diff --git a/java/src/org/broadinstitute/sting/bwa/CreateBWTFromReference.java b/java/src/org/broadinstitute/sting/bwa/CreateBWTFromReference.java
index 93a1588a8..04d6a730d 100755
--- a/java/src/org/broadinstitute/sting/bwa/CreateBWTFromReference.java
+++ b/java/src/org/broadinstitute/sting/bwa/CreateBWTFromReference.java
@@ -99,6 +99,13 @@ public class CreateBWTFromReference {
         return compressedSuffixArray;
     }
 
+    private int[] createInversedCompressedSuffixArray( int[] compressedSuffixArray ) {
+        int[] inverseCompressedSuffixArray = new int[compressedSuffixArray.length];
+        for( int i = 0; i < compressedSuffixArray.length; i++ )
+            inverseCompressedSuffixArray[compressedSuffixArray[i]] = i;
+        return inverseCompressedSuffixArray;
+    }
+
     private byte[] createBWT( String sequence, int[] suffixArray ) {
         byte[] bwt = new byte[suffixArray.length];
         for( int i = 0; i < suffixArray.length; i++ ) {
@@ -111,16 +118,19 @@ public class CreateBWTFromReference {
     }
 
     public static void main( String argv[] ) throws IOException {
-        if( argv.length != 2 ) {
-            System.out.println("USAGE: CreateBWTFromReference <input>.fasta <output>");
+        if( argv.length != 3 ) {
+            System.out.println("USAGE: CreateBWTFromReference <input>.fasta <output bwt> <output sa>");
             return;
         }
 
         String inputFileName = argv[0];
         File inputFile = new File(inputFileName);
 
-        String outputFileName = argv[1];
-        File outputFile = new File(outputFileName);
+        String bwtFileName = argv[1];
+        File bwtFile = new File(bwtFileName);
+
+        String saFileName = argv[2];
+        File saFile = new File(saFileName);
 
         CreateBWTFromReference creator = new CreateBWTFromReference();
 
@@ -144,6 +154,12 @@ public class CreateBWTFromReference {
             reconstructedInverseSA = compressedSuffixArray[reconstructedInverseSA];
         }
 
+        // Create the data structure for the inverse compressed suffix array and print diagnostics.
+        int[] inverseCompressedSuffixArray = creator.createInversedCompressedSuffixArray(compressedSuffixArray);
+        for( int i = 0; i < 8; i++ ) {
+            System.out.printf("inverseCompressedSuffixArray[%d] = %d%n", i, inverseCompressedSuffixArray[i]);
+        }
+
         // Count the occurences of each given base.
         int[] occurrences = creator.countOccurrences(sequence);
         System.out.printf("Occurrences: a=%d, c=%d, g=%d, t=%d%n",occurrences[0],occurrences[1],occurrences[2],occurrences[3]);
@@ -152,27 +168,39 @@ public class CreateBWTFromReference {
         byte[] bwt = creator.createBWT(sequence, suffixArray);
 
         String bwtAsString = new String(bwt);
-        System.out.printf("BWT:%n");
+        //System.out.printf("BWT:%n");
         while( bwtAsString.length() > 0 ) {
             int end = Math.min( 80, bwtAsString.length() );
             //System.out.printf("%s%n", bwtAsString.substring(0,end));
             bwtAsString = bwtAsString.substring(end);
         }
 
-        OutputStream outputStream = new BufferedOutputStream(new FileOutputStream(outputFile));
+        OutputStream bwtOutputStream = new BufferedOutputStream(new FileOutputStream(bwtFile));
 
         ByteBuffer buffer = ByteBuffer.allocate(4).order(ByteOrder.LITTLE_ENDIAN);
         buffer.putInt(inverseSuffixArray[0]);
-        outputStream.write(buffer.array());
-        outputStream.flush();
+        bwtOutputStream.write(buffer.array());
+        bwtOutputStream.flush();
 
-        OccurrenceOutputStream occurrenceWriter = new OccurrenceOutputStream(outputStream);
+        PackedIntOutputStream occurrenceWriter = new PackedIntOutputStream(bwtOutputStream);
         occurrenceWriter.write(occurrences);
         occurrenceWriter.flush();
 
-        WordPackedOutputStream bwtOutputStream = new WordPackedOutputStream(outputStream,ByteOrder.LITTLE_ENDIAN);
-        bwtOutputStream.write(bwt);
-        bwtOutputStream.close();
+        WordPackedOutputStream sequenceOutputStream = new WordPackedOutputStream(bwtOutputStream,ByteOrder.LITTLE_ENDIAN);
+        sequenceOutputStream.write(bwt);
+        sequenceOutputStream.close();
+
+        OutputStream saOutputStream = new BufferedOutputStream(new FileOutputStream(saFile));
+        PackedIntOutputStream saIntWriter = new PackedIntOutputStream(saOutputStream);
+
+        // SA file format is 'primary' (= SA-1[0]?), occurrence array, interval, sequence length, SA[]
+        saIntWriter.write(inverseSuffixArray[0]);
+        saIntWriter.write(occurrences);
+        saIntWriter.write(1);
+        saIntWriter.write(suffixArray.length-1);
+        saIntWriter.write(suffixArray, 1, suffixArray.length-1);
+
+        saIntWriter.close();
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/bwa/OccurrenceOutputStream.java b/java/src/org/broadinstitute/sting/bwa/PackedIntOutputStream.java
similarity index 70%
rename from java/src/org/broadinstitute/sting/bwa/OccurrenceOutputStream.java
rename to java/src/org/broadinstitute/sting/bwa/PackedIntOutputStream.java
index 9b3bb2d7e..c530676b7 100755
--- a/java/src/org/broadinstitute/sting/bwa/OccurrenceOutputStream.java
+++ b/java/src/org/broadinstitute/sting/bwa/PackedIntOutputStream.java
@@ -37,7 +37,7 @@ import java.nio.ByteOrder;
  * @author mhanna
  * @version 0.1
  */
-public class OccurrenceOutputStream {
+public class PackedIntOutputStream {
     /**
      * How many bytes does it take to hold an integer in Java?
      */
@@ -49,35 +49,47 @@ public class OccurrenceOutputStream {
     private final OutputStream targetOutputStream;
 
     /**
-     * Create a new OccurrenceArrayOutputStream, writing to the given target file.
+     * Create a new PackedIntOutputStream, writing to the given target file.
      * @param outputFile target output file.
      * @throws IOException if an I/O error occurs.
      */
-    public OccurrenceOutputStream( File outputFile ) throws IOException {
+    public PackedIntOutputStream( File outputFile ) throws IOException {
         this(new FileOutputStream(outputFile));
     }
 
     /**
-     * Write occurrence array to the given OutputStream.
-     * @param outputStream Output stream to which to write packed bases.
+     * Write packed ints to the given OutputStream.
+     * @param outputStream Output stream to which to write packed ints.
      * @throws IOException if an I/O error occurs.
      */
-    public OccurrenceOutputStream( OutputStream outputStream ) throws IOException {
+    public PackedIntOutputStream( OutputStream outputStream ) throws IOException {
         this.targetOutputStream = outputStream;
     }
 
     /**
-     * Write the cumulative occurrences to the output stream.
-     * @param occurrences occurrences to write.  occurrences.length must match alphabet size.
+     * Write the data to the output stream.
+     * @param datum datum to write. 
      * @throws IOException if an I/O error occurs.
      */
-    public void write( int[] occurrences ) throws IOException {
-        if( occurrences.length > BytePackedOutputStream.ALPHABET_SIZE )
-            throw new StingException("Wrong number of occurrence data points; expected " + BytePackedOutputStream.ALPHABET_SIZE);
-        ByteBuffer buffer = ByteBuffer.allocate(INT_SIZE_IN_BYTES*occurrences.length).order(ByteOrder.LITTLE_ENDIAN);
-        for(int occurrence: occurrences)
-            buffer.putInt(occurrence);
-        targetOutputStream.write(buffer.array());        
+    public void write( int datum ) throws IOException {
+        ByteBuffer buffer = ByteBuffer.allocate(INT_SIZE_IN_BYTES).order(ByteOrder.LITTLE_ENDIAN);
+        buffer.putInt(datum);
+        targetOutputStream.write(buffer.array());
+    }
+
+    /**
+     * Write the data to the output stream.
+     * @param data data to write.  occurrences.length must match alphabet size.
+     * @throws IOException if an I/O error occurs.
+     */
+    public void write( int[] data ) throws IOException {
+        for(int datum: data)
+            write(datum);
+    }
+
+    public void write( int[] data, int offset, int length ) throws IOException {
+        for( int i = offset; i < offset+length; i++ )
+            write(data[i]);
     }
 
     /**