diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java
index 9c03a9bb4..d5276254f 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java
@@ -394,7 +394,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             throw new RuntimeException("Entropy threshold must be a fraction between 0 and 1");
 
         try {
-            referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
+            referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile, false, true);
         }
         catch(FileNotFoundException ex) {
             throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile,ex);
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java
index 598c13d90..a456008a5 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java
@@ -125,8 +125,9 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile {
      * @param fasta The file to open.
      * @param cacheSize the size of the cache to use in this CachingIndexedFastaReader, must be >= 0
      * @param preserveCase If true, we will keep the case of the underlying bases in the FASTA, otherwise everything is converted to upper case
+     * @param preserveIUPAC If true, we will keep the IUPAC bases in the FASTA, otherwise they are converted to Ns
      */
-    public CachingIndexedFastaSequenceFile(final File fasta, final long cacheSize, final boolean preserveCase, final boolean  preserveIUPAC) throws FileNotFoundException {
+    public CachingIndexedFastaSequenceFile(final File fasta, final long cacheSize, final boolean preserveCase, final boolean preserveIUPAC) throws FileNotFoundException {
         super(fasta);
         if ( cacheSize < 0 ) throw new IllegalArgumentException("cacheSize must be > 0");
         this.cacheSize = cacheSize;
@@ -172,6 +173,19 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile {
         this(fasta, DEFAULT_CACHE_SIZE, preserveCase, false);
     }
 
+    /**
+     * Open the given indexed fasta sequence file.  Throw an exception if the file cannot be opened.
+     *
+     * Looks for a index file for fasta on disk
+     *
+     * @param fasta The file to open.
+     * @param preserveCase If true, we will keep the case of the underlying bases in the FASTA, otherwise everything is converted to upper case
+     * @param preserveIUPAC If true, we will keep the IUPAC bases in the FASTA, otherwise they are converted to Ns
+     */
+    public CachingIndexedFastaSequenceFile(final File fasta, final boolean preserveCase, final boolean preserveIUPAC) throws FileNotFoundException {
+        this(fasta, DEFAULT_CACHE_SIZE, preserveCase, preserveIUPAC);
+    }
+
     /**
      * Create reference data source from fasta file, after performing several preliminary checks on the file.
      * This static utility was refactored from the constructor of ReferenceDataSource.
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
index 17cdb0938..ef8565dba 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
@@ -236,7 +236,7 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testIupacChanges() throws FileNotFoundException, InterruptedException {
         final String testFasta = privateTestDir + "iupacFASTA.fasta";
-        final CachingIndexedFastaSequenceFile iupacPreserving = new CachingIndexedFastaSequenceFile(new File(testFasta), CachingIndexedFastaSequenceFile.DEFAULT_CACHE_SIZE, false, true);
+        final CachingIndexedFastaSequenceFile iupacPreserving = new CachingIndexedFastaSequenceFile(new File(testFasta), false, true);
         final CachingIndexedFastaSequenceFile makeNs = new CachingIndexedFastaSequenceFile(new File(testFasta));
 
         int preservingNs = 0;