diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
index 65d211b2e..052d0b5f2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
@@ -55,7 +55,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
             return new Pair<GenomeLoc, String>(context.getLocation(), "");
         }
 
-        String refBase = String.valueOf(ref.getBaseAsChar());
+        String refBase = String.valueOf((char)ref.getBase());
 
         Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref);
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
index 92613ec87..6be2336c0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
@@ -56,7 +56,7 @@ public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, Gen
     }
 
 	public Pair<GenomeLoc, String> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
-        return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf(ref.getBase()));
+        return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf((char)ref.getBase()));
 	}
 
     public GenomeLoc reduceInit() {
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
index 3b6819735..b13f5919a 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
@@ -9,11 +9,19 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
     @Test
     public void testIntervals() {
 
-        WalkerTestSpec spec1 = new WalkerTestSpec(
+        String md5_1 = "328d2d52cedfdc52da7d1abff487633d";
+
+        WalkerTestSpec spec1a = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
                  1,
-                 Arrays.asList("328d2d52cedfdc52da7d1abff487633d"));
-        executeTest("testFastaReference", spec1);
+                 Arrays.asList(md5_1));
+        executeTest("testFastaReference", spec1a);
+
+        WalkerTestSpec spec1b = new WalkerTestSpec(
+                "-T FastaReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
+                 1,
+                 Arrays.asList(md5_1));
+        executeTest("testFastaReference", spec1b);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -B:snpmask,dbsnp /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
@@ -21,10 +29,10 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
                  Arrays.asList("3a48986c3832a768b478c3e95f994b0f"));
         executeTest("testFastaAlternateReferenceIndels", spec2);
 
-        WalkerTestSpec spec4 = new WalkerTestSpec(
+        WalkerTestSpec spec3 = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:snps,GeliText " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.geli.calls -B:snpmask,dbsnp /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s",
                  1,
                  Arrays.asList("82705a88f6fc25880dd2331183531d9a"));
-        executeTest("testFastaAlternateReferenceSnps", spec4);
+        executeTest("testFastaAlternateReferenceSnps", spec3);
     }
 }