Restoring accidentially deleted unit test

public/java/test/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDataUnitTest.java

@@ -0,0 +1,48 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import org.testng.Assert;
+import org.broadinstitute.sting.BaseTest;
+
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * 
+ * @author aaron 
+ * 
+ * Class ReferenceOrderedDataUnitTest
+ *
+ * some functionality to test parts of the reference ordered data system that I've added.  This is by NO MEANS
+ * a complete test suite, but additions would be extremely welcome
+ */
+public class ReferenceOrderedDataUnitTest extends BaseTest {
+    @Test
+    public void extractRodsFromFileTest() {
+        String file = validationDataLocation + "testRODFileImpl.csv";
+        List<String> lst = new ArrayList<String>();
+        ReferenceOrderedData.extractRodsFromFile(lst,file);
+        Assert.assertEquals(lst.size(), 6);
+        int index = 0;
+        for (String entry: lst) {
+            String first = entry.subSequence(0,entry.indexOf(",")).toString();            
+            Assert.assertTrue(first.equals("rod" + String.valueOf(++index)));
+        }
+    }
+    @Test
+    public void extractRodsFromMultiFileTest() {
+        String file = validationDataLocation + "testRODFileImpl.csv";
+        String file2 = validationDataLocation + "testRODFileImpl2.csv";
+        List<String> lst = new ArrayList<String>();
+        ReferenceOrderedData.extractRodsFromFile(lst,file);
+        ReferenceOrderedData.extractRodsFromFile(lst,file2);
+        Assert.assertEquals(lst.size(), 12);
+        int index = 0;
+        for (String entry: lst) {
+            String first = entry.subSequence(0,entry.indexOf(",")).toString();
+            Assert.assertTrue(first.equals("rod" + String.valueOf(++index)));
+        }
+    }
+}