diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
index c6753efb2..63fb84c8d 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
@@ -208,7 +208,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
                     if (base == 'T'){numTs++;}
                     if (base == 'G'){numGs++;}
                     //consider base in likelihood calculations if it looks good and has high mapping score
-                    G.add(base, qual);
+                    G.add(base, qual, ! read.getReadNegativeStrandFlag());
                 }
             }
 
diff --git a/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/java/src/org/broadinstitute/sting/utils/BaseUtils.java
index beb8d5062..68a65dd53 100644
--- a/java/src/org/broadinstitute/sting/utils/BaseUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/BaseUtils.java
@@ -197,7 +197,7 @@ public class BaseUtils {
      * @param base  the base [AaCcGgTt]
      * @return the complementary base, or the input base if it's not one of the understood ones
      */
-    static public byte simpleComplement(char base) {
+    static public char simpleComplement(char base) {
         switch (base) {
             case 'A':
             case 'a': return 'T';
@@ -207,7 +207,7 @@ public class BaseUtils {
             case 'g': return 'C';
             case 'T':
             case 't': return 'A';
-            default: return (byte) base;
+            default: return base;
         }
     }
 
@@ -221,7 +221,7 @@ public class BaseUtils {
         byte[] rcbases = new byte[bases.length];
 
         for (int i = 0; i < bases.length; i++) {
-            rcbases[i] = simpleComplement((char) bases[bases.length - 1 - i]);
+            rcbases[i] = (byte)simpleComplement((char) bases[bases.length - 1 - i]);
         }
 
         return rcbases;