/*
 * The MIT License
 *
 * 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 net.sf.samtools.util;/*
 * The MIT License
 *
 * 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.
 */

import net.sf.picard.PicardException;

import java.io.File;
import java.io.IOException;

public class TestUtil {

    public static File getTempDirecory(final String prefix, final String suffix) {
        final File tempDirectory;
        try {
            tempDirectory = File.createTempFile(prefix, suffix);
        } catch (IOException e) {
            throw new PicardException("Failed to create temporary file.", e);
        }
        if (!tempDirectory.delete())
            throw new PicardException("Failed to delete file: " + tempDirectory);
        if (!tempDirectory.mkdir())
            throw new PicardException("Failed to make directory: " + tempDirectory);
        tempDirectory.deleteOnExit();
        return tempDirectory;
    }
    
    /**
     * Little test utility to help tests that create multiple levels of subdirectories
     * clean up after themselves.
     *
     * @param directory The directory to be deleted (along with its subdirectories)
     */
    public static void recursiveDelete(final File directory) {
        for (final File f : directory.listFiles()) {
            if (f.isDirectory()) {
                recursiveDelete(f);
            }
            f.delete();
        }
    }
}

@@ -1172,1182 +1172,36 @@
 til;
-/*%0A * The MIT License%0A *%0A * Copyright (c) 2010 The Broad Institute%0A *%0A * Permission is hereby granted, free of charge, to any person obtaining a copy%0A * of this software and associated documentation files (the %22Software%22), to deal%0A * in the Software without restriction, including without limitation the rights%0A * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell%0A * copies of the Software, and to permit persons to whom the Software is%0A * furnished to do so, subject to the following conditions:%0A *%0A * The above copyright notice and this permission notice shall be included in%0A * all copies or substantial portions of the Software.%0A *%0A * THE SOFTWARE IS PROVIDED %22AS IS%22, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR%0A * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,%0A * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE%0A * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER%0A * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,%0A * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN%0A * THE SOFTWARE.%0A */%0A%0Aimport net.sf.picard.Picard
+%0A%0Aimport net.sf.samtools.SAM
 Exce
@@ -1527,38 +1527,35 @@
       throw new 
-Picard
+SAM
 Exception(%22Faile
@@ -1649,38 +1649,35 @@
       throw new 
-Picard
+SAM
 Exception(%22Faile
@@ -1776,14 +1776,11 @@
 new 
-Picard
+SAM
 Exce

Replace PicardException with SamException because net.sf.samtools code cannot reference net.sf.picard code.