diff --git a/c/bwa/bwa_gateway.cpp b/c/bwa/bwa_gateway.cpp
index a5fb045ec..d73d4ef86 100644
--- a/c/bwa/bwa_gateway.cpp
+++ b/c/bwa/bwa_gateway.cpp
@@ -24,6 +24,9 @@ BWA::BWA(const char* ann_filename,
   bwts[1] = bwt_restore_bwt(reverse_bwt_filename);
   bwt_restore_sa(reverse_sa_filename, bwts[1]);
   load_default_options();
+
+  // initialize the bwase subsystem
+  bwase_initialize();
 }
 
 BWA::~BWA() {
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
index 50cba3151..143f0a073 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
@@ -55,7 +55,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
     @Override
     public boolean filter(char[] ref, SAMRecord read) {
         return true;
-        //return read.getReadName().contains("SL-XBC:1:76:604:397#0");
+        //return read.getReadName().contains("SL-XBC:1:61:1719:1512#0");
     }
 
     /**
@@ -84,7 +84,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
                 matches &= (alignment.getCigar().equals(read.getCigar()));
                 int mapQDelta = Math.abs(alignment.getMappingQuality()-read.getMappingQuality());
                 maxMapQDelta = Math.max(mapQDelta,maxMapQDelta);
-                //matches &= (alignment.getMappingQuality() == read.getMappingQuality());
+                matches &= (alignment.getMappingQuality() == read.getMappingQuality());
                 if(matches) break;
             }
         }