/*
 * Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *      http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

/*
 * Copyright (C) 2003 EBI, GRL
 * 
 * This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
 * 
 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
 * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation,
 * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 */
package org.ensembl.healthcheck.testcase.variation;

import java.util.Map;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.generic.ComparePreviousVersionBase;

/**
 * Compare the number of reads per individual between the current database and the database on the secondary server.
 */

public class ComparePreviousVersionReadCoverage extends ComparePreviousVersionBase {

	/**
	 * Create a new testcase.
	 */
	public ComparePreviousVersionReadCoverage() {

		addToGroup("variation-release");
		setDescription("Compare the number of reads for each individual with read coverage in the current database with those from the equivalent database on the secondary server");
		setTeamResponsible(Team.VARIATION);

	}

	protected Map getCounts(DatabaseRegistryEntry dbre) {
		return getCountsBySQL(dbre, "SELECT i.name, COUNT(*) FROM read_coverage rc JOIN individual i ON (i.individual_id = rc.individual_id) GROUP BY i.name");

	}

	// ------------------------------------------------------------------------

	protected String entityDescription() {

		return "number of reads for individual";

	}

	// ------------------------------------------------------------------------

	protected double threshold() {

		return 1;

	}

        // ------------------------------------------------------------------------

        protected double minimum() {

                return 0;

        }

	// ------------------------------------------------------------------------

} 

Add health check for read coverage data