|
|
*
|
|
* @param string $callsetId
|
|
* The ID of the callset to be deleted.
|
|
* @param array $optParams Optional parameters.
|
|
*/
|
|
public function delete($callsetId, $optParams = array())
|
|
{
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$params = array('callsetId' => $callsetId);
|
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$params = array_merge($params, $optParams);
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return $this->call('delete', array($params));
|
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}
|
|
/**
|
|
* Gets a callset by ID. (callsets.get)
|
|
*
|
|
* @param string $callsetId
|
|
* The ID of the callset.
|
|
* @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 callset. This method supports patch semantics. (callsets.patch)
|
|
*
|
|
* @param string $callsetId
|
|
* The ID of the callset 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 callsets matching the criteria. (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 callset. (callsets.update)
|
|
*
|
|
* @param string $callsetId
|
|
* The ID of the callset 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 $optParams Optional parameters.
|
|
*
|
|
* @opt_param string pageToken
|
|
* The continuation token, which is used to page through large result sets. To get the next page of
|
|
* results, set this parameter to the value of "nextPageToken" from the previous response.
|
|
* @opt_param string maxResults
|
|
* The maximum number of results returned by this request.
|
|
* @opt_param string projectId
|
|
* Only return datasets which belong to this Google Developers Console project. Only accepts
|
|
* project numbers.
|
|
* @return Google_Service_Genomics_ListDatasetsResponse
|
|
*/
|
|
public function listDatasets($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 "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 readsets. Reads search operates over a
|
|
* genomic coordinate space of reference sequence & position defined over the
|
|
* reference sequences to which the requested readsets 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 readset
|
|
* IDs yields all reads in those readsets, 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. (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 "readsets" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $readsets = $genomicsService->readsets;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_Readsets_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Deletes a readset. (readsets.delete)
|
|
*
|
|
* @param string $readsetId
|
|
* The ID of the readset to be deleted. The caller must have WRITE permissions to the dataset
|
|
* associated with this readset.
|
|
* @param array $optParams Optional parameters.
|
|
*/
|
|
public function delete($readsetId, $optParams = array())
|
|
{
|
|
$params = array('readsetId' => $readsetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('delete', array($params));
|
|
}
|
|
/**
|
|
* Exports readsets 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.
|
|
* (readsets.export)
|
|
*
|
|
* @param Google_ExportReadsetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ExportReadsetsResponse
|
|
*/
|
|
public function export(Google_Service_Genomics_ExportReadsetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('export', array($params), "Google_Service_Genomics_ExportReadsetsResponse");
|
|
}
|
|
/**
|
|
* Gets a readset by ID. (readsets.get)
|
|
*
|
|
* @param string $readsetId
|
|
* The ID of the readset.
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Readset
|
|
*/
|
|
public function get($readsetId, $optParams = array())
|
|
{
|
|
$params = array('readsetId' => $readsetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('get', array($params), "Google_Service_Genomics_Readset");
|
|
}
|
|
/**
|
|
* Creates readsets 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. (readsets.import)
|
|
*
|
|
* @param Google_ImportReadsetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ImportReadsetsResponse
|
|
*/
|
|
public function import(Google_Service_Genomics_ImportReadsetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('import', array($params), "Google_Service_Genomics_ImportReadsetsResponse");
|
|
}
|
|
/**
|
|
* Updates a readset. This method supports patch semantics. (readsets.patch)
|
|
*
|
|
* @param string $readsetId
|
|
* The ID of the readset to be updated. The caller must have WRITE permissions to the dataset
|
|
* associated with this readset.
|
|
* @param Google_Readset $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Readset
|
|
*/
|
|
public function patch($readsetId, Google_Service_Genomics_Readset $postBody, $optParams = array())
|
|
{
|
|
$params = array('readsetId' => $readsetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('patch', array($params), "Google_Service_Genomics_Readset");
|
|
}
|
|
/**
|
|
* Gets a list of readsets matching the criteria. (readsets.search)
|
|
*
|
|
* @param Google_SearchReadsetsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_SearchReadsetsResponse
|
|
*/
|
|
public function search(Google_Service_Genomics_SearchReadsetsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('search', array($params), "Google_Service_Genomics_SearchReadsetsResponse");
|
|
}
|
|
/**
|
|
* Updates a readset. (readsets.update)
|
|
*
|
|
* @param string $readsetId
|
|
* The ID of the readset to be updated. The caller must have WRITE permissions to the dataset
|
|
* associated with this readset.
|
|
* @param Google_Readset $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Readset
|
|
*/
|
|
public function update($readsetId, Google_Service_Genomics_Readset $postBody, $optParams = array())
|
|
{
|
|
$params = array('readsetId' => $readsetId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('update', array($params), "Google_Service_Genomics_Readset");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* The "coveragebuckets" collection of methods.
|
|
* Typical usage is:
|
|
* <code>
|
|
* $genomicsService = new Google_Service_Genomics(...);
|
|
* $coveragebuckets = $genomicsService->coveragebuckets;
|
|
* </code>
|
|
*/
|
|
class Google_Service_Genomics_ReadsetsCoveragebuckets_Resource extends Google_Service_Resource
|
|
{
|
|
|
|
/**
|
|
* Lists fixed width coverage buckets for a readset, 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 various bucket widths, enabling various coverage
|
|
* "zoom levels". The caller must have READ permissions for the target readset.
|
|
* (coveragebuckets.listReadsetsCoveragebuckets)
|
|
*
|
|
* @param string $readsetId
|
|
* Required. The ID of the readset over which coverage is requested.
|
|
* @param array $optParams Optional parameters.
|
|
*
|
|
* @opt_param string range.sequenceStart
|
|
* The start position of the range on the reference, 1-based inclusive. If specified, sequenceName
|
|
* must also be specified.
|
|
* @opt_param string maxResults
|
|
* The maximum number of results to return in a single page. If unspecified, defaults to 1024. The
|
|
* maximum value is 2048.
|
|
* @opt_param string range.sequenceName
|
|
* The reference sequence name, for example "chr1", "1", or "chrX".
|
|
* @opt_param string pageToken
|
|
* The continuation token, which is used to page through large result sets. To get the next page of
|
|
* results, set this parameter to the value of "nextPageToken" from the previous response.
|
|
* @opt_param string targetBucketWidth
|
|
* The desired width of each reported coverage bucket in base pairs. This will be rounded down to
|
|
* the nearest precomputed bucket width; the value of which is returned as bucket_width in the
|
|
* response. Defaults to infinity (each bucket spans an entire reference sequence) or the length of
|
|
* the target range, if specified. The smallest precomputed bucket_width is currently 2048 base
|
|
* pairs; this is subject to change.
|
|
* @opt_param string range.sequenceEnd
|
|
* The end position of the range on the reference, 1-based exclusive. If specified, sequenceName
|
|
* must also be specified.
|
|
* @return Google_Service_Genomics_ListCoverageBucketsResponse
|
|
*/
|
|
public function listReadsetsCoveragebuckets($readsetId, $optParams = array())
|
|
{
|
|
$params = array('readsetId' => $readsetId);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('list', array($params), "Google_Service_Genomics_ListCoverageBucketsResponse");
|
|
}
|
|
}
|
|
|
|
/**
|
|
* 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));
|
|
}
|
|
/**
|
|
* Exports variant data to an external destination. (variants.export)
|
|
*
|
|
* @param Google_ExportVariantsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ExportVariantsResponse
|
|
*/
|
|
public function export(Google_Service_Genomics_ExportVariantsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('export', array($params), "Google_Service_Genomics_ExportVariantsResponse");
|
|
}
|
|
/**
|
|
* 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 summary of all the variant data in a dataset. (variants.getSummary)
|
|
*
|
|
* @param array $optParams Optional parameters.
|
|
*
|
|
* @opt_param string datasetId
|
|
* Required. The ID of the dataset to get variant summary information for.
|
|
* @return Google_Service_Genomics_GetVariantsSummaryResponse
|
|
*/
|
|
public function getSummary($optParams = array())
|
|
{
|
|
$params = array();
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('getSummary', array($params), "Google_Service_Genomics_GetVariantsSummaryResponse");
|
|
}
|
|
/**
|
|
* Creates variant data by asynchronously importing the provided information.
|
|
* (variants.import)
|
|
*
|
|
* @param Google_ImportVariantsRequest $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_ImportVariantsResponse
|
|
*/
|
|
public function import(Google_Service_Genomics_ImportVariantsRequest $postBody, $optParams = array())
|
|
{
|
|
$params = array('postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('import', array($params), "Google_Service_Genomics_ImportVariantsResponse");
|
|
}
|
|
/**
|
|
* Updates a variant. This method supports patch semantics. (variants.patch)
|
|
*
|
|
* @param string $variantId
|
|
* The ID of the variant to be updated..
|
|
* @param Google_Variant $postBody
|
|
* @param array $optParams Optional parameters.
|
|
* @return Google_Service_Genomics_Variant
|
|
*/
|
|
public function patch($variantId, Google_Service_Genomics_Variant $postBody, $optParams = array())
|
|
{
|
|
$params = array('variantId' => $variantId, 'postBody' => $postBody);
|
|
$params = array_merge($params, $optParams);
|
|
return $this->call('patch', array($params), "Google_Service_Genomics_Variant");
|
|
}
|
|
/**
|
|
* Gets a list of variants matching the criteria. (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. (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");
|
|
}
|
|
}
|
|
|
|
|
|
|
|
|
|
class Google_Service_Genomics_Beacon extends Google_Model
|
|
{
|
|
public $exists;
|
|
|
|
public function setExists($exists)
|
|
{
|
|
$this->exists = $exists;
|
|
}
|
|
|
|
public function getExists()
|
|
{
|
|
return $this->exists;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Call extends Google_Collection
|
|
{
|
|
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
|
|
{
|
|
|
|
}
|
|
|
|
class Google_Service_Genomics_Callset extends Google_Model
|
|
{
|
|
public $created;
|
|
public $datasetId;
|
|
public $id;
|
|
public $info;
|
|
public $name;
|
|
|
|
public function setCreated($created)
|
|
{
|
|
$this->created = $created;
|
|
}
|
|
|
|
public function getCreated()
|
|
{
|
|
return $this->created;
|
|
}
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
|
|
public function setInfo($info)
|
|
{
|
|
$this->info = $info;
|
|
}
|
|
|
|
public function getInfo()
|
|
{
|
|
return $this->info;
|
|
}
|
|
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_CallsetInfo extends Google_Model
|
|
{
|
|
|
|
}
|
|
|
|
class Google_Service_Genomics_ContigBound extends Google_Model
|
|
{
|
|
public $contig;
|
|
public $upperBound;
|
|
|
|
public function setContig($contig)
|
|
{
|
|
$this->contig = $contig;
|
|
}
|
|
|
|
public function getContig()
|
|
{
|
|
return $this->contig;
|
|
}
|
|
|
|
public function setUpperBound($upperBound)
|
|
{
|
|
$this->upperBound = $upperBound;
|
|
}
|
|
|
|
public function getUpperBound()
|
|
{
|
|
return $this->upperBound;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_CoverageBucket extends Google_Model
|
|
{
|
|
public $meanCoverage;
|
|
protected $rangeType = 'Google_Service_Genomics_GenomicRange';
|
|
protected $rangeDataType = '';
|
|
|
|
public function setMeanCoverage($meanCoverage)
|
|
{
|
|
$this->meanCoverage = $meanCoverage;
|
|
}
|
|
|
|
public function getMeanCoverage()
|
|
{
|
|
return $this->meanCoverage;
|
|
}
|
|
|
|
public function setRange(Google_Service_Genomics_GenomicRange $range)
|
|
{
|
|
$this->range = $range;
|
|
}
|
|
|
|
public function getRange()
|
|
{
|
|
return $this->range;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Dataset extends Google_Model
|
|
{
|
|
public $id;
|
|
public $isPublic;
|
|
public $name;
|
|
public $projectId;
|
|
|
|
public function setId($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 $this->name;
|
|
}
|
|
|
|
public function setProjectId($projectId)
|
|
{
|
|
$this->projectId = $projectId;
|
|
}
|
|
|
|
public function getProjectId()
|
|
{
|
|
return $this->projectId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExperimentalCreateJobRequest extends Google_Collection
|
|
{
|
|
public $align;
|
|
public $callVariants;
|
|
public $gcsOutputPath;
|
|
public $pairedSourceUris;
|
|
public $projectId;
|
|
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 $this->pairedSourceUris;
|
|
}
|
|
|
|
public function setProjectId($projectId)
|
|
{
|
|
$this->projectId = $projectId;
|
|
}
|
|
|
|
public function getProjectId()
|
|
{
|
|
return $this->projectId;
|
|
}
|
|
|
|
public function setSourceUris($sourceUris)
|
|
{
|
|
$this->sourceUris = $sourceUris;
|
|
}
|
|
|
|
public function getSourceUris()
|
|
{
|
|
return $this->sourceUris;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExperimentalCreateJobResponse extends Google_Model
|
|
{
|
|
public $jobId;
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExportReadsetsRequest extends Google_Collection
|
|
{
|
|
public $exportUri;
|
|
public $projectId;
|
|
public $readsetIds;
|
|
|
|
public function setExportUri($exportUri)
|
|
{
|
|
$this->exportUri = $exportUri;
|
|
}
|
|
|
|
public function getExportUri()
|
|
{
|
|
return $this->exportUri;
|
|
}
|
|
|
|
public function setProjectId($projectId)
|
|
{
|
|
$this->projectId = $projectId;
|
|
}
|
|
|
|
public function getProjectId()
|
|
{
|
|
return $this->projectId;
|
|
}
|
|
|
|
public function setReadsetIds($readsetIds)
|
|
{
|
|
$this->readsetIds = $readsetIds;
|
|
}
|
|
|
|
public function getReadsetIds()
|
|
{
|
|
return $this->readsetIds;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExportReadsetsResponse extends Google_Model
|
|
{
|
|
public $jobId;
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExportVariantsRequest extends Google_Collection
|
|
{
|
|
public $bigqueryDataset;
|
|
public $bigqueryTable;
|
|
public $callsetIds;
|
|
public $datasetId;
|
|
public $format;
|
|
public $projectId;
|
|
|
|
public function setBigqueryDataset($bigqueryDataset)
|
|
{
|
|
$this->bigqueryDataset = $bigqueryDataset;
|
|
}
|
|
|
|
public function getBigqueryDataset()
|
|
{
|
|
return $this->bigqueryDataset;
|
|
}
|
|
|
|
public function setBigqueryTable($bigqueryTable)
|
|
{
|
|
$this->bigqueryTable = $bigqueryTable;
|
|
}
|
|
|
|
public function getBigqueryTable()
|
|
{
|
|
return $this->bigqueryTable;
|
|
}
|
|
|
|
public function setCallsetIds($callsetIds)
|
|
{
|
|
$this->callsetIds = $callsetIds;
|
|
}
|
|
|
|
public function getCallsetIds()
|
|
{
|
|
return $this->callsetIds;
|
|
}
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
|
|
public function setFormat($format)
|
|
{
|
|
$this->format = $format;
|
|
}
|
|
|
|
public function getFormat()
|
|
{
|
|
return $this->format;
|
|
}
|
|
|
|
public function setProjectId($projectId)
|
|
{
|
|
$this->projectId = $projectId;
|
|
}
|
|
|
|
public function getProjectId()
|
|
{
|
|
return $this->projectId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ExportVariantsResponse extends Google_Model
|
|
{
|
|
public $jobId;
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_GenomicRange extends Google_Model
|
|
{
|
|
public $sequenceEnd;
|
|
public $sequenceName;
|
|
public $sequenceStart;
|
|
|
|
public function setSequenceEnd($sequenceEnd)
|
|
{
|
|
$this->sequenceEnd = $sequenceEnd;
|
|
}
|
|
|
|
public function getSequenceEnd()
|
|
{
|
|
return $this->sequenceEnd;
|
|
}
|
|
|
|
public function setSequenceName($sequenceName)
|
|
{
|
|
$this->sequenceName = $sequenceName;
|
|
}
|
|
|
|
public function getSequenceName()
|
|
{
|
|
return $this->sequenceName;
|
|
}
|
|
|
|
public function setSequenceStart($sequenceStart)
|
|
{
|
|
$this->sequenceStart = $sequenceStart;
|
|
}
|
|
|
|
public function getSequenceStart()
|
|
{
|
|
return $this->sequenceStart;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_GetVariantsSummaryResponse extends Google_Collection
|
|
{
|
|
protected $contigBoundsType = 'Google_Service_Genomics_ContigBound';
|
|
protected $contigBoundsDataType = 'array';
|
|
protected $metadataType = 'Google_Service_Genomics_Metadata';
|
|
protected $metadataDataType = 'array';
|
|
|
|
public function setContigBounds($contigBounds)
|
|
{
|
|
$this->contigBounds = $contigBounds;
|
|
}
|
|
|
|
public function getContigBounds()
|
|
{
|
|
return $this->contigBounds;
|
|
}
|
|
|
|
public function setMetadata($metadata)
|
|
{
|
|
$this->metadata = $metadata;
|
|
}
|
|
|
|
public function getMetadata()
|
|
{
|
|
return $this->metadata;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Header extends Google_Model
|
|
{
|
|
public $sortingOrder;
|
|
public $version;
|
|
|
|
public function setSortingOrder($sortingOrder)
|
|
{
|
|
$this->sortingOrder = $sortingOrder;
|
|
}
|
|
|
|
public function getSortingOrder()
|
|
{
|
|
return $this->sortingOrder;
|
|
}
|
|
|
|
public function setVersion($version)
|
|
{
|
|
$this->version = $version;
|
|
}
|
|
|
|
public function getVersion()
|
|
{
|
|
return $this->version;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_HeaderSection extends Google_Collection
|
|
{
|
|
public $comments;
|
|
public $fileUri;
|
|
public $filename;
|
|
protected $headersType = 'Google_Service_Genomics_Header';
|
|
protected $headersDataType = 'array';
|
|
protected $programsType = 'Google_Service_Genomics_Program';
|
|
protected $programsDataType = 'array';
|
|
protected $readGroupsType = 'Google_Service_Genomics_ReadGroup';
|
|
protected $readGroupsDataType = 'array';
|
|
protected $refSequencesType = 'Google_Service_Genomics_ReferenceSequence';
|
|
protected $refSequencesDataType = 'array';
|
|
|
|
public function setComments($comments)
|
|
{
|
|
$this->comments = $comments;
|
|
}
|
|
|
|
public function getComments()
|
|
{
|
|
return $this->comments;
|
|
}
|
|
|
|
public function setFileUri($fileUri)
|
|
{
|
|
$this->fileUri = $fileUri;
|
|
}
|
|
|
|
public function getFileUri()
|
|
{
|
|
return $this->fileUri;
|
|
}
|
|
|
|
public function setFilename($filename)
|
|
{
|
|
$this->filename = $filename;
|
|
}
|
|
|
|
public function getFilename()
|
|
{
|
|
return $this->filename;
|
|
}
|
|
|
|
public function setHeaders($headers)
|
|
{
|
|
$this->headers = $headers;
|
|
}
|
|
|
|
public function getHeaders()
|
|
{
|
|
return $this->headers;
|
|
}
|
|
|
|
public function setPrograms($programs)
|
|
{
|
|
$this->programs = $programs;
|
|
}
|
|
|
|
public function getPrograms()
|
|
{
|
|
return $this->programs;
|
|
}
|
|
|
|
public function setReadGroups($readGroups)
|
|
{
|
|
$this->readGroups = $readGroups;
|
|
}
|
|
|
|
public function getReadGroups()
|
|
{
|
|
return $this->readGroups;
|
|
}
|
|
|
|
public function setRefSequences($refSequences)
|
|
{
|
|
$this->refSequences = $refSequences;
|
|
}
|
|
|
|
public function getRefSequences()
|
|
{
|
|
return $this->refSequences;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ImportReadsetsRequest extends Google_Collection
|
|
{
|
|
public $datasetId;
|
|
public $sourceUris;
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
|
|
public function setSourceUris($sourceUris)
|
|
{
|
|
$this->sourceUris = $sourceUris;
|
|
}
|
|
|
|
public function getSourceUris()
|
|
{
|
|
return $this->sourceUris;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ImportReadsetsResponse extends Google_Model
|
|
{
|
|
public $jobId;
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ImportVariantsRequest extends Google_Collection
|
|
{
|
|
public $datasetId;
|
|
public $sourceUris;
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
|
|
public function setSourceUris($sourceUris)
|
|
{
|
|
$this->sourceUris = $sourceUris;
|
|
}
|
|
|
|
public function getSourceUris()
|
|
{
|
|
return $this->sourceUris;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ImportVariantsResponse extends Google_Model
|
|
{
|
|
public $jobId;
|
|
|
|
public function setJobId($jobId)
|
|
{
|
|
$this->jobId = $jobId;
|
|
}
|
|
|
|
public function getJobId()
|
|
{
|
|
return $this->jobId;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_Job extends Google_Collection
|
|
{
|
|
public $created;
|
|
public $description;
|
|
public $errors;
|
|
public $id;
|
|
public $importedIds;
|
|
public $projectId;
|
|
public $status;
|
|
public $warnings;
|
|
|
|
public function setCreated($created)
|
|
{
|
|
$this->created = $created;
|
|
}
|
|
|
|
public function getCreated()
|
|
{
|
|
return $this->created;
|
|
}
|
|
|
|
public function setDescription($description)
|
|
{
|
|
$this->description = $description;
|
|
}
|
|
|
|
public function getDescription()
|
|
{
|
|
return $this->description;
|
|
}
|
|
|
|
public function setErrors($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 $this->importedIds;
|
|
}
|
|
|
|
public function setProjectId($projectId)
|
|
{
|
|
$this->projectId = $projectId;
|
|
}
|
|
|
|
public function getProjectId()
|
|
{
|
|
return $this->projectId;
|
|
}
|
|
|
|
public function setStatus($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_ListCoverageBucketsResponse extends Google_Collection
|
|
{
|
|
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 $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_Metadata extends Google_Model
|
|
{
|
|
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
|
|
{
|
|
|
|
}
|
|
|
|
class Google_Service_Genomics_Program extends Google_Model
|
|
{
|
|
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_Read extends Google_Model
|
|
{
|
|
public $alignedBases;
|
|
public $baseQuality;
|
|
public $cigar;
|
|
public $flags;
|
|
public $id;
|
|
public $mappingQuality;
|
|
public $matePosition;
|
|
public $mateReferenceSequenceName;
|
|
public $name;
|
|
public $originalBases;
|
|
public $position;
|
|
public $readsetId;
|
|
public $referenceSequenceName;
|
|
public $tags;
|
|
public $templateLength;
|
|
|
|
public function setAlignedBases($alignedBases)
|
|
{
|
|
$this->alignedBases = $alignedBases;
|
|
}
|
|
|
|
public function getAlignedBases()
|
|
{
|
|
return $this->alignedBases;
|
|
}
|
|
|
|
public function setBaseQuality($baseQuality)
|
|
{
|
|
$this->baseQuality = $baseQuality;
|
|
}
|
|
|
|
public function getBaseQuality()
|
|
{
|
|
return $this->baseQuality;
|
|
}
|
|
|
|
public function setCigar($cigar)
|
|
{
|
|
$this->cigar = $cigar;
|
|
}
|
|
|
|
public function getCigar()
|
|
{
|
|
return $this->cigar;
|
|
}
|
|
|
|
public function setFlags($flags)
|
|
{
|
|
$this->flags = $flags;
|
|
}
|
|
|
|
public function getFlags()
|
|
{
|
|
return $this->flags;
|
|
}
|
|
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
|
|
public function setMappingQuality($mappingQuality)
|
|
{
|
|
$this->mappingQuality = $mappingQuality;
|
|
}
|
|
|
|
public function getMappingQuality()
|
|
{
|
|
return $this->mappingQuality;
|
|
}
|
|
|
|
public function setMatePosition($matePosition)
|
|
{
|
|
$this->matePosition = $matePosition;
|
|
}
|
|
|
|
public function getMatePosition()
|
|
{
|
|
return $this->matePosition;
|
|
}
|
|
|
|
public function setMateReferenceSequenceName($mateReferenceSequenceName)
|
|
{
|
|
$this->mateReferenceSequenceName = $mateReferenceSequenceName;
|
|
}
|
|
|
|
public function getMateReferenceSequenceName()
|
|
{
|
|
return $this->mateReferenceSequenceName;
|
|
}
|
|
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
|
|
public function setOriginalBases($originalBases)
|
|
{
|
|
$this->originalBases = $originalBases;
|
|
}
|
|
|
|
public function getOriginalBases()
|
|
{
|
|
return $this->originalBases;
|
|
}
|
|
|
|
public function setPosition($position)
|
|
{
|
|
$this->position = $position;
|
|
}
|
|
|
|
public function getPosition()
|
|
{
|
|
return $this->position;
|
|
}
|
|
|
|
public function setReadsetId($readsetId)
|
|
{
|
|
$this->readsetId = $readsetId;
|
|
}
|
|
|
|
public function getReadsetId()
|
|
{
|
|
return $this->readsetId;
|
|
}
|
|
|
|
public function setReferenceSequenceName($referenceSequenceName)
|
|
{
|
|
$this->referenceSequenceName = $referenceSequenceName;
|
|
}
|
|
|
|
public function getReferenceSequenceName()
|
|
{
|
|
return $this->referenceSequenceName;
|
|
}
|
|
|
|
public function setTags($tags)
|
|
{
|
|
$this->tags = $tags;
|
|
}
|
|
|
|
public function getTags()
|
|
{
|
|
return $this->tags;
|
|
}
|
|
|
|
public function setTemplateLength($templateLength)
|
|
{
|
|
$this->templateLength = $templateLength;
|
|
}
|
|
|
|
public function getTemplateLength()
|
|
{
|
|
return $this->templateLength;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ReadGroup extends Google_Model
|
|
{
|
|
public $date;
|
|
public $description;
|
|
public $flowOrder;
|
|
public $id;
|
|
public $keySequence;
|
|
public $library;
|
|
public $platformUnit;
|
|
public $predictedInsertSize;
|
|
public $processingProgram;
|
|
public $sample;
|
|
public $sequencingCenterName;
|
|
public $sequencingTechnology;
|
|
|
|
public function setDate($date)
|
|
{
|
|
$this->date = $date;
|
|
}
|
|
|
|
public function getDate()
|
|
{
|
|
return $this->date;
|
|
}
|
|
|
|
public function setDescription($description)
|
|
{
|
|
$this->description = $description;
|
|
}
|
|
|
|
public function getDescription()
|
|
{
|
|
return $this->description;
|
|
}
|
|
|
|
public function setFlowOrder($flowOrder)
|
|
{
|
|
$this->flowOrder = $flowOrder;
|
|
}
|
|
|
|
public function getFlowOrder()
|
|
{
|
|
return $this->flowOrder;
|
|
}
|
|
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
|
|
public function setKeySequence($keySequence)
|
|
{
|
|
$this->keySequence = $keySequence;
|
|
}
|
|
|
|
public function getKeySequence()
|
|
{
|
|
return $this->keySequence;
|
|
}
|
|
|
|
public function setLibrary($library)
|
|
{
|
|
$this->library = $library;
|
|
}
|
|
|
|
public function getLibrary()
|
|
{
|
|
return $this->library;
|
|
}
|
|
|
|
public function setPlatformUnit($platformUnit)
|
|
{
|
|
$this->platformUnit = $platformUnit;
|
|
}
|
|
|
|
public function getPlatformUnit()
|
|
{
|
|
return $this->platformUnit;
|
|
}
|
|
|
|
public function setPredictedInsertSize($predictedInsertSize)
|
|
{
|
|
$this->predictedInsertSize = $predictedInsertSize;
|
|
}
|
|
|
|
public function getPredictedInsertSize()
|
|
{
|
|
return $this->predictedInsertSize;
|
|
}
|
|
|
|
public function setProcessingProgram($processingProgram)
|
|
{
|
|
$this->processingProgram = $processingProgram;
|
|
}
|
|
|
|
public function getProcessingProgram()
|
|
{
|
|
return $this->processingProgram;
|
|
}
|
|
|
|
public function setSample($sample)
|
|
{
|
|
$this->sample = $sample;
|
|
}
|
|
|
|
public function getSample()
|
|
{
|
|
return $this->sample;
|
|
}
|
|
|
|
public function setSequencingCenterName($sequencingCenterName)
|
|
{
|
|
$this->sequencingCenterName = $sequencingCenterName;
|
|
}
|
|
|
|
public function getSequencingCenterName()
|
|
{
|
|
return $this->sequencingCenterName;
|
|
}
|
|
|
|
public function setSequencingTechnology($sequencingTechnology)
|
|
{
|
|
$this->sequencingTechnology = $sequencingTechnology;
|
|
}
|
|
|
|
public function getSequencingTechnology()
|
|
{
|
|
return $this->sequencingTechnology;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ReadTags extends Google_Model
|
|
{
|
|
|
|
}
|
|
|
|
class Google_Service_Genomics_Readset extends Google_Collection
|
|
{
|
|
public $datasetId;
|
|
protected $fileDataType = 'Google_Service_Genomics_HeaderSection';
|
|
protected $fileDataDataType = 'array';
|
|
public $id;
|
|
public $name;
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
|
|
public function setFileData($fileData)
|
|
{
|
|
$this->fileData = $fileData;
|
|
}
|
|
|
|
public function getFileData()
|
|
{
|
|
return $this->fileData;
|
|
}
|
|
|
|
public function setId($id)
|
|
{
|
|
$this->id = $id;
|
|
}
|
|
|
|
public function getId()
|
|
{
|
|
return $this->id;
|
|
}
|
|
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_ReferenceSequence extends Google_Model
|
|
{
|
|
public $assemblyId;
|
|
public $length;
|
|
public $md5Checksum;
|
|
public $name;
|
|
public $species;
|
|
public $uri;
|
|
|
|
public function setAssemblyId($assemblyId)
|
|
{
|
|
$this->assemblyId = $assemblyId;
|
|
}
|
|
|
|
public function getAssemblyId()
|
|
{
|
|
return $this->assemblyId;
|
|
}
|
|
|
|
public function setLength($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 $this->name;
|
|
}
|
|
|
|
public function setSpecies($species)
|
|
{
|
|
$this->species = $species;
|
|
}
|
|
|
|
public function getSpecies()
|
|
{
|
|
return $this->species;
|
|
}
|
|
|
|
public function setUri($uri)
|
|
{
|
|
$this->uri = $uri;
|
|
}
|
|
|
|
public function getUri()
|
|
{
|
|
return $this->uri;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchCallsetsRequest extends Google_Collection
|
|
{
|
|
public $datasetIds;
|
|
public $maxResults;
|
|
public $name;
|
|
public $pageToken;
|
|
|
|
public function setDatasetIds($datasetIds)
|
|
{
|
|
$this->datasetIds = $datasetIds;
|
|
}
|
|
|
|
public function getDatasetIds()
|
|
{
|
|
return $this->datasetIds;
|
|
}
|
|
|
|
public function setMaxResults($maxResults)
|
|
{
|
|
$this->maxResults = $maxResults;
|
|
}
|
|
|
|
public function getMaxResults()
|
|
{
|
|
return $this->maxResults;
|
|
}
|
|
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchCallsetsResponse extends Google_Collection
|
|
{
|
|
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
|
|
{
|
|
public $createdAfter;
|
|
public $createdBefore;
|
|
public $maxResults;
|
|
public $pageToken;
|
|
public $projectId;
|
|
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 $this->createdBefore;
|
|
}
|
|
|
|
public function setMaxResults($maxResults)
|
|
{
|
|
$this->maxResults = $maxResults;
|
|
}
|
|
|
|
public function getMaxResults()
|
|
{
|
|
return $this->maxResults;
|
|
}
|
|
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
|
|
public function setProjectId($projectId)
|
|
{
|
|
$this->projectId = $projectId;
|
|
}
|
|
|
|
public function getProjectId()
|
|
{
|
|
return $this->projectId;
|
|
}
|
|
|
|
public function setStatus($status)
|
|
{
|
|
$this->status = $status;
|
|
}
|
|
|
|
public function getStatus()
|
|
{
|
|
return $this->status;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchJobsResponse extends Google_Collection
|
|
{
|
|
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_SearchReadsRequest extends Google_Collection
|
|
{
|
|
public $maxResults;
|
|
public $pageToken;
|
|
public $readsetIds;
|
|
public $sequenceEnd;
|
|
public $sequenceName;
|
|
public $sequenceStart;
|
|
|
|
public function setMaxResults($maxResults)
|
|
{
|
|
$this->maxResults = $maxResults;
|
|
}
|
|
|
|
public function getMaxResults()
|
|
{
|
|
return $this->maxResults;
|
|
}
|
|
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
|
|
public function setReadsetIds($readsetIds)
|
|
{
|
|
$this->readsetIds = $readsetIds;
|
|
}
|
|
|
|
public function getReadsetIds()
|
|
{
|
|
return $this->readsetIds;
|
|
}
|
|
|
|
public function setSequenceEnd($sequenceEnd)
|
|
{
|
|
$this->sequenceEnd = $sequenceEnd;
|
|
}
|
|
|
|
public function getSequenceEnd()
|
|
{
|
|
return $this->sequenceEnd;
|
|
}
|
|
|
|
public function setSequenceName($sequenceName)
|
|
{
|
|
$this->sequenceName = $sequenceName;
|
|
}
|
|
|
|
public function getSequenceName()
|
|
{
|
|
return $this->sequenceName;
|
|
}
|
|
|
|
public function setSequenceStart($sequenceStart)
|
|
{
|
|
$this->sequenceStart = $sequenceStart;
|
|
}
|
|
|
|
public function getSequenceStart()
|
|
{
|
|
return $this->sequenceStart;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchReadsResponse extends Google_Collection
|
|
{
|
|
public $nextPageToken;
|
|
protected $readsType = 'Google_Service_Genomics_Read';
|
|
protected $readsDataType = 'array';
|
|
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
|
|
public function setReads($reads)
|
|
{
|
|
$this->reads = $reads;
|
|
}
|
|
|
|
public function getReads()
|
|
{
|
|
return $this->reads;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchReadsetsRequest extends Google_Collection
|
|
{
|
|
public $datasetIds;
|
|
public $maxResults;
|
|
public $name;
|
|
public $pageToken;
|
|
|
|
public function setDatasetIds($datasetIds)
|
|
{
|
|
$this->datasetIds = $datasetIds;
|
|
}
|
|
|
|
public function getDatasetIds()
|
|
{
|
|
return $this->datasetIds;
|
|
}
|
|
|
|
public function setMaxResults($maxResults)
|
|
{
|
|
$this->maxResults = $maxResults;
|
|
}
|
|
|
|
public function getMaxResults()
|
|
{
|
|
return $this->maxResults;
|
|
}
|
|
|
|
public function setName($name)
|
|
{
|
|
$this->name = $name;
|
|
}
|
|
|
|
public function getName()
|
|
{
|
|
return $this->name;
|
|
}
|
|
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchReadsetsResponse extends Google_Collection
|
|
{
|
|
public $nextPageToken;
|
|
protected $readsetsType = 'Google_Service_Genomics_Readset';
|
|
protected $readsetsDataType = 'array';
|
|
|
|
public function setNextPageToken($nextPageToken)
|
|
{
|
|
$this->nextPageToken = $nextPageToken;
|
|
}
|
|
|
|
public function getNextPageToken()
|
|
{
|
|
return $this->nextPageToken;
|
|
}
|
|
|
|
public function setReadsets($readsets)
|
|
{
|
|
$this->readsets = $readsets;
|
|
}
|
|
|
|
public function getReadsets()
|
|
{
|
|
return $this->readsets;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchVariantsRequest extends Google_Collection
|
|
{
|
|
public $callsetIds;
|
|
public $callsetNames;
|
|
public $contig;
|
|
public $datasetId;
|
|
public $endPosition;
|
|
public $maxResults;
|
|
public $pageToken;
|
|
public $startPosition;
|
|
public $variantName;
|
|
|
|
public function setCallsetIds($callsetIds)
|
|
{
|
|
$this->callsetIds = $callsetIds;
|
|
}
|
|
|
|
public function getCallsetIds()
|
|
{
|
|
return $this->callsetIds;
|
|
}
|
|
|
|
public function setCallsetNames($callsetNames)
|
|
{
|
|
$this->callsetNames = $callsetNames;
|
|
}
|
|
|
|
public function getCallsetNames()
|
|
{
|
|
return $this->callsetNames;
|
|
}
|
|
|
|
public function setContig($contig)
|
|
{
|
|
$this->contig = $contig;
|
|
}
|
|
|
|
public function getContig()
|
|
{
|
|
return $this->contig;
|
|
}
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
|
|
public function setEndPosition($endPosition)
|
|
{
|
|
$this->endPosition = $endPosition;
|
|
}
|
|
|
|
public function getEndPosition()
|
|
{
|
|
return $this->endPosition;
|
|
}
|
|
|
|
public function setMaxResults($maxResults)
|
|
{
|
|
$this->maxResults = $maxResults;
|
|
}
|
|
|
|
public function getMaxResults()
|
|
{
|
|
return $this->maxResults;
|
|
}
|
|
|
|
public function setPageToken($pageToken)
|
|
{
|
|
$this->pageToken = $pageToken;
|
|
}
|
|
|
|
public function getPageToken()
|
|
{
|
|
return $this->pageToken;
|
|
}
|
|
|
|
public function setStartPosition($startPosition)
|
|
{
|
|
$this->startPosition = $startPosition;
|
|
}
|
|
|
|
public function getStartPosition()
|
|
{
|
|
return $this->startPosition;
|
|
}
|
|
|
|
public function setVariantName($variantName)
|
|
{
|
|
$this->variantName = $variantName;
|
|
}
|
|
|
|
public function getVariantName()
|
|
{
|
|
return $this->variantName;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_SearchVariantsResponse extends Google_Collection
|
|
{
|
|
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
|
|
{
|
|
public $alternateBases;
|
|
protected $callsType = 'Google_Service_Genomics_Call';
|
|
protected $callsDataType = 'array';
|
|
public $contig;
|
|
public $created;
|
|
public $datasetId;
|
|
public $end;
|
|
public $id;
|
|
public $info;
|
|
public $names;
|
|
public $position;
|
|
public $referenceBases;
|
|
|
|
public function setAlternateBases($alternateBases)
|
|
{
|
|
$this->alternateBases = $alternateBases;
|
|
}
|
|
|
|
public function getAlternateBases()
|
|
{
|
|
return $this->alternateBases;
|
|
}
|
|
|
|
public function setCalls($calls)
|
|
{
|
|
$this->calls = $calls;
|
|
}
|
|
|
|
public function getCalls()
|
|
{
|
|
return $this->calls;
|
|
}
|
|
|
|
public function setContig($contig)
|
|
{
|
|
$this->contig = $contig;
|
|
}
|
|
|
|
public function getContig()
|
|
{
|
|
return $this->contig;
|
|
}
|
|
|
|
public function setCreated($created)
|
|
{
|
|
$this->created = $created;
|
|
}
|
|
|
|
public function getCreated()
|
|
{
|
|
return $this->created;
|
|
}
|
|
|
|
public function setDatasetId($datasetId)
|
|
{
|
|
$this->datasetId = $datasetId;
|
|
}
|
|
|
|
public function getDatasetId()
|
|
{
|
|
return $this->datasetId;
|
|
}
|
|
|
|
public function setEnd($end)
|
|
{
|
|
$this->end = $end;
|
|
}
|
|
|
|
public function getEnd()
|
|
{
|
|
return $this->end;
|
|
}
|
|
|
|
public function setId($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 $this->names;
|
|
}
|
|
|
|
public function setPosition($position)
|
|
{
|
|
$this->position = $position;
|
|
}
|
|
|
|
public function getPosition()
|
|
{
|
|
return $this->position;
|
|
}
|
|
|
|
public function setReferenceBases($referenceBases)
|
|
{
|
|
$this->referenceBases = $referenceBases;
|
|
}
|
|
|
|
public function getReferenceBases()
|
|
{
|
|
return $this->referenceBases;
|
|
}
|
|
}
|
|
|
|
class Google_Service_Genomics_VariantInfo extends Google_Model
|
|
{
|
|
|
|
}
|