diff --git a/java/test/org/broadinstitute/sting/utils/RefHangerTest.java b/java/test/org/broadinstitute/sting/utils/RefHangerTest.java
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+++ b/java/test/org/broadinstitute/sting/utils/RefHangerTest.java
@@ -0,0 +1,213 @@
+// our package
+package org.broadinstitute.sting.utils;
+
+
+// the imports for unit testing.
+
+import org.junit.*;
+import static org.junit.Assert.assertTrue;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
+import org.broadinstitute.sting.utils.RefHanger;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Basic unit test for RefHanger
+ *
+ * interface functions:
+    public RefHanger();
+    public void clear();
+    protected int getLeftOffset();
+    protected int getRightOffset();
+    protected int getOffset(GenomeLoc loc);
+    public GenomeLoc getLeftLoc();
+    public GenomeLoc getRightLoc();
+    public boolean hasLocation(GenomeLoc loc);
+    public boolean isEmpty();
+    public boolean hasHangers();
+    public Hanger popLeft();
+    public void dropLeft();
+    public Hanger getLeft();
+    public Hanger getHanger(int relativePos);
+    public Hanger getHanger(GenomeLoc pos);
+    public int size();
+    public void pushLeft(GenomeLoc pos);
+    public void pushLeft(GenomeLoc pos, T datum);
+    public void pushLeft(GenomeLoc pos, ArrayList<T> data);
+    public void pushRight(GenomeLoc pos);
+    public void pushRight(GenomeLoc pos, T datum);
+    public void pushRight(GenomeLoc pos, ArrayList<T> data);
+    public boolean ensurePos(GenomeLoc pos);
+    public void extendData(GenomeLoc pos, T datum);
+    public void addData(List<GenomeLoc> positions, List<T> dataByPos);
+    public void expandingPut1(final GenomeLoc loc, T datum);
+    public void printState();
+    public void expandingPut(GenomeLoc pos, T datum);
+
+ */
+public class RefHangerTest extends BaseTest {
+    private static FastaSequenceFile2 seq;
+    private GenomeLoc startLoc;
+    private RefHanger<Integer> emptyHanger;
+
+    /**
+     * chrM:1 is the start.
+     * 1: 1 2 3
+     * 2: 4 5
+     * 3: 6
+     * 4: 7 8
+     * 5: 9 10
+     */
+    private static RefHanger<Integer> filledHanger;
+    private static List<Integer> l1, l2, l3, l4, l5;
+    private static GenomeLoc p1, p2, p3, p4, p5;
+
+    @BeforeClass
+    public static void init() {
+        // sequence
+        seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        GenomeLoc.setupRefContigOrdering(seq);
+
+        System.out.printf("Filled hanger is %n%s%n", makeFilledHanger());
+    }
+
+    private static RefHanger makeFilledHanger() {
+        RefHanger<Integer> filledHanger = new RefHanger<Integer>();
+        l1 = Arrays.asList(1, 2, 3);
+        l2 = Arrays.asList(4, 5);
+        l3 = Arrays.asList(6);
+        l4 = Arrays.asList(7, 8);
+        l5 = Arrays.asList(9, 10);
+        p1 = new GenomeLoc(0, 1, 1);
+        p2 = new GenomeLoc(p1).nextLoc();
+        p3 = new GenomeLoc(p2).nextLoc();
+        p4 = new GenomeLoc(p3).nextLoc();
+        p5 = new GenomeLoc(p4).nextLoc();
+
+        filledHanger.addDataList(Arrays.asList(p1, p2, p3, p4, p5),
+                                 Arrays.asList(l1, l2, l3, l4, l5));
+        return filledHanger;
+    }
+
+    @Before
+    public void setupHanger() {
+        startLoc = new GenomeLoc(0, 1, 1);  // chrM 1
+        emptyHanger = new RefHanger<Integer>();
+        filledHanger = makeFilledHanger();
+
+        //System.out.printf("Filled hanger is %n%s%n", filledHanger);
+
+        //GenomeLoc two = new GenomeLoc();
+    }
+
+    /**
+     * Tests that we got a string parameter in correctly
+     */
+    @Test
+    public void testEmpty() {
+        logger.warn("Executing testEmpty");
+        assertTrue(emptyHanger.size() == 0);
+        assertTrue(emptyHanger.getLeftOffset() == 0);
+        assertTrue(emptyHanger.getRightOffset() == 0);
+    }
+
+    @Test (expected=IndexOutOfBoundsException.class )
+    public void testEmptyGet() {
+        logger.warn("Executing testEmptyGet");
+        emptyHanger.getHanger(0);
+    }
+
+    @Test
+    public void testFilledFilling() {
+        logger.warn("Executing testFilledFilling");
+        testBaseFilledHanger();
+    }
+
+    private void testBaseFilledHanger() {
+        assertTrue(filledHanger.size() == 5);
+        assertTrue(! filledHanger.isEmpty());
+        assertTrue(filledHanger.hasHangers());
+        assertTrue(filledHanger.getLeftOffset() == 0);
+        assertTrue(filledHanger.getRightOffset() == 4);
+        assertTrue(filledHanger.getOffset(p1) == 0);
+        assertTrue(filledHanger.getOffset(p2) == 1);
+        assertTrue(filledHanger.getOffset(p3) == 2);
+        assertTrue(filledHanger.getOffset(p4) == 3);
+        assertTrue(filledHanger.getOffset(p5) == 4);
+        assertTrue(filledHanger.getLeftLoc().compareTo(p1) == 0);
+        assertTrue(filledHanger.getRightLoc().compareTo(p5) == 0);
+        assertTrue(filledHanger.getLoc(2).compareTo(p3) == 0);
+        assertTrue(filledHanger.hasLocation(p1));
+        assertTrue(filledHanger.hasLocation(p2));
+        assertTrue(filledHanger.hasLocation(p3));
+        assertTrue(filledHanger.hasLocation(p4));
+        assertTrue(filledHanger.hasLocation(p5));
+        assertTrue(! filledHanger.hasLocation(new GenomeLoc(0, 6, 6)));
+
+        assertTrue(filledHanger.getHanger(0) != null);
+        assertTrue(filledHanger.getHanger(1) != null);
+        assertTrue((int)(Integer)filledHanger.getHanger(0).data.get(0) == 1);
+        assertTrue((int)(Integer)filledHanger.getHanger(1).data.get(0) == 4);
+        assertTrue((int)(Integer)filledHanger.getHanger(p1).data.get(0) == 1);
+        assertTrue((int)(Integer)filledHanger.getHanger(p2).data.get(0) == 4);
+    }
+
+    @Test
+    public void testClear() {
+        logger.warn("Executing testClear");        
+        assertTrue(filledHanger.size() == 5);
+        assertTrue(! filledHanger.isEmpty());
+        assertTrue(filledHanger.hasHangers());
+
+        filledHanger.clear();
+
+        assertTrue(filledHanger.size() == 0);
+        assertTrue(filledHanger.isEmpty());
+        assertTrue(! filledHanger.hasHangers());
+    }
+
+    @Test
+    public void testPopLeft() {
+        logger.warn("Executing testPopLeft");
+        filledHanger.popLeft();
+        assertTrue(filledHanger.size() == 4);
+        assertTrue(filledHanger.getRightOffset() == 3);
+        assertTrue(filledHanger.getOffset(p2) == 0);
+        assertTrue(filledHanger.getOffset(p3) == 1);
+        assertTrue(filledHanger.getOffset(p4) == 2);
+        assertTrue(filledHanger.getOffset(p5) == 3);
+        assertTrue(! filledHanger.hasLocation(p1));
+        assertTrue(filledHanger.hasLocation(p2));
+        assertTrue(filledHanger.hasLocation(p3));
+        assertTrue(filledHanger.hasLocation(p4));
+        assertTrue(filledHanger.hasLocation(p5));
+    }
+
+    @Test
+    public void testDoublePopLeft() {
+        logger.warn("Executing testDoublePopLeft");
+        filledHanger.popLeft();
+        filledHanger.popLeft();
+        assertTrue(filledHanger.size() == 3);
+        assertTrue(filledHanger.getRightOffset() == 2);
+        assertTrue(filledHanger.getOffset(p3) == 0);
+        assertTrue(filledHanger.getOffset(p4) == 1);
+        assertTrue(filledHanger.getOffset(p5) == 2);
+        assertTrue(! filledHanger.hasLocation(p1));
+        assertTrue(! filledHanger.hasLocation(p2));
+        assertTrue(filledHanger.hasLocation(p3));
+        assertTrue(filledHanger.hasLocation(p4));
+        assertTrue(filledHanger.hasLocation(p5));
+    }
+
+    @Test
+    public void testPopPushLeft() {
+        logger.warn("Executing testPopPushLeft");
+        filledHanger.popLeft();
+        filledHanger.pushLeft(p1, l1);
+        testBaseFilledHanger();
+    }
+}
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