/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.track;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.ui.AbstractHeadedTest;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/**
* @author Jim Robinson
* @date 10/3/11
*/
public class TrackLoaderTestHeaded extends AbstractHeadedTest {
TrackLoader trackLoader;
@Before
public void setUp() throws Exception {
super.setUp();
trackLoader = new TrackLoader();
}
@Test
public void testFilesHeaded() throws Exception {
String ex_filename = "/vcf/example4-last-gsnap-2_fixed.vcf";
Genome genome = TestUtils.loadGenome();
List<String> finames = new ArrayList<String>(Arrays.asList(TrackLoaderTest.filenamesTryIndex));
finames.add(ex_filename);
for (String finame : finames) {
TrackLoaderTest.tstLoadFi(trackLoader, TestUtils.DATA_DIR + finame, null, genome, true);
}
}
@Test
public void testReadVCF() throws Exception {
String file = TestUtils.DATA_DIR + "vcf/outputPileup.flt1.vcf";
TestUtils.createIndex(file);
ResourceLocator locator = new ResourceLocator(file);
//For files with 1 record, this threw a null pointer exception prior to r1595
List<Track> tracks = igv.load(locator);
Assert.assertEquals(1, tracks.size());
}
@Test
public void testLoadBAMFtpHeaded() throws Exception{
String path = "ftp://ftp.broadinstitute.org/pub/igv/TEST/HG00171.hg18.bam";
Integer expected_tracks = 2;
TrackLoaderTest.tstLoadFi(trackLoader, path, expected_tracks, genome, false);
}
}