/*
* Copyright (c) 2007-2013 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.feature.tribble.reader;
import org.broad.igv.util.FileUtils;
import org.broad.igv.util.HttpUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.AbstractFeatureReader;
import java.io.IOException;
import java.net.URL;
public class IGVComponentMethods extends AbstractFeatureReader.ComponentMethods {
public boolean isTabix(String resourcePath, String tabxIndex) throws IOException {
ResourceLocator locator = new ResourceLocator(resourcePath);
if (tabxIndex == null) {
if (HttpUtils.isRemoteURL(locator.getPath())) {
final URL url = new URL(locator.getPath());
String path = url.getPath();
String indexPath = path + ".tbi"; // Strip off parameters
tabxIndex = locator.getPath().replace(path, indexPath);
} else {
tabxIndex = locator.getPath() + ".tbi";
}
}
boolean isTabix = (locator.getPath().endsWith(".gz") || locator.getPath().endsWith(".bgz")) && FileUtils.resourceExists(tabxIndex);
if(isTabix) {
locator.setIndexPath(tabxIndex);
}
return isTabix;
}
}