diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SAMToFastqAndSqWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SAMToFastqAndSqWalker.java
deleted file mode 100644
index 42994053f..000000000
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SAMToFastqAndSqWalker.java
+++ /dev/null
@@ -1,74 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers;
-
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
-import net.sf.samtools.SAMRecord;
-
-import java.io.*;
-
-public class SAMToFastqAndSqWalker extends ReadWalker<Integer, Integer> {
-    @Argument(fullName="FASTQFILE", doc="Output path for Fastq file")
-    public File FASTQFILE;
-
-    @Argument(fullName="SQFILE", shortName="SQ", doc="Output path for secondary quality map (readName => SAM SQ field)", required=false)
-    public File SQFILE;
-
-    private PrintWriter fastqbw;
-    private PrintWriter sqbw;
-
-    private boolean ready = false;
-    
-    public Integer map(char[] ref, SAMRecord read) {
-        if (!ready) {
-            try {
-                fastqbw = new PrintWriter(FASTQFILE);
-
-                if (SQFILE != null) {
-                    sqbw = new PrintWriter(SQFILE);
-                }
-
-                ready = true;
-            } catch (IOException e) {
-                err.println("Unable to open output files.");
-                System.exit(1);
-            }
-        }
-
-        String bases = read.getReadString();
-        String quals = read.getBaseQualityString();
-        byte[] sqs   = (byte[]) read.getAttribute("SQ");
-
-        fastqbw.println("@" + read.getReadName());
-        fastqbw.println(bases);
-
-        fastqbw.println("+" + read.getReadName());
-        fastqbw.println(quals);
-
-        if (sqbw != null && sqs != null) {
-            sqbw.print(read.getReadName() + "\t" + "SQ:H:");
-
-            for (byte sq : sqs) {
-                sqbw.printf("%02X", sq);
-            }
-            sqbw.println();
-        }
-
-        return null;
-    }
-
-    public Integer reduceInit() {
-        return null;
-    }
-
-    public Integer reduce(Integer value, Integer sum) {
-        return null;
-    }
-
-    public void onTraversalDone(Integer sum) {
-        fastqbw.close();
-
-        if (sqbw != null) {
-            sqbw.close();
-        }
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/BamToFastqWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/BamToFastqWalker.java
index aa7406ae7..0c1772900 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/BamToFastqWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/BamToFastqWalker.java
@@ -6,6 +6,8 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import net.sf.samtools.SAMRecord;
 
+import java.io.*;
+
 // create a fastq file from a bam file
 
 @WalkerName("BamToFastq")
@@ -14,6 +16,21 @@ public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
     @Argument(fullName="re_reverse", shortName="reverse", doc="re-reverse bases and quals of reads from the negative strand", required=false)
     private Boolean RE_REVERSE = false;
 
+    @Argument(fullName="SQFile", shortName="SQ", doc="Output path for secondary quality map (readName => SAM SQ field)", required=false)
+    String SQFile = null;
+
+    private PrintWriter sqbw = null;
+
+    public void initialize() {
+        if ( SQFile != null ) {
+            try {
+                sqbw = new PrintWriter(SQFile);
+            } catch (IOException e) {
+                throw new RuntimeException("Unable to open sq output file: " + SQFile);
+            }
+        }
+    }
+
 	public Integer map(char[] ref, SAMRecord read) {
         out.println("@" + read.getReadName());
         if ( !RE_REVERSE || !read.getReadNegativeStrandFlag() ) {
@@ -26,6 +43,17 @@ public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
             out.println(BaseUtils.reverse(read.getBaseQualityString()));
         }
 
+        if ( sqbw != null ) {
+            byte[] sqs = (byte[])read.getAttribute("SQ");
+            if ( sqs != null ) {
+                sqbw.print(read.getReadName() + "\t" + "SQ:H:");
+                for ( byte sq : sqs ) {
+                    sqbw.printf("%02X", sq);
+                }
+                sqbw.println();
+            }
+        }
+
         return 1;
 	}
 
@@ -38,6 +66,8 @@ public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
 	}
 
     public void onTraversalDone(Integer sum) {
+        if ( sqbw != null )
+            sqbw.close();
         logger.info("Number of reads converted: " + sum);
     }
 }
\ No newline at end of file