It helps if I check the new base class in with my changes

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@404 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/BaseTest.java

@@ -0,0 +1,158 @@
+package org.broadinstitute.sting;
+
+import org.apache.log4j.*;
+import org.junit.*;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.Enumeration;
+
+/**
+ *
+ * User: aaron
+ * Date: Apr 14, 2009
+ * Time: 10:24:30 AM
+ *
+ * The Broad Institute
+ * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
+ * This software and its documentation are copyright 2009 by the
+ * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
+ *
+ * This software is supplied without any warranty or guaranteed support whatsoever. Neither
+ * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
+ *
+ */
+
+
+/**
+ * @author aaron
+ * @version 1.0
+ * @date Apr 14, 2009
+ * <p/>
+ * Class BaseTest
+ * <p/>
+ * A descriptions should go here. Blame aaron if it's missing.
+ */
+public abstract class BaseTest {
+    /** our log, which we want to capture anything from org.broadinstitute.sting */
+    public static Logger logger = Logger.getRootLogger();// .getLogger(CommandLineProgram.class);
+
+    protected static String seqLocation = "/seq";
+    protected static String oneKGLocation = "/broad/1KG";
+
+    protected static boolean alreadySetup = false;
+
+    /** before the class starts up */
+    @BeforeClass
+    public static void baseStartup() {
+        if (!alreadySetup) {
+            alreadySetup = true;
+            // setup a basic log configuration
+            BasicConfigurator.configure();
+
+            // setup our log layout
+            PatternLayout layout = new PatternLayout();
+            layout.setConversionPattern("TEST %C{1} - %d{HH:mm:ss,SSS} - %m%n");
+
+            // now set the layout of all the loggers to our layout
+            Enumeration<Appender> en = logger.getAllAppenders();
+            for (; en.hasMoreElements();) {
+                Appender app = en.nextElement();
+                app.setLayout(layout);
+            }
+            logger.setLevel(Level.WARN);
+
+            // find our file sources
+            try {
+                findFileLocations();
+            } catch (IOException e) {
+                logger.fatal("We can't locate the base /seq and /broad/1KG directories, for the following reason: " + e.getMessage());
+                e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+                throw new RuntimeException("BaseTest setup failed: findFileLocations emited exception with a reason: " + e.getMessage());
+            }
+        }
+    }
+
+    public static void findFileLocations() throws IOException {
+        // if either doesn't exist
+        if (!fileExist(seqLocation) || !fileExist(oneKGLocation)) {
+            String workDir = System.getProperty("user.dir");
+
+            if (!fileExist("test.conf")) {
+                throw new IOException("Unable to find both data directories or your test.conf, make sure it's placed in the base Sting directory");
+            }
+
+            BufferedReader inputStream = new BufferedReader(new FileReader("test.conf"));
+
+            String line = "";
+            while ((line = inputStream.readLine()) != null) {
+                String[] array = line.split("=");
+
+                // check the length
+                if (array.length != 2) {
+                    throw new IOException("Line : " + line + ", split != 2");
+                }
+                // clean up the right side
+                if (array[1].contains("\n")) {
+                    array[1] = array[1].substring(0, array[1].indexOf("\n") - 1);
+                }
+                // check to see if the right side exists
+                if (!fileExist(array[1])) {
+                    throw new IOException("Line : " + line + ", right side doesn't exist");
+                }
+                // check to see what type it is
+                if (array[0].equals("seq")) {
+                    seqLocation = array[1];
+                } else if (array[0].equals("1KG")) {
+                    oneKGLocation = array[1];
+
+                } else {
+                    throw new IOException("Line : " + line + ", unknown left side");
+                }
+            }
+
+        }
+
+    }
+
+    /**
+     * test if the file exists
+     *
+     * @param file name as a string
+     * @return true if it exists
+     */
+    public static boolean fileExist(String file) {
+        File temp = new File(file);
+        return temp.exists();
+
+    }
+
+
+    /**
+     * this test is here so that we can always pass when this test is run
+     */
+    @Test
+    public void basicTest() {
+
+    }
+
+    /** after the class runs */
+    @AfterClass
+    public static void baseShutdown() {
+
+    }
+
+    // pass through to the junit 3 calls, which are not annotated
+    @Before
+    final public void baseSetup() throws Exception {
+
+    }
+
+    @After
+    public void baseTearDown() throws Exception {
+
+    }
+
+}