diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
index 5004292f1..dca0b2e62 100755
--- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
@@ -155,12 +155,14 @@ public class ArtificialSAMUtils {
         record.setCigar(new Cigar(elements));
         record.setProperPairFlag(false);
 
-        // our reads are all 'A's by default
+        // our reads and quals are all 'A's by default
         byte[] c = new byte[length];
+        byte[] q = new byte[length];
         for (int x = 0; x < length; x++)
-            c[x] = 'A';
+            c[x] = q[x] = 'A';
         record.setReadBases(c);
-        
+        record.setBaseQualities(q);
+
         if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
             record.setReadUmappedFlag(true);
         }
diff --git a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index a7a00150d..d25f6803c 100755
--- a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -55,7 +55,8 @@ public class GATKSAMRecord extends SAMRecord {
             setAttribute(attribute.tag, attribute.value);
 
         // if we are using original quals, set them now if t hey are present in the record
-        if ( GenomeAnalysisEngine.instance.getArguments().useOriginalBaseQualities ) {
+        if ( GenomeAnalysisEngine.instance != null &&
+                GenomeAnalysisEngine.instance.getArguments().useOriginalBaseQualities ) {
             byte[] originalQuals = mRecord.getOriginalBaseQualities();
             if ( originalQuals != null )
                 mRecord.setBaseQualities(originalQuals);