diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java
new file mode 100755
index 000000000..317b320d3
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java
@@ -0,0 +1,83 @@
+package org.broadinstitute.sting.utils.sam;
+
+import net.sf.samtools.SAMFileHeader;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+
+public class GATKSAMRecordUnitTest extends BaseTest {
+    GATKSAMRecord read, reducedRead;
+    final static String BASES = "ACTG";
+    final static String QUALS = "!+5?";
+    final private static byte[] REDUCED_READ_COUNTS = new byte[]{10, 20, 30, 40, 1};
+    final private static byte[] REDUCED_READ_COUNTS_TAG = new byte[]{10, 10, 20, 30, -9};  // just the offsets
+
+    @BeforeClass
+    public void init() {
+        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
+        read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length());
+        read.setReadUnmappedFlag(true);
+        read.setReadBases(new String(BASES).getBytes());
+        read.setBaseQualityString(new String(QUALS));
+
+        reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length());
+        reducedRead.setReadBases(BASES.getBytes());
+        reducedRead.setBaseQualityString(QUALS);
+        reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, REDUCED_READ_COUNTS_TAG);
+    }
+
+    @Test
+    public void testReducedReads() {
+        Assert.assertFalse(read.isReducedRead(), "isReducedRead is false for normal read");
+        Assert.assertEquals(read.getReducedReadCounts(), null, "No reduced read tag in normal read");
+
+        Assert.assertTrue(reducedRead.isReducedRead(), "isReducedRead is true for reduced read");
+        for (int i = 0; i < reducedRead.getReadLength(); i++) {
+            Assert.assertEquals(reducedRead.getReducedCount(i), REDUCED_READ_COUNTS[i], "Reduced read count not set to the expected value at " + i);
+        }
+    }
+
+    @Test
+    public void testReducedReadPileupElement() {
+        PileupElement readp = new PileupElement(read, 0, false);
+        PileupElement reducedreadp = new PileupElement(reducedRead, 0, false);
+
+        Assert.assertFalse(readp.getRead().isReducedRead());
+
+        Assert.assertTrue(reducedreadp.getRead().isReducedRead());
+        Assert.assertEquals(reducedreadp.getRepresentativeCount(), REDUCED_READ_COUNTS[0]);
+        Assert.assertEquals(reducedreadp.getQual(), readp.getQual());
+    }
+
+    @Test
+    public void testGetOriginalAlignments() {
+        final byte [] bases = {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
+        final byte [] quals = {20 , 20 , 20 , 20 , 20 , 20 , 20 , 20 };
+        GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, "6M");
+
+        // A regular read with all matches
+        Assert.assertEquals(read.getAlignmentStart(), read.getOriginalAlignmentStart());
+        Assert.assertEquals(read.getAlignmentEnd(), read.getOriginalAlignmentEnd());
+
+        // Alignment start shifted
+        int alignmentShift = 2;
+        read.setAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_START_SHIFT, alignmentShift);
+        Assert.assertEquals(read.getAlignmentStart() + alignmentShift, read.getOriginalAlignmentStart());
+        Assert.assertEquals(read.getAlignmentEnd(), read.getOriginalAlignmentEnd());
+
+        // Both alignments shifted
+        read.setAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_END_SHIFT, alignmentShift);
+        Assert.assertEquals(read.getAlignmentStart() + alignmentShift, read.getOriginalAlignmentStart());
+        Assert.assertEquals(read.getAlignmentEnd() - alignmentShift, read.getOriginalAlignmentEnd());
+
+        // Alignment end shifted
+        read.setAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_START_SHIFT, null);
+        Assert.assertEquals(read.getAlignmentStart(), read.getOriginalAlignmentStart());
+        Assert.assertEquals(read.getAlignmentEnd() - alignmentShift, read.getOriginalAlignmentEnd());
+        
+    }
+
+}
diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
index b7a22ca1a..7598f62a6 100755
--- a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
@@ -1,57 +1,11 @@
 package org.broadinstitute.sting.utils.sam;
 
-import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.testng.Assert;
-import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
 
 
 public class ReadUtilsUnitTest extends BaseTest {
-    GATKSAMRecord read, reducedRead;
-    final static String BASES = "ACTG";
-    final static String QUALS = "!+5?";
-    final private static byte[] REDUCED_READ_COUNTS = new byte[]{10, 20, 30, 40, 1};
-    final private static byte[] REDUCED_READ_COUNTS_TAG = new byte[]{10, 10, 20, 30, -9};  // just the offsets
-
-    @BeforeTest
-    public void init() {
-        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
-        read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length());
-        read.setReadUnmappedFlag(true);
-        read.setReadBases(new String(BASES).getBytes());
-        read.setBaseQualityString(new String(QUALS));
-
-        reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length());
-        reducedRead.setReadBases(BASES.getBytes());
-        reducedRead.setBaseQualityString(QUALS);
-        reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, REDUCED_READ_COUNTS_TAG);
-    }
-
-    @Test
-    public void testReducedReads() {
-        Assert.assertFalse(read.isReducedRead(), "isReducedRead is false for normal read");
-        Assert.assertEquals(read.getReducedReadCounts(), null, "No reduced read tag in normal read");
-
-        Assert.assertTrue(reducedRead.isReducedRead(), "isReducedRead is true for reduced read");
-        for (int i = 0; i < reducedRead.getReadLength(); i++) {
-            Assert.assertEquals(reducedRead.getReducedCount(i), REDUCED_READ_COUNTS[i], "Reduced read count not set to the expected value at " + i);
-        }
-    }
-
-    @Test
-    public void testReducedReadPileupElement() {
-        PileupElement readp = new PileupElement(read, 0, false, false, false);
-        PileupElement reducedreadp = new PileupElement(reducedRead, 0, false, false, false);
-
-        Assert.assertFalse(readp.getRead().isReducedRead());
-
-        Assert.assertTrue(reducedreadp.getRead().isReducedRead());
-        Assert.assertEquals(reducedreadp.getRepresentativeCount(), REDUCED_READ_COUNTS[0]);
-        Assert.assertEquals(reducedreadp.getQual(), readp.getQual());
-    }
-
     @Test
     public void testGetAdaptorBoundary() {
         final byte[] bases = {'A', 'C', 'G', 'T', 'A', 'C', 'G', 'T'};