/*
 * Copyright (c) 2010, The Broad Institute 
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 * OTHER DEALINGS IN THE SOFTWARE.
 */

package org.broadinstitute.sting.gatk.walkers.coverage;

import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;

import java.util.Arrays;

public class CompareCallableLociWalkerIntegrationTest extends WalkerTest {
    final static String commonArgs = "-R " + hg18Reference + " -T CompareCallableLoci -B:comp1,Bed " + validationDataLocation + "1kg_slx.chr1_10mb.callable.bed -B:comp2,Bed " + validationDataLocation + "ga2_slx.chr1_10mb.callable.bed -o %s";

    @Test
    public void testCompareCallableLociWalker1() {
        String gatk_args = commonArgs + " -L chr1:1-10,000,000";
        WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList("70efebac55ff210bb022e9e22ed80a95"));
        executeTest("CompareCallableLoci Walker", spec);
    }
}
