diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/Marshal.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/Marshal.java
index f61cb6f..90def56 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/Marshal.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/Marshal.java
@@ -34,6 +34,10 @@
 //                + ((bytes[offset + 6] & 0xff) << 8) + ((bytes[offset + 7] & 0xff) << 0);
     }
     
+    public static float getFloat(byte[] bytes, int offset) {   
+        return ByteBuffer.wrap(bytes, offset, 4).getFloat();
+    }
+    
     public static void putInt(int val, byte[] bytes, int offset) {
         bytes[offset] = (byte)((val >>> 24) & 0xFF);        
         bytes[offset + 1] = (byte)((val >>> 16) & 0xFF);
@@ -54,6 +58,11 @@
 //        bytes[offset + 7] = (byte)((val >>> 0) & 0xFF);
     }
     
+    public static void putFloat(float val, byte[] bytes, int offset) {
+        ByteBuffer byteBuffer = ByteBuffer.allocate(4);
+        System.arraycopy(byteBuffer.putFloat(val).array(), 0, bytes, offset, 4);
+    }
+    
     public static int hashBytes(byte[] bytes, int offset, int length) {
         int hash = 1;
         for (int i = offset; i < offset + length; i++)
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/IntermediateNodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/IntermediateNodeWritable.java
deleted file mode 100644
index 3826f86..0000000
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/IntermediateNodeWritable.java
+++ /dev/null
@@ -1,144 +0,0 @@
-package edu.uci.ics.genomix.oldtype;
-
-import java.io.DataInput;
-import java.io.DataOutput;
-import java.io.IOException;
-import java.io.Serializable;
-
-import org.apache.hadoop.io.WritableComparable;
-
-import edu.uci.ics.genomix.type.KmerListWritable;
-import edu.uci.ics.genomix.type.PositionWritable;
-
-public class IntermediateNodeWritable implements WritableComparable<IntermediateNodeWritable>, Serializable{
-
-    private static final long serialVersionUID = 1L;
-    public static final IntermediateNodeWritable EMPTY_NODE = new IntermediateNodeWritable();
-    
-    private KmerListWritable forwardForwardList;
-    private KmerListWritable forwardReverseList;
-    private KmerListWritable reverseForwardList;
-    private KmerListWritable reverseReverseList;
-    private PositionWritable nodeId;
-    
-    public IntermediateNodeWritable(){
-        forwardForwardList = new KmerListWritable();
-        forwardReverseList = new KmerListWritable();
-        reverseForwardList = new KmerListWritable();
-        reverseReverseList = new KmerListWritable();
-        nodeId = new PositionWritable();
-    }
-    
-    public IntermediateNodeWritable(KmerListWritable FFList, KmerListWritable FRList,
-            KmerListWritable RFList, KmerListWritable RRList, PositionWritable uniqueKey) {
-        this();
-        set(FFList, FRList, RFList, RRList, uniqueKey);
-    }
-    
-    public void set(IntermediateNodeWritable node){
-        set(node.forwardForwardList, node.forwardReverseList, node.reverseForwardList, 
-                node.reverseReverseList, node.nodeId);
-    }
-    
-    public void set(KmerListWritable FFList, KmerListWritable FRList,
-            KmerListWritable RFList, KmerListWritable RRList, PositionWritable uniqueKey) {
-        this.forwardForwardList.set(FFList);
-        this.forwardReverseList.set(FRList);
-        this.reverseForwardList.set(RFList);
-        this.reverseReverseList.set(RRList);
-        this.nodeId.set(uniqueKey);
-    }
-    
-    public KmerListWritable getFFList() {
-        return forwardForwardList;
-    }
-
-    public void setFFList(KmerListWritable forwardForwardList) {
-        this.forwardForwardList.set(forwardForwardList);
-    }
-
-    public KmerListWritable getFRList() {
-        return forwardReverseList;
-    }
-
-    public void setFRList(KmerListWritable forwardReverseList) {
-        this.forwardReverseList.set(forwardReverseList);
-    }
-
-    public KmerListWritable getRFList() {
-        return reverseForwardList;
-    }
-
-    public void setRFList(KmerListWritable reverseForwardList) {
-        this.reverseForwardList.set(reverseForwardList);
-    }
-
-    public KmerListWritable getRRList() {
-        return reverseReverseList;
-    }
-
-    public void setRRList(KmerListWritable reverseReverseList) {
-        this.reverseReverseList.set(reverseReverseList);
-    }
-
-	public PositionWritable getNodeId() {
-        return nodeId;
-    }
-
-    public void setNodeId(PositionWritable nodeId) {
-        this.nodeId.set(nodeId);
-    }
-
-    @Override
-    public void readFields(DataInput in) throws IOException {
-        this.forwardForwardList.readFields(in);
-        this.forwardReverseList.readFields(in);
-        this.reverseForwardList.readFields(in);
-        this.reverseReverseList.readFields(in);
-        this.nodeId.readFields(in);
-    }
-
-    @Override
-    public void write(DataOutput out) throws IOException {
-        this.forwardForwardList.write(out);
-        this.forwardReverseList.write(out);
-        this.reverseForwardList.write(out);
-        this.reverseReverseList.write(out);
-        this.nodeId.write(out);
-    }
-
-    @Override
-    public int compareTo(IntermediateNodeWritable other) {
-        // TODO Auto-generated method stub
-        return this.nodeId.compareTo(other.nodeId);
-    }
-    
-    @Override
-    public int hashCode() {
-        return this.nodeId.hashCode();
-    }
-    
-    @Override
-    public boolean equals(Object o) {
-        if (o instanceof IntermediateNodeWritable) {
-            IntermediateNodeWritable nw = (IntermediateNodeWritable) o;
-            return (this.forwardForwardList.equals(nw.forwardForwardList)
-                    && this.forwardReverseList.equals(nw.forwardReverseList)
-                    && this.reverseForwardList.equals(nw.reverseForwardList)
-                    && this.reverseReverseList.equals(nw.reverseReverseList) && (this.nodeId.equals(nw.nodeId)));
-        }
-        return false;
-    }
-    
-    @Override
-    public String toString() {
-        StringBuilder sbuilder = new StringBuilder();
-        sbuilder.append('(');
-        sbuilder.append(nodeId.toString()).append('\t');
-        sbuilder.append(forwardForwardList.toString()).append('\t');
-        sbuilder.append(forwardReverseList.toString()).append('\t');
-        sbuilder.append(reverseForwardList.toString()).append('\t');
-        sbuilder.append(reverseReverseList.toString()).append('\t').append(')');
-        return sbuilder.toString();
-    }
-}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
index 65233d8..bbba2fb 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
@@ -25,192 +25,177 @@
 import org.apache.hadoop.io.WritableComparator;
 
 import edu.uci.ics.genomix.data.KmerUtil;
-import edu.uci.ics.genomix.oldtype.NodeWritable.DirectionFlag;
+import edu.uci.ics.genomix.data.Marshal;
 
 /**
- * Variable kmer length byteswritable
- * It was used to generate the graph in which phase the kmer length doesn't change.
- * Thus the kmerByteSize of bytes doesn't change either.
+ * Fixed, static-length Kmer used as the key and edge values of each
+ * NodeWritable. Kmer length should be set once during configuration and should
+ * never change.
  */
 public class KmerBytesWritable extends BinaryComparable implements Serializable, WritableComparable<BinaryComparable> {
-    /**
-	 * 
-	 */
-    private static final long serialVersionUID = 1L;
-    private static final byte[] EMPTY_BYTES = {};
 
-    public int kmerByteSize;
+    private static final long serialVersionUID = 1L;
+    protected static final byte[] EMPTY_BYTES = {};
+
+    protected static int lettersInKmer;
+    protected static int bytesUsed;
     protected byte[] bytes;
     protected int offset;
-    protected int kmerlength;
 
-    public KmerBytesWritable() {
-        this(0, EMPTY_BYTES, 0);
-    }
-
-    public KmerBytesWritable(int k, byte[] storage, int offset) {
-        setNewReference(k, storage, offset);
-    }
-
-    public KmerBytesWritable(int k, String kmer) {
-        setNewReference(kmer.length(), kmer.getBytes(), 0);
+    /**
+     * set the *GLOBAL* kmer length to the given k value.
+     * NOTE: this will invalidate ALL previously created kmers. This function
+     * should be called before any kmers are created
+     */
+    public static void setGlobalKmerLength(int k) {
+        bytesUsed = KmerUtil.getByteNumFromK(k);
+        lettersInKmer = k;
     }
 
     /**
-     * Initial Kmer space by kmerlength
-     * 
-     * @param k
-     *            kmerlength
+     * Initialize as empty kmer
      */
-    public KmerBytesWritable(int k) {
-        this.kmerlength = k;
-        this.kmerByteSize = KmerUtil.getByteNumFromK(kmerlength);
-        if (k > 0) {
-            this.bytes = new byte[this.kmerByteSize];
-        } else {
-            this.bytes = EMPTY_BYTES;
-        }
-        this.offset = 0;
+    public KmerBytesWritable() {
+        bytes = new byte[bytesUsed];
+        offset = 0;
     }
 
-    public KmerBytesWritable(KmerBytesWritable right) {
-        this(right.kmerlength);
-        set(right);
+    /**
+     * Copy contents of kmer string
+     */
+    public KmerBytesWritable(String kmer) {
+        this();
+        setByRead(kmer.getBytes(), 0);
+    }
+
+    /**
+     * Set as reference to existing data
+     */
+    public KmerBytesWritable(byte[] newStorage, int newOffset) {
+        setAsReference(newStorage, newOffset);
+    }
+
+    /**
+     * copy kmer in other
+     * 
+     * @param other
+     */
+    public KmerBytesWritable(KmerBytesWritable other) {
+        this();
+        setAsCopy(other);
+    }
+    
+    /**
+     * copy kmer in other
+     * 
+     * @param other
+     */
+    public KmerBytesWritable(VKmerBytesWritable other) {
+        this();
+        setAsCopy(other);
     }
 
     /**
      * Deep copy of the given kmer
      * 
-     * @param newData
+     * @param other
      */
-    public void set(KmerBytesWritable newData) {
-        if (newData == null) {
-            this.set(0, EMPTY_BYTES, 0);
-        } else {
-            this.set(newData.kmerlength, newData.bytes, newData.getOffset());
+    public void setAsCopy(KmerBytesWritable other) {
+        if (lettersInKmer > 0) {
+            System.arraycopy(other.bytes, other.offset, bytes, offset, bytesUsed);
         }
     }
+    
+    /**
+     * Deep copy of the given kmer
+     * 
+     * @param other
+     */
+    public void setAsCopy(VKmerBytesWritable other) {
+        if (other.lettersInKmer != lettersInKmer) {
+            throw new IllegalArgumentException("Provided VKmer (" + other + ") is of an incompatible length (was " + other.getKmerLetterLength() + ", should be " + lettersInKmer + ")!");
+        }
+        if (lettersInKmer > 0) {
+            System.arraycopy(other.bytes, other.kmerStartOffset, bytes, offset, bytesUsed);
+        }
+    }
+
 
     /**
      * Deep copy of the given bytes data
-     * It will not change the kmerlength
+     * 
+     * @param newData
+     * @param newOffset
+     */
+    public void setAsCopy(byte[] newData, int newOffset) {
+        if (newData.length - newOffset < bytesUsed) {
+            throw new IllegalArgumentException("Requested " + bytesUsed + " bytes (k=" + lettersInKmer
+                    + ") but buffer has only " + (newData.length - newOffset) + " bytes");
+        }
+        System.arraycopy(newData, newOffset, bytes, offset, bytesUsed);
+    }
+
+    /**
+     * Point this datablock to the given bytes array It works like the pointer
+     * to new datablock.
+     * 
+     * @param newData
+     * @param newOffset
+     */
+    public void setAsReference(byte[] newData, int newOffset) {
+        if (newData.length - newOffset < bytesUsed) {
+            throw new IllegalArgumentException("Requested " + bytesUsed + " bytes (k=" + lettersInKmer
+                    + ") but buffer has only " + (newData.length - newOffset) + " bytes");
+        }
+        bytes = newData;
+        offset = newOffset;
+    }
+    
+    /**
+     * Point this datablock to the given kmer's byte array It works like the pointer
+     * to new datablock.
      * 
      * @param newData
      * @param offset
      */
-    public void set(byte[] newData, int offset) {
-        if (kmerlength > 0) {
-            System.arraycopy(newData, offset, bytes, this.offset, kmerByteSize);
+    public void setAsReference(VKmerBytesWritable other) {
+        if (other.lettersInKmer != lettersInKmer) {
+            throw new IllegalArgumentException("Provided VKmer (" + other + ") is of an incompatible length (was " + other.getKmerLetterLength() + ", should be " + lettersInKmer + ")!");
         }
+        bytes = other.bytes;
+        offset = other.kmerStartOffset;
     }
 
     /**
-     * Deep copy of the given data, and also set to new kmerlength
-     * 
-     * @param k
-     *            : new kmer length
-     * @param newData
-     *            : data storage
-     * @param offset
-     *            : start offset
-     */
-    public void set(int k, byte[] newData, int offset) {
-        reset(k);
-        if (k > 0) {
-            System.arraycopy(newData, offset, bytes, this.offset, kmerByteSize);
-        }
-    }
-
-    /**
-     * Reset array by kmerlength
-     * 
-     * @param k
-     */
-    public void reset(int k) {
-        this.kmerlength = k;
-        setSize(KmerUtil.getByteNumFromK(k));
-        clearLeadBit();
-    }
-
-    /**
-     * Point this datablock to the given bytes array
-     * It works like the pointer to new datablock.
-     * kmerlength will not change
-     * 
-     * @param newData
-     * @param offset
-     */
-    public void setNewReference(byte[] newData, int offset) {
-        this.bytes = newData;
-        this.offset = offset;
-        if (newData.length - offset < kmerByteSize) {
-            throw new IllegalArgumentException("Not given enough space");
-        }
-    }
-
-    /**
-     * Point this datablock to the given bytes array
-     * It works like the pointer to new datablock.
-     * It also set the new kmerlength
-     * 
-     * @param k
-     * @param newData
-     * @param offset
-     */
-    public void setNewReference(int k, byte[] newData, int offset) {
-        this.kmerlength = k;
-        this.kmerByteSize = KmerUtil.getByteNumFromK(k);
-        setNewReference(newData, offset);
-    }
-
-    protected void setSize(int size) {
-        if (size > getCapacity()) {
-            setCapacity((size * 3 / 2));
-        }
-        this.kmerByteSize = size;
-    }
-
-    protected int getCapacity() {
-        return bytes.length;
-    }
-
-    protected void setCapacity(int new_cap) {
-        if (new_cap != getCapacity()) {
-            byte[] new_data = new byte[new_cap];
-            if (new_cap < kmerByteSize) {
-                kmerByteSize = new_cap;
-            }
-            if (kmerByteSize != 0) {
-                System.arraycopy(bytes, offset, new_data, 0, kmerByteSize);
-            }
-            bytes = new_data;
-            offset = 0;
-        }
-    }
-
-    /**
-     * Get one genecode (A|G|C|T) from the given kmer index
-     * e.g. Get the 4th gene of the kmer ACGTA will return T
+     * Get one genecode (A|G|C|T) from the given kmer index e.g. Get the 4th
+     * gene of the kmer ACGTA will return T
      * 
      * @param pos
      * @return
      */
     public byte getGeneCodeAtPosition(int pos) {
-        if (pos >= kmerlength) {
-            throw new IllegalArgumentException("gene position out of bound");
+        if (pos >= lettersInKmer || pos < 0) {
+            throw new ArrayIndexOutOfBoundsException("Gene position (" + pos + ") out of bounds for k=" + lettersInKmer);
         }
         return geneCodeAtPosition(pos);
     }
-    
-    // unchecked version of above. Used when kmerlength is inaccurate (mid-merge)
+
+    /**
+     * unchecked version of getGeneCodeAtPosition. Used when kmerlength is
+     * inaccurate (mid-merge)
+     */
     private byte geneCodeAtPosition(int pos) {
         int posByte = pos / 4;
         int shift = (pos % 4) << 1;
-        return (byte) ((bytes[offset + kmerByteSize - 1 - posByte] >> shift) & 0x3);
+        return (byte) ((bytes[offset + bytesUsed - 1 - posByte] >> shift) & 0x3);
+    }
+
+    public static int getKmerLength() {
+        return lettersInKmer;
     }
     
-    public int getKmerLength() {
-        return this.kmerlength;
+    public static int getBytesPerKmer() {
+        return bytesUsed;
     }
 
     @Override
@@ -224,23 +209,22 @@
 
     @Override
     public int getLength() {
-        return kmerByteSize;
+        return bytesUsed;
     }
 
     /**
      * Read Kmer from read text into bytes array e.g. AATAG will compress as
      * [0x000G, 0xATAA]
      * 
-     * @param k
-     * @param array
+     * @param stringBytes
      * @param start
      */
-    public void setByRead(byte[] array, int start) {
+    public void setByRead(byte[] stringBytes, int start) {
         byte l = 0;
         int bytecount = 0;
-        int bcount = this.kmerByteSize - 1;
-        for (int i = start; i < start + kmerlength && i < array.length; i++) {
-            byte code = GeneCode.getCodeFromSymbol(array[i]);
+        int bcount = this.bytesUsed - 1;
+        for (int i = start; i < start + lettersInKmer && i < stringBytes.length; i++) {
+            byte code = GeneCode.getCodeFromSymbol(stringBytes[i]);
             l |= (byte) (code << bytecount);
             bytecount += 2;
             if (bytecount == 8) {
@@ -254,15 +238,9 @@
         }
     }
 
-    public void setByRead(int k, byte[] array, int start) {
-        reset(k);
-        setByRead(array, start);
-    }
-
     /**
-     * Compress Reversed read into bytes array
-     * e.g. AATAG will paired to CTATT, and then compress as
-     * [0x000T,0xTATC]
+     * Compress Reversed read into bytes array e.g. AATAG will paired to CTATT,
+     * and then compress as [0x000T,0xTATC]
      * 
      * @param input
      *            array
@@ -272,9 +250,10 @@
     public void setByReadReverse(byte[] array, int start) {
         byte l = 0;
         int bytecount = 0;
-        int bcount = kmerByteSize - 1;
-//        for (int i = start + kmerlength - 1; i >= 0 && i < array.length; i--) {
-        for (int i = start + kmerlength - 1; i >= start && i < array.length; i--) {
+        int bcount = bytesUsed - 1;
+        // for (int i = start + kmerlength - 1; i >= 0 && i < array.length; i--)
+        // {
+        for (int i = start + lettersInKmer - 1; i >= start && i < array.length; i--) {
             byte code = GeneCode.getPairedCodeFromSymbol(array[i]);
             l |= (byte) (code << bytecount);
             bytecount += 2;
@@ -289,11 +268,6 @@
         }
     }
 
-    public void setByReadReverse(int k, byte[] array, int start) {
-        reset(k);
-        setByReadReverse(array, start);
-    }
-
     /**
      * Shift Kmer to accept new char input
      * 
@@ -313,12 +287,12 @@
      * @return the shift out gene, in gene code format
      */
     public byte shiftKmerWithNextCode(byte c) {
-        byte output = (byte) (bytes[offset + kmerByteSize - 1] & 0x03);
-        for (int i = kmerByteSize - 1; i > 0; i--) {
+        byte output = (byte) (bytes[offset + bytesUsed - 1] & 0x03);
+        for (int i = bytesUsed - 1; i > 0; i--) {
             byte in = (byte) (bytes[offset + i - 1] & 0x03);
             bytes[offset + i] = (byte) (((bytes[offset + i] >>> 2) & 0x3f) | (in << 6));
         }
-        int pos = ((kmerlength - 1) % 4) << 1;
+        int pos = ((lettersInKmer - 1) % 4) << 1;
         byte code = (byte) (c << pos);
         bytes[offset] = (byte) (((bytes[offset] >>> 2) & 0x3f) | code);
         clearLeadBit();
@@ -344,152 +318,17 @@
      * @return the shiftout gene, in gene code format
      */
     public byte shiftKmerWithPreCode(byte c) {
-        int pos = ((kmerlength - 1) % 4) << 1;
+        int pos = ((lettersInKmer - 1) % 4) << 1;
         byte output = (byte) ((bytes[offset] >> pos) & 0x03);
-        for (int i = 0; i < kmerByteSize - 1; i++) {
+        for (int i = 0; i < bytesUsed - 1; i++) {
             byte in = (byte) ((bytes[offset + i + 1] >> 6) & 0x03);
             bytes[offset + i] = (byte) ((bytes[offset + i] << 2) | in);
         }
-        bytes[offset + kmerByteSize - 1] = (byte) ((bytes[offset + kmerByteSize - 1] << 2) | c);
+        bytes[offset + bytesUsed - 1] = (byte) ((bytes[offset + bytesUsed - 1] << 2) | c);
         clearLeadBit();
         return output;
     }
 
-    /**
-     * Merge Kmer with the next connected Kmer
-     * e.g. AAGCTAA merge with AACAACC, if the initial kmerSize = 3
-     * then it will return AAGCTAACAACC
-     * 
-     * @param initialKmerSize
-     *            : the initial kmerSize
-     * @param kmer
-     *            : the next kmer
-     */
-    public void mergeWithFFKmer(int initialKmerSize, KmerBytesWritable kmer) {
-        int preKmerLength = kmerlength;
-        int preSize = kmerByteSize;
-        this.kmerlength += kmer.kmerlength - initialKmerSize + 1;
-        setSize(KmerUtil.getByteNumFromK(kmerlength));
-        for (int i = 1; i <= preSize; i++) {
-            bytes[offset + kmerByteSize - i] = bytes[offset + preSize - i];
-        }
-        for (int k = initialKmerSize - 1; k < kmer.getKmerLength(); k += 4) {
-            byte onebyte = getOneByteFromKmerAtPosition(k, kmer.getBytes(), kmer.getOffset(), kmer.getLength());
-            appendOneByteAtPosition(preKmerLength + k - initialKmerSize + 1, onebyte, bytes, offset, kmerByteSize);
-        }
-        clearLeadBit();
-    }
-
-    /**
-     * Merge Kmer with the next connected Kmer, when that Kmer needs to be reverse-complemented
-     * e.g. AAGCTAA merge with GGTTGTT, if the initial kmerSize = 3
-     * then it will return AAGCTAACAACC
-     * 
-     * A merge B =>  A B~
-     * 
-     * @param initialKmerSize
-     *            : the initial kmerSize
-     * @param kmer
-     *            : the next kmer
-     */
-    public void mergeWithFRKmer(int initialKmerSize, KmerBytesWritable kmer) {
-        int preSize = kmerByteSize;
-        int preKmerLength = kmerlength;
-        this.kmerlength += kmer.kmerlength - initialKmerSize + 1;
-        setSize(KmerUtil.getByteNumFromK(kmerlength));
-        // copy prefix into right-side of buffer
-        for (int i = 1; i <= preSize; i++) {
-            bytes[offset + kmerByteSize - i] = bytes[offset + preSize - i];
-        }
-
-        int bytecount = (preKmerLength % 4) * 2;
-        int bcount = kmerByteSize - preSize - bytecount / 8; // may overlap previous kmer
-        byte l = bcount == kmerByteSize - preSize ? bytes[offset + bcount] : 0x00;
-        bytecount %= 8;
-        for (int i = kmer.kmerlength - initialKmerSize; i >= 0; i--) {
-            byte code = GeneCode.getPairedGeneCode(kmer.getGeneCodeAtPosition(i));
-            l |= (byte) (code << bytecount);
-            bytecount += 2;
-            if (bytecount == 8) {
-                bytes[offset + bcount--] = l;
-                l = 0;
-                bytecount = 0;
-            }
-        }
-        if (bcount >= 0) {
-            bytes[offset] = l;
-        }
-    }
-
-    /**
-     * Merge Kmer with the previous connected Kmer, when that kmer needs to be reverse-complemented
-     * e.g. AACAACC merge with TTCTGCC, if the initial kmerSize = 3
-     * then it will return GGCAGAACAACC
-     * 
-     * @param initialKmerSize
-     *            : the initial kmerSize
-     * @param preKmer
-     *            : the previous kmer
-     */
-    public void mergeWithRFKmer(int initialKmerSize, KmerBytesWritable preKmer) {
-        KmerBytesWritable reversed = new KmerBytesWritable(preKmer.kmerlength);
-        reversed.setByReadReverse(preKmer.toString().getBytes(), 0);
-        mergeWithRRKmer(initialKmerSize, reversed);
-    }
-
-    /**
-     * Merge Kmer with the previous connected Kmer
-     * e.g. AACAACC merge with AAGCTAA, if the initial kmerSize = 3
-     * then it will return AAGCTAACAACC
-     * 
-     * @param initialKmerSize
-     *            : the initial kmerSize
-     * @param preKmer
-     *            : the previous kmer
-     */
-    public void mergeWithRRKmer(int initialKmerSize, KmerBytesWritable preKmer) {
-        int preKmerLength = kmerlength;
-        int preSize = kmerByteSize;
-        this.kmerlength += preKmer.kmerlength - initialKmerSize + 1;
-        setSize(KmerUtil.getByteNumFromK(kmerlength));
-        byte cacheByte = getOneByteFromKmerAtPosition(0, bytes, offset, preSize);
-
-        // copy prekmer
-        for (int k = 0; k < preKmer.kmerlength - initialKmerSize + 1; k += 4) {
-            byte onebyte = getOneByteFromKmerAtPosition(k, preKmer.bytes, preKmer.offset, preKmer.kmerByteSize);
-            appendOneByteAtPosition(k, onebyte, bytes, offset, kmerByteSize);
-        }
-
-        // copy current kmer
-        int k = 4;
-        for (; k < preKmerLength; k += 4) {
-            byte onebyte = getOneByteFromKmerAtPosition(k, bytes, offset, preSize);
-            appendOneByteAtPosition(preKmer.kmerlength - initialKmerSize + k - 4 + 1, cacheByte, bytes, offset, kmerByteSize);
-            cacheByte = onebyte;
-        }
-        appendOneByteAtPosition(preKmer.kmerlength - initialKmerSize + k - 4 + 1, cacheByte, bytes, offset, kmerByteSize);
-        clearLeadBit();
-    }
-    
-    public void mergeWithKmerInDir(byte dir, int initialKmerSize, KmerBytesWritable kmer) {
-        switch(dir & DirectionFlag.DIR_MASK) {
-            case DirectionFlag.DIR_FF:
-                mergeWithFFKmer(initialKmerSize, kmer);
-                break;
-            case DirectionFlag.DIR_FR:
-                mergeWithFRKmer(initialKmerSize, kmer);
-                break;
-            case DirectionFlag.DIR_RF:
-                mergeWithRFKmer(initialKmerSize, kmer);
-                break;
-            case DirectionFlag.DIR_RR:
-                mergeWithRRKmer(initialKmerSize, kmer);
-                break;
-            default:
-                throw new RuntimeException("Direciotn not recognized: " + dir);
-        }
-    }
-
     public static void appendOneByteAtPosition(int k, byte onebyte, byte[] buffer, int start, int length) {
         int position = start + length - 1 - k / 4;
         if (position < start) {
@@ -518,63 +357,53 @@
     }
 
     protected void clearLeadBit() {
-        if (kmerlength % 4 != 0) {
-            bytes[offset] &= (1 << ((kmerlength % 4) << 1)) - 1;
+        if (lettersInKmer % 4 != 0) {
+            bytes[offset] &= (1 << ((lettersInKmer % 4) << 1)) - 1;
         }
     }
 
     @Override
     public void readFields(DataInput in) throws IOException {
-        this.kmerlength = in.readInt();
-        this.kmerByteSize = KmerUtil.getByteNumFromK(kmerlength);
-        if (this.kmerlength > 0) {
-            if (this.bytes.length < this.kmerByteSize) {
-                this.bytes = new byte[this.kmerByteSize];
-                this.offset = 0;
-            }
-            in.readFully(bytes, offset, kmerByteSize);
-        }
+        in.readFully(bytes, offset, bytesUsed);
     }
 
     @Override
     public void write(DataOutput out) throws IOException {
-        out.writeInt(kmerlength);
-        if (kmerlength > 0) {
-            out.write(bytes, offset, kmerByteSize);
-        }
+        out.write(bytes, offset, bytesUsed);
     }
 
     @Override
     public int hashCode() {
-        return super.hashCode() * 31 + this.kmerlength;
+        return Marshal.hashBytes(bytes, offset, bytesUsed);
     }
 
     @Override
     public boolean equals(Object right_obj) {
-        if (right_obj instanceof KmerBytesWritable)
-            return this.kmerlength == ((KmerBytesWritable) right_obj).kmerlength && super.equals(right_obj);
+        if (right_obj instanceof KmerBytesWritable) {
+            // since these may be backed by storage of different sizes, we have to manually check each byte
+            KmerBytesWritable right = (KmerBytesWritable) right_obj;
+            for (int i=0; i < bytesUsed; i++) {
+                if (bytes[offset + i] != right.bytes[right.offset + i]) {
+                    return false;
+                }
+            }
+            return true;
+        }
         return false;
     }
 
     @Override
     public String toString() {
-        return KmerUtil.recoverKmerFrom(this.kmerlength, this.getBytes(), offset, this.getLength());
+        return KmerUtil.recoverKmerFrom(lettersInKmer, bytes, offset, bytesUsed);
     }
 
     public static class Comparator extends WritableComparator {
-        public final int LEAD_BYTES = 4;
-
         public Comparator() {
             super(KmerBytesWritable.class);
         }
 
         public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) {
-            int kmerlength1 = readInt(b1, s1);
-            int kmerlength2 = readInt(b2, s2);
-            if (kmerlength1 == kmerlength2) {
-                return compareBytes(b1, s1 + LEAD_BYTES, l1 - LEAD_BYTES, b2, s2 + LEAD_BYTES, l2 - LEAD_BYTES);
-            }
-            return kmerlength1 - kmerlength2;
+            return compareBytes(b1, s1, l1, b2, s2, l2);
         }
     }
 
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java
index d2e3a94..16df821 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java
@@ -16,10 +16,10 @@
 package edu.uci.ics.genomix.type;
 
 public class KmerBytesWritableFactory {
-    private KmerBytesWritable kmer;
+    private VKmerBytesWritable kmer;
 
     public KmerBytesWritableFactory(int k) {
-        kmer = new KmerBytesWritable(k);
+        kmer = new VKmerBytesWritable(k);
     }
 
     /**
@@ -30,7 +30,7 @@
      * @param array
      * @param start
      */
-    public KmerBytesWritable getKmerByRead(int k, byte[] array, int start) {
+    public VKmerBytesWritable getKmerByRead(int k, byte[] array, int start) {
         kmer.reset(k);
         kmer.setByRead(array, start);
         return kmer;
@@ -43,7 +43,7 @@
      * @param array
      * @param start
      */
-    public KmerBytesWritable getKmerByReadReverse(int k, byte[] array, int start) {
+    public VKmerBytesWritable getKmerByReadReverse(int k, byte[] array, int start) {
         kmer.reset(k);
         kmer.setByReadReverse(array, start);
         return kmer;
@@ -59,28 +59,28 @@
      * @param kmerChain
      * @return LastKmer bytes array
      */
-    public KmerBytesWritable getLastKmerFromChain(int lastK, final KmerBytesWritable kmerChain) {
-        if (lastK > kmerChain.getKmerLength()) {
+    public VKmerBytesWritable getLastKmerFromChain(int lastK, final VKmerBytesWritable kmerChain) {
+        if (lastK > kmerChain.getKmerLetterLength()) {
             return null;
         }
-        if (lastK == kmerChain.getKmerLength()) {
-            kmer.set(kmerChain);
+        if (lastK == kmerChain.getKmerLetterLength()) {
+            kmer.setAsCopy(kmerChain);
             return kmer;
         }
         kmer.reset(lastK);
 
         /** from end to start */
-        int byteInChain = kmerChain.getLength() - 1 - (kmerChain.getKmerLength() - lastK) / 4;
-        int posInByteOfChain = ((kmerChain.getKmerLength() - lastK) % 4) << 1; // *2
-        int byteInKmer = kmer.getLength() - 1;
+        int byteInChain = kmerChain.getKmerByteLength() - 1 - (kmerChain.getKmerLetterLength() - lastK) / 4;
+        int posInByteOfChain = ((kmerChain.getKmerLetterLength() - lastK) % 4) << 1; // *2
+        int byteInKmer = kmer.getKmerByteLength() - 1;
         for (; byteInKmer >= 0 && byteInChain > 0; byteInKmer--, byteInChain--) {
-            kmer.getBytes()[byteInKmer] = (byte) ((0xff & kmerChain.getBytes()[byteInChain]) >> posInByteOfChain);
-            kmer.getBytes()[byteInKmer] |= ((kmerChain.getBytes()[byteInChain - 1] << (8 - posInByteOfChain)));
+            kmer.getBytes()[byteInKmer + kmer.getKmerOffset()] = (byte) ((0xff & kmerChain.getBytes()[byteInChain + kmerChain.getKmerOffset()]) >> posInByteOfChain);
+            kmer.getBytes()[byteInKmer + kmer.getKmerOffset()] |= ((kmerChain.getBytes()[byteInChain  + kmerChain.getKmerOffset() - 1] << (8 - posInByteOfChain)));
         }
 
         /** last kmer byte */
         if (byteInKmer == 0) {
-            kmer.getBytes()[0] = (byte) ((kmerChain.getBytes()[0] & 0xff) >> posInByteOfChain);
+            kmer.getBytes()[0 + kmer.getKmerOffset()] = (byte) ((kmerChain.getBytes()[0 + kmerChain.getKmerOffset()] & 0xff) >> posInByteOfChain);
         }
         kmer.clearLeadBit();
         return kmer;
@@ -95,52 +95,52 @@
      * @param kmerChain
      * @return FirstKmer bytes array
      */
-    public KmerBytesWritable getFirstKmerFromChain(int firstK, final KmerBytesWritable kmerChain) {
-        if (firstK > kmerChain.getKmerLength()) {
+    public VKmerBytesWritable getFirstKmerFromChain(int firstK, final VKmerBytesWritable kmerChain) {
+        if (firstK > kmerChain.getKmerLetterLength()) {
             return null;
         }
-        if (firstK == kmerChain.getKmerLength()) {
-            kmer.set(kmerChain);
+        if (firstK == kmerChain.getKmerLetterLength()) {
+            kmer.setAsCopy(kmerChain);
             return kmer;
         }
         kmer.reset(firstK);
 
         int i = 1;
-        for (; i < kmer.getLength(); i++) {
-            kmer.getBytes()[kmer.getLength() - i] = kmerChain.getBytes()[kmerChain.getLength() - i];
+        for (; i < kmer.getKmerByteLength(); i++) {
+            kmer.getBytes()[kmer.getKmerOffset() + kmer.getKmerByteLength() - i] = kmerChain.getBytes()[kmerChain.getKmerOffset() + kmerChain.getKmerByteLength() - i];
         }
         int posInByteOfChain = (firstK % 4) << 1; // *2
         if (posInByteOfChain == 0) {
-            kmer.getBytes()[0] = kmerChain.getBytes()[kmerChain.getLength() - i];
+            kmer.getBytes()[0 + kmer.getKmerOffset()] = kmerChain.getBytes()[kmerChain.getKmerOffset() + kmerChain.getKmerByteLength() - i];
         } else {
-            kmer.getBytes()[0] = (byte) (kmerChain.getBytes()[kmerChain.getLength() - i] & ((1 << posInByteOfChain) - 1));
+            kmer.getBytes()[0 + kmer.getKmerOffset()] = (byte) (kmerChain.getBytes()[kmerChain.getKmerOffset() + kmerChain.getKmerByteLength() - i] & ((1 << posInByteOfChain) - 1));
         }
         kmer.clearLeadBit();
         return kmer;
     }
 
-    public KmerBytesWritable getSubKmerFromChain(int startK, int kSize, final KmerBytesWritable kmerChain) {
-        if (startK + kSize > kmerChain.getKmerLength()) {
+    public VKmerBytesWritable getSubKmerFromChain(int startK, int kSize, final VKmerBytesWritable kmerChain) {
+        if (startK + kSize > kmerChain.getKmerLetterLength()) {
             return null;
         }
-        if (startK == 0 && kSize == kmerChain.getKmerLength()) {
-            kmer.set(kmerChain);
+        if (startK == 0 && kSize == kmerChain.getKmerLetterLength()) {
+            kmer.setAsCopy(kmerChain);
             return kmer;
         }
         kmer.reset(kSize);
 
         /** from end to start */
-        int byteInChain = kmerChain.getLength() - 1 - startK / 4;
+        int byteInChain = kmerChain.getKmerByteLength() - 1 - startK / 4;
         int posInByteOfChain = startK % 4 << 1; // *2
-        int byteInKmer = kmer.getLength() - 1;
+        int byteInKmer = kmer.getKmerByteLength() - 1;
         for (; byteInKmer >= 0 && byteInChain > 0; byteInKmer--, byteInChain--) {
-            kmer.getBytes()[byteInKmer] = (byte) ((0xff & kmerChain.getBytes()[byteInChain]) >> posInByteOfChain);
-            kmer.getBytes()[byteInKmer] |= ((kmerChain.getBytes()[byteInChain - 1] << (8 - posInByteOfChain)));
+            kmer.getBytes()[byteInKmer + kmer.getKmerOffset()] = (byte) ((0xff & kmerChain.getBytes()[byteInChain + kmerChain.getKmerOffset()]) >> posInByteOfChain);
+            kmer.getBytes()[byteInKmer + kmer.getKmerOffset()] |= ((kmerChain.getBytes()[byteInChain + kmerChain.getKmerOffset() - 1] << (8 - posInByteOfChain)));
         }
 
         /** last kmer byte */
         if (byteInKmer == 0) {
-            kmer.getBytes()[0] = (byte) ((kmerChain.getBytes()[0] & 0xff) >> posInByteOfChain);
+            kmer.getBytes()[0 + kmer.getKmerOffset()] = (byte) ((kmerChain.getBytes()[0 + kmerChain.getKmerOffset()] & 0xff) >> posInByteOfChain);
         }
         kmer.clearLeadBit();
         return kmer;
@@ -159,15 +159,15 @@
      *            : next neighbor in gene-code format
      * @return the merged Kmer, this K of this Kmer is k+1
      */
-    public KmerBytesWritable mergeKmerWithNextCode(final KmerBytesWritable kmer, byte nextCode) {
-        this.kmer.reset(kmer.getKmerLength() + 1);
-        for (int i = 1; i <= kmer.getLength(); i++) {
-            this.kmer.getBytes()[this.kmer.getLength() - i] = kmer.getBytes()[kmer.getLength() - i];
+    public VKmerBytesWritable mergeKmerWithNextCode(final VKmerBytesWritable kmer, byte nextCode) {
+        this.kmer.reset(kmer.getKmerLetterLength() + 1);
+        for (int i = 1; i <= kmer.getKmerByteLength(); i++) {
+            this.kmer.getBytes()[this.kmer.getKmerOffset() + this.kmer.getKmerByteLength() - i] = kmer.getBytes()[kmer.getKmerOffset() + kmer.getKmerByteLength() - i];
         }
-        if (this.kmer.getLength() > kmer.getLength()) {
-            this.kmer.getBytes()[0] = (byte) (nextCode & 0x3);
+        if (this.kmer.getKmerByteLength() > kmer.getKmerByteLength()) {
+            this.kmer.getBytes()[0 + kmer.getKmerOffset()] = (byte) (nextCode & 0x3);
         } else {
-            this.kmer.getBytes()[0] = (byte) (kmer.getBytes()[0] | ((nextCode & 0x3) << ((kmer.getKmerLength() % 4) << 1)));
+            this.kmer.getBytes()[0 + kmer.getKmerOffset()] = (byte) (kmer.getBytes()[0 + kmer.getKmerOffset()] | ((nextCode & 0x3) << ((kmer.getKmerLetterLength() % 4) << 1)));
         }
         this.kmer.clearLeadBit();
         return this.kmer;
@@ -186,17 +186,17 @@
      *            : next neighbor in gene-code format
      * @return the merged Kmer,this K of this Kmer is k+1
      */
-    public KmerBytesWritable mergeKmerWithPreCode(final KmerBytesWritable kmer, byte preCode) {
-        this.kmer.reset(kmer.getKmerLength() + 1);
+    public VKmerBytesWritable mergeKmerWithPreCode(final VKmerBytesWritable kmer, byte preCode) {
+        this.kmer.reset(kmer.getKmerLetterLength() + 1);
         int byteInMergedKmer = 0;
-        if (kmer.getKmerLength() % 4 == 0) {
-            this.kmer.getBytes()[0] = (byte) ((kmer.getBytes()[0] >> 6) & 0x3);
+        if (kmer.getKmerLetterLength() % 4 == 0) {
+            this.kmer.getBytes()[0 + kmer.getKmerOffset()] = (byte) ((kmer.getBytes()[0 + kmer.getKmerOffset()] >> 6) & 0x3);
             byteInMergedKmer++;
         }
-        for (int i = 0; i < kmer.getLength() - 1; i++, byteInMergedKmer++) {
-            this.kmer.getBytes()[byteInMergedKmer] = (byte) ((kmer.getBytes()[i] << 2) | ((kmer.getBytes()[i + 1] >> 6) & 0x3));
+        for (int i = 0; i < kmer.getKmerByteLength() - 1; i++, byteInMergedKmer++) {
+            this.kmer.getBytes()[byteInMergedKmer + kmer.getKmerOffset()] = (byte) ((kmer.getBytes()[i + kmer.getKmerOffset()] << 2) | ((kmer.getBytes()[i + kmer.getKmerOffset() + 1] >> 6) & 0x3));
         }
-        this.kmer.getBytes()[byteInMergedKmer] = (byte) ((kmer.getBytes()[kmer.getLength() - 1] << 2) | (preCode & 0x3));
+        this.kmer.getBytes()[byteInMergedKmer + kmer.getKmerOffset()] = (byte) ((kmer.getBytes()[kmer.getKmerOffset() + kmer.getKmerByteLength() - 1] << 2) | (preCode & 0x3));
         this.kmer.clearLeadBit();
         return this.kmer;
     }
@@ -215,28 +215,28 @@
      *            : bytes array of next kmer
      * @return merged kmer, the new k is @preK + @nextK
      */
-    public KmerBytesWritable mergeTwoKmer(final KmerBytesWritable preKmer, final KmerBytesWritable nextKmer) {
-        kmer.reset(preKmer.getKmerLength() + nextKmer.getKmerLength());
+    public VKmerBytesWritable mergeTwoKmer(final VKmerBytesWritable preKmer, final VKmerBytesWritable nextKmer) {
+        kmer.reset(preKmer.getKmerLetterLength() + nextKmer.getKmerLetterLength());
         int i = 1;
-        for (; i <= preKmer.getLength(); i++) {
-            kmer.getBytes()[kmer.getLength() - i] = preKmer.getBytes()[preKmer.getLength() - i];
+        for (; i <= preKmer.getKmerByteLength(); i++) {
+            kmer.getBytes()[kmer.getKmerOffset() + kmer.getKmerByteLength() - i] = preKmer.getBytes()[preKmer.getKmerOffset() + preKmer.getKmerByteLength() - i];
         }
         if (i > 1) {
             i--;
         }
-        if (preKmer.getKmerLength() % 4 == 0) {
-            for (int j = 1; j <= nextKmer.getLength(); j++) {
-                kmer.getBytes()[kmer.getLength() - i - j] = nextKmer.getBytes()[nextKmer.getLength() - j];
+        if (preKmer.getKmerLetterLength() % 4 == 0) {
+            for (int j = 1; j <= nextKmer.getKmerByteLength(); j++) {
+                kmer.getBytes()[kmer.getKmerOffset() + kmer.getKmerByteLength() - i - j] = nextKmer.getBytes()[nextKmer.getKmerOffset() + nextKmer.getKmerByteLength() - j];
             }
         } else {
-            int posNeedToMove = ((preKmer.getKmerLength() % 4) << 1);
-            kmer.getBytes()[kmer.getLength() - i] |= nextKmer.getBytes()[nextKmer.getLength() - 1] << posNeedToMove;
-            for (int j = 1; j < nextKmer.getLength(); j++) {
-                kmer.getBytes()[kmer.getLength() - i - j] = (byte) (((nextKmer.getBytes()[nextKmer.getLength() - j] & 0xff) >> (8 - posNeedToMove)) | (nextKmer
-                        .getBytes()[nextKmer.getLength() - j - 1] << posNeedToMove));
+            int posNeedToMove = ((preKmer.getKmerLetterLength() % 4) << 1);
+            kmer.getBytes()[kmer.getKmerOffset() + kmer.getKmerByteLength() - i] |= nextKmer.getBytes()[nextKmer.getKmerOffset() + nextKmer.getKmerByteLength() - 1] << posNeedToMove;
+            for (int j = 1; j < nextKmer.getKmerByteLength(); j++) {
+                kmer.getBytes()[kmer.getKmerOffset() + kmer.getKmerByteLength() - i - j] = (byte) (((nextKmer.getBytes()[nextKmer.getKmerOffset() + nextKmer.getKmerByteLength() - j] & 0xff) >> (8 - posNeedToMove)) | (nextKmer
+                        .getBytes()[nextKmer.getKmerOffset() + nextKmer.getKmerByteLength() - j - 1] << posNeedToMove));
             }
-            if (nextKmer.getKmerLength() % 4 == 0 || (nextKmer.getKmerLength() % 4) * 2 + posNeedToMove > 8) {
-                kmer.getBytes()[0] = (byte) ((0xff & nextKmer.getBytes()[0]) >> (8 - posNeedToMove));
+            if (nextKmer.getKmerLetterLength() % 4 == 0 || (nextKmer.getKmerLetterLength() % 4) * 2 + posNeedToMove > 8) {
+                kmer.getBytes()[0 + kmer.getKmerOffset()] = (byte) ((0xff & nextKmer.getBytes()[0 + nextKmer.getKmerOffset()]) >> (8 - posNeedToMove));
             }
         }
         kmer.clearLeadBit();
@@ -255,8 +255,8 @@
      *            : input genecode
      * @return new created kmer that shifted by afterCode, the K will not change
      */
-    public KmerBytesWritable shiftKmerWithNextCode(final KmerBytesWritable kmer, byte afterCode) {
-        this.kmer.set(kmer);
+    public VKmerBytesWritable shiftKmerWithNextCode(final VKmerBytesWritable kmer, byte afterCode) {
+        this.kmer.setAsCopy(kmer);
         this.kmer.shiftKmerWithNextCode(afterCode);
         return this.kmer;
     }
@@ -273,8 +273,8 @@
      *            : input genecode
      * @return new created kmer that shifted by preCode, the K will not change
      */
-    public KmerBytesWritable shiftKmerWithPreCode(final KmerBytesWritable kmer, byte preCode) {
-        this.kmer.set(kmer);
+    public VKmerBytesWritable shiftKmerWithPreCode(final VKmerBytesWritable kmer, byte preCode) {
+        this.kmer.setAsCopy(kmer);
         this.kmer.shiftKmerWithPreCode(preCode);
         return this.kmer;
     }
@@ -284,22 +284,22 @@
      * 
      * @param kmer
      */
-    public KmerBytesWritable reverse(final KmerBytesWritable kmer) {
-        this.kmer.reset(kmer.getKmerLength());
+    public VKmerBytesWritable reverse(final VKmerBytesWritable kmer) {
+        this.kmer.reset(kmer.getKmerLetterLength());
 
-        int curPosAtKmer = ((kmer.getKmerLength() - 1) % 4) << 1;
+        int curPosAtKmer = ((kmer.getKmerLetterLength() - 1) % 4) << 1;
         int curByteAtKmer = 0;
 
         int curPosAtReverse = 0;
-        int curByteAtReverse = this.kmer.getLength() - 1;
-        this.kmer.getBytes()[curByteAtReverse] = 0;
-        for (int i = 0; i < kmer.getKmerLength(); i++) {
-            byte gene = (byte) ((kmer.getBytes()[curByteAtKmer] >> curPosAtKmer) & 0x03);
-            this.kmer.getBytes()[curByteAtReverse] |= gene << curPosAtReverse;
+        int curByteAtReverse = this.kmer.getKmerByteLength() - 1;
+        this.kmer.getBytes()[curByteAtReverse + this.kmer.getKmerOffset()] = 0;
+        for (int i = 0; i < kmer.getKmerLetterLength(); i++) {
+            byte gene = (byte) ((kmer.getBytes()[curByteAtKmer + kmer.getKmerOffset()] >> curPosAtKmer) & 0x03);
+            this.kmer.getBytes()[curByteAtReverse + this.kmer.getKmerOffset()] |= gene << curPosAtReverse;
             curPosAtReverse += 2;
             if (curPosAtReverse >= 8) {
                 curPosAtReverse = 0;
-                this.kmer.getBytes()[--curByteAtReverse] = 0;
+                this.kmer.getBytes()[--curByteAtReverse + this.kmer.getKmerOffset()] = 0;
             }
             curPosAtKmer -= 2;
             if (curPosAtKmer < 0) {
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java
deleted file mode 100644
index 1d8d871..0000000
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java
+++ /dev/null
@@ -1,244 +0,0 @@
-package edu.uci.ics.genomix.type;
-
-import java.io.DataInput;
-import java.io.DataOutput;
-import java.io.IOException;
-import java.io.Serializable;
-import java.util.Iterator;
-import java.util.List;
-
-import org.apache.hadoop.io.BinaryComparable;
-import org.apache.hadoop.io.Writable;
-
-import edu.uci.ics.genomix.data.KmerUtil;
-import edu.uci.ics.genomix.data.Marshal;
-
-public class KmerListWritable extends BinaryComparable
-    implements Writable, Iterable<KmerBytesWritable>, Serializable{
-    private static final long serialVersionUID = 1L;
-    protected byte[] storage;
-    protected int offset;
-    protected int valueCount;
-    public int kmerByteSize = 0; 
-    public int kmerlength = 0;
-    protected static final byte[] EMPTY = {};
-    
-    protected KmerBytesWritable posIter = new KmerBytesWritable();
-    
-    public KmerListWritable() {
-        this.storage = EMPTY;
-        this.valueCount = 0;
-        this.offset = 0;
-    }
-    
-    public KmerListWritable(int kmerlength) {
-        this();
-        this.kmerlength = kmerlength;
-        this.kmerByteSize = KmerUtil.getByteNumFromK(kmerlength);
-    }
-    
-    public KmerListWritable(int kmerlength, int count, byte[] data, int offset) {
-        this.kmerlength = kmerlength;
-        this.kmerByteSize = KmerUtil.getByteNumFromK(kmerlength);
-        setNewReference(count, data, offset);
-    }
-    
-    public KmerListWritable(List<KmerBytesWritable> kmers) {
-        this();
-        setSize(kmers.size());  // reserve space for all elements
-        for (KmerBytesWritable kmer : kmers) {
-            append(kmer);
-        }
-    }
-    
-    public void setNewReference(int count, byte[] data, int offset) {
-        this.valueCount = count;
-        this.storage = data;
-        this.offset = offset;
-    }
-    
-    public void append(KmerBytesWritable kmer){
-        if(kmer != null){
-            kmerByteSize = kmer.kmerByteSize;
-            kmerlength = kmer.kmerlength;
-            setSize((1 + valueCount) * kmerByteSize); 
-            System.arraycopy(kmer.getBytes(), 0, storage, offset + valueCount * kmerByteSize, kmerByteSize);
-            valueCount += 1;
-        }
-    }
-    
-    /*
-     * Append the otherList to the end of myList
-     */
-    public void appendList(KmerListWritable otherList) {
-        if (otherList.valueCount > 0) {
-            setSize((valueCount + otherList.valueCount) * kmerByteSize);
-            // copy contents of otherList into the end of my storage
-            System.arraycopy(otherList.storage, otherList.offset,
-                    storage, offset + valueCount * kmerByteSize, 
-                    otherList.valueCount * kmerByteSize);
-            valueCount += otherList.valueCount;
-        }
-    }
-    
-    protected void setSize(int size) {
-        if (size > getCapacity()) {
-            setCapacity((size * 3 / 2));
-        }
-    }
-    
-    protected int getCapacity() {
-        return storage.length - offset;
-    }
-
-    protected void setCapacity(int new_cap) {
-        if (new_cap > getCapacity()) {
-            byte[] new_data = new byte[new_cap];
-            if (storage.length - offset > 0) {
-                System.arraycopy(storage, offset, new_data, 0, storage.length - offset);
-            }
-            storage = new_data;
-            offset = 0;
-        }
-    }
-    
-    public void reset() {
-        this.reset(0);
-    }
-    
-    public void reset(int kmerSize) {
-        kmerlength = kmerSize;
-        kmerByteSize = KmerUtil.getByteNumFromK(kmerlength);
-        storage = EMPTY;
-        valueCount = 0;
-        offset = 0;
-    }
-    
-    public KmerBytesWritable getPosition(int i) {
-        if (i >= valueCount) {
-            throw new ArrayIndexOutOfBoundsException("No such positions");
-        }
-        posIter.setNewReference(kmerlength, storage, offset + i * kmerByteSize);
-        return posIter;
-    }
-    
-    public void set(KmerListWritable otherList) {
-        this.kmerlength = otherList.kmerlength;
-        this.kmerByteSize = otherList.kmerByteSize;
-        set(otherList.valueCount, otherList.storage, otherList.offset);
-    }
-
-    public void set(int valueCount, byte[] newData, int offset) {
-        this.valueCount = valueCount;
-        setSize(valueCount * kmerByteSize);
-        if (valueCount > 0) {
-            System.arraycopy(newData, offset, storage, this.offset, valueCount * kmerByteSize);
-        }
-    }
-    
-    @Override
-    public Iterator<KmerBytesWritable> iterator() {
-        Iterator<KmerBytesWritable> it = new Iterator<KmerBytesWritable>() {
-
-            private int currentIndex = 0;
-
-            @Override
-            public boolean hasNext() {
-                return currentIndex < valueCount;
-            }
-
-            @Override
-            public KmerBytesWritable next() {
-                return getPosition(currentIndex++);
-            }
-
-            @Override
-            public void remove() {
-                if(currentIndex < valueCount)
-                    System.arraycopy(storage, offset + currentIndex * kmerByteSize, 
-                          storage, offset + (currentIndex - 1) * kmerByteSize, 
-                          (valueCount - currentIndex) * kmerByteSize);
-                valueCount--;
-                currentIndex--;
-            }
-        };
-        return it;
-    }
-    
-    /*
-     * remove the first instance of @toRemove. Uses a linear scan.  Throws an exception if not in this list.
-     */
-    public void remove(KmerBytesWritable toRemove, boolean ignoreMissing) {
-        Iterator<KmerBytesWritable> posIterator = this.iterator();
-        while (posIterator.hasNext()) {
-            if(toRemove.equals(posIterator.next())) {
-                posIterator.remove();
-                return;
-            }
-        }
-        if (!ignoreMissing) {
-            throw new ArrayIndexOutOfBoundsException("the KmerBytesWritable `" + toRemove.toString() + "` was not found in this list.");
-        }
-    }
-    
-    public void remove(KmerBytesWritable toRemove) {
-        remove(toRemove, false);
-    }
-
-    @Override
-    public void readFields(DataInput in) throws IOException {
-        this.valueCount = in.readInt();
-        setSize(valueCount * kmerByteSize);//kmerByteSize
-        in.readFully(storage, offset, valueCount * kmerByteSize);//kmerByteSize
-    }
-
-    @Override
-    public void write(DataOutput out) throws IOException {
-        out.writeInt(valueCount);
-        out.write(storage, offset, valueCount * kmerByteSize);
-    }
-    
-    public int getCountOfPosition() {
-        return valueCount;
-    }
-
-    public byte[] getByteArray() {
-        return storage;
-    }
-
-    public int getStartOffset() {
-        return offset;
-    }
-    
-    public int getLength() {
-        return valueCount * kmerByteSize;
-    }
-    
-    
-    @Override
-    public String toString() {
-        StringBuilder sbuilder = new StringBuilder();
-        sbuilder.append('[');
-        for(int i = 0; i < valueCount; i++){
-            sbuilder.append(getPosition(i).toString());
-            sbuilder.append(',');
-        }
-        if (valueCount > 0) {
-            sbuilder.setCharAt(sbuilder.length() - 1, ']');
-        } else {
-            sbuilder.append(']');
-        }
-        return sbuilder.toString();
-    }
-    
-    @Override
-    public int hashCode() {
-        return Marshal.hashBytes(getByteArray(), getStartOffset(), getLength());
-    }
-
-    @Override
-    public byte[] getBytes() {
-        
-        return null;
-    }
-}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
index efa87f7..35e55d5 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
@@ -1,25 +1,33 @@
 package edu.uci.ics.genomix.type;
 
+import java.io.ByteArrayOutputStream;
 import java.io.DataInput;
 import java.io.DataOutput;
+import java.io.DataOutputStream;
 import java.io.IOException;
 import java.io.Serializable;
+import java.util.Comparator;
 
+import org.apache.hadoop.io.DataOutputBuffer;
 import org.apache.hadoop.io.WritableComparable;
 
+import edu.uci.ics.genomix.data.Marshal;
+
 
 public class NodeWritable implements WritableComparable<NodeWritable>, Serializable{
 
     private static final long serialVersionUID = 1L;
-    public static final NodeWritable EMPTY_NODE = new NodeWritable(0);
+    public static final NodeWritable EMPTY_NODE = new NodeWritable();
+    
+    private static final int SIZE_FLOAT = 4;
     
     private PositionListWritable nodeIdList;
-    private KmerListWritable forwardForwardList;
-    private KmerListWritable forwardReverseList;
-    private KmerListWritable reverseForwardList;
-    private KmerListWritable reverseReverseList;
-    private KmerBytesWritable kmer;
-    private int kmerlength = 0;
+    private VKmerListWritable forwardForwardList;
+    private VKmerListWritable forwardReverseList;
+    private VKmerListWritable reverseForwardList;
+    private VKmerListWritable reverseReverseList;
+    private VKmerBytesWritable kmer;
+    private float averageCoverage;
     
     // merge/update directions
     public static class DirectionFlag {
@@ -31,49 +39,45 @@
     }
     
     public NodeWritable() {
-        this(0);
-    }
-    
-    public NodeWritable(int kmerlenth) {
-        this.kmerlength = kmerlenth;
         nodeIdList = new PositionListWritable();
-        forwardForwardList = new KmerListWritable(kmerlenth);
-        forwardReverseList = new KmerListWritable(kmerlenth);
-        reverseForwardList = new KmerListWritable(kmerlenth);
-        reverseReverseList = new KmerListWritable(kmerlenth);
-        kmer = new KmerBytesWritable(); //in graph construction - not set kmerlength Optimization: VKmer
+        forwardForwardList = new VKmerListWritable();
+        forwardReverseList = new VKmerListWritable();
+        reverseForwardList = new VKmerListWritable();
+        reverseReverseList = new VKmerListWritable();
+        kmer = new VKmerBytesWritable();  // in graph construction - not set kmerlength Optimization: VKmer
+        averageCoverage = 0;
     }
     
-    public NodeWritable(PositionListWritable nodeIdList, KmerListWritable FFList, KmerListWritable FRList,
-            KmerListWritable RFList, KmerListWritable RRList, KmerBytesWritable kmer) {
-        this(kmer.getKmerLength());
-        set(nodeIdList, FFList, FRList, RFList, RRList, kmer);
+    public NodeWritable(PositionListWritable nodeIdList, VKmerListWritable FFList, VKmerListWritable FRList,
+            VKmerListWritable RFList, VKmerListWritable RRList, VKmerBytesWritable kmer, float coverage) {
+        this();
+        set(nodeIdList, FFList, FRList, RFList, RRList, kmer, coverage);
     }
     
     public void set(NodeWritable node){
-        this.kmerlength = node.kmerlength;
         set(node.nodeIdList, node.forwardForwardList, node.forwardReverseList, node.reverseForwardList, 
-                node.reverseReverseList, node.kmer);
+                node.reverseReverseList, node.kmer, node.averageCoverage);
     }
     
-    public void set(PositionListWritable nodeIdList, KmerListWritable FFList, KmerListWritable FRList,
-            KmerListWritable RFList, KmerListWritable RRList, KmerBytesWritable kmer) {
+    public void set(PositionListWritable nodeIdList, VKmerListWritable FFList, VKmerListWritable FRList,
+            VKmerListWritable RFList, VKmerListWritable RRList, VKmerBytesWritable kmer2, float coverage) {
         this.nodeIdList.set(nodeIdList);
-        this.forwardForwardList.set(FFList);
-        this.forwardReverseList.set(FRList);
-        this.reverseForwardList.set(RFList);
-        this.reverseReverseList.set(RRList);
-        this.kmer.set(kmer);
+        this.forwardForwardList.setCopy(FFList);
+        this.forwardReverseList.setCopy(FRList);
+        this.reverseForwardList.setCopy(RFList);
+        this.reverseReverseList.setCopy(RRList);
+        this.kmer.setAsCopy(kmer2);
+        this.averageCoverage = coverage;
     }
 
-    public void reset(int kmerSize) {
-        this.kmerlength = kmerSize;
+    public void reset() {
         this.nodeIdList.reset();
-        this.forwardForwardList.reset(kmerSize);
-        this.forwardReverseList.reset(kmerSize);
-        this.reverseForwardList.reset(kmerSize);
-        this.reverseReverseList.reset(kmerSize);
+        this.forwardForwardList.reset();
+        this.forwardReverseList.reset();
+        this.reverseForwardList.reset();
+        this.reverseReverseList.reset();
         this.kmer.reset(0);
+        averageCoverage = 0;
     }
     
     
@@ -85,59 +89,51 @@
         this.nodeIdList.set(nodeIdList);
     }
 
-    public KmerBytesWritable getKmer() {
+    public VKmerBytesWritable getKmer() {
         return kmer;
     }
 
-    public void setKmer(KmerBytesWritable kmer) {
-        this.kmer.set(kmer);
+    public void setKmer(VKmerBytesWritable kmer) {
+        this.kmer.setAsCopy(kmer);
     }
     
-    public int getKmerlength() {
-        return kmerlength;
-    }
-
-    public void setKmerlength(int kmerlength) {
-        this.kmerlength = kmerlength;
-    }
-
-    public int getCount() {
-        return kmer.getKmerLength();
+    public int getKmerLength() {
+        return kmer.getKmerLetterLength();
     }
     
-    public KmerListWritable getFFList() {
+    public VKmerListWritable getFFList() {
         return forwardForwardList;
     }
 
-    public KmerListWritable getFRList() {
+    public VKmerListWritable getFRList() {
         return forwardReverseList;
     }
 
-    public KmerListWritable getRFList() {
+    public VKmerListWritable getRFList() {
         return reverseForwardList;
     }
 
-    public KmerListWritable getRRList() {
+    public VKmerListWritable getRRList() {
         return reverseReverseList;
     }
     
-	public void setFFList(KmerListWritable forwardForwardList) {
-		this.forwardForwardList.set(forwardForwardList);
+	public void setFFList(VKmerListWritable forwardForwardList) {
+		this.forwardForwardList.setCopy(forwardForwardList);
 	}
 
-	public void setFRList(KmerListWritable forwardReverseList) {
-		this.forwardReverseList.set(forwardReverseList);
+	public void setFRList(VKmerListWritable forwardReverseList) {
+		this.forwardReverseList.setCopy(forwardReverseList);
 	}
 
-	public void setRFList(KmerListWritable reverseForwardList) {
-		this.reverseForwardList.set(reverseForwardList);
+	public void setRFList(VKmerListWritable reverseForwardList) {
+		this.reverseForwardList.setCopy(reverseForwardList);
 	}
 
-	public void setRRList(KmerListWritable reverseReverseList) {
-		this.reverseReverseList.set(reverseReverseList);
+	public void setRRList(VKmerListWritable reverseReverseList) {
+		this.reverseReverseList.setCopy(reverseReverseList);
 	}
 
-	public KmerListWritable getListFromDir(byte dir) {
+	public VKmerListWritable getListFromDir(byte dir) {
         switch (dir & DirectionFlag.DIR_MASK) {
             case DirectionFlag.DIR_FF:
                 return getFFList();
@@ -152,27 +148,114 @@
         }
     }
 	
+	/**
+	 * Update my coverage to be the average of this and other. Used when merging paths.
+	 */
+	public void mergeCoverage(NodeWritable other) {
+	    // sequence considered in the average doesn't include anything overlapping with other kmers
+	    float adjustedLength = kmer.getKmerLetterLength() + other.kmer.getKmerLetterLength() - (KmerBytesWritable.getKmerLength() - 1) * 2;
+	    
+	    float myCount = (kmer.getKmerLetterLength() - KmerBytesWritable.getKmerLength() - 1) * averageCoverage;
+	    float otherCount = (other.kmer.getKmerLetterLength() - KmerBytesWritable.getKmerLength() - 1) * other.averageCoverage;
+	    averageCoverage = (myCount + otherCount) / adjustedLength;
+	}
+	
+	/**
+	 * Update my coverage as if all the reads in other became my own 
+	 */
+	public void addCoverage(NodeWritable other) {
+	    float myAdjustedLength = kmer.getKmerLetterLength() - KmerBytesWritable.getKmerLength() - 1;
+	    float otherAdjustedLength = other.kmer.getKmerLetterLength() - KmerBytesWritable.getKmerLength() - 1; 
+	    averageCoverage += other.averageCoverage * (otherAdjustedLength / myAdjustedLength);
+	}
+	
+	public void setAvgCoverage(float coverage) {
+	    averageCoverage = coverage;
+	}
+	
+	public float getAvgCoverage() {
+	    return averageCoverage;
+	}
+	
+	/**
+	 * Returns the length of the byte-array version of this node
+	 */
+	public int getSerializedLength() {
+	    return nodeIdList.getLength() + forwardForwardList.getLength() + forwardReverseList.getLength() + 
+	            reverseForwardList.getLength() + reverseReverseList.getLength() + kmer.getLength() + SIZE_FLOAT;
+	}
+	
+	/**
+     * Return this Node's representation as a new byte array 
+     */
+    public byte[] marshalToByteArray() throws IOException {
+        ByteArrayOutputStream baos = new ByteArrayOutputStream(getSerializedLength());
+        DataOutputStream out = new DataOutputStream(baos);
+        write(out);
+        return baos.toByteArray();
+    }
+    
+    public void setAsCopy(byte[] data, int offset) {
+        int curOffset = offset;
+        nodeIdList.set(data, curOffset);
+        
+        curOffset += nodeIdList.getLength();
+        forwardForwardList.setCopy(data, curOffset);
+        curOffset += forwardForwardList.getLength();
+        forwardReverseList.setCopy(data, curOffset);
+        curOffset += forwardReverseList.getLength();
+        reverseForwardList.setCopy(data, curOffset);
+        curOffset += reverseForwardList.getLength();
+        reverseReverseList.setCopy(data, curOffset);
+        
+        curOffset += reverseReverseList.getLength();
+        kmer.setAsCopy(data, curOffset);
+        
+        curOffset += kmer.getLength();
+        averageCoverage = Marshal.getFloat(data, curOffset);
+    }
+    
+    public void setAsReference(byte[] data, int offset) {
+        int curOffset = offset;
+        nodeIdList.setNewReference(data, curOffset);
+        
+        curOffset += nodeIdList.getLength();
+        forwardForwardList.setNewReference(data, curOffset);
+        curOffset += forwardForwardList.getLength();
+        forwardReverseList.setNewReference(data, curOffset);
+        curOffset += forwardReverseList.getLength();
+        reverseForwardList.setNewReference(data, curOffset);
+        curOffset += reverseForwardList.getLength();
+        reverseReverseList.setNewReference(data, curOffset);
+        
+        curOffset += reverseReverseList.getLength();
+        kmer.setAsReference(data, curOffset);
+        
+        curOffset += kmer.getLength();
+        averageCoverage = Marshal.getFloat(data, curOffset);
+    }
+	
     @Override
     public void write(DataOutput out) throws IOException {
-        out.writeInt(kmerlength);
         this.nodeIdList.write(out);
         this.forwardForwardList.write(out);
         this.forwardReverseList.write(out);
         this.reverseForwardList.write(out);
         this.reverseReverseList.write(out);
         this.kmer.write(out);
+        out.writeFloat(averageCoverage);
     }
 
     @Override
     public void readFields(DataInput in) throws IOException {
-        this.kmerlength = in.readInt();
-        reset(kmerlength);
+        reset();
         this.nodeIdList.readFields(in);
         this.forwardForwardList.readFields(in);
         this.forwardReverseList.readFields(in);
         this.reverseForwardList.readFields(in);
         this.reverseReverseList.readFields(in);
         this.kmer.readFields(in);
+        averageCoverage = in.readFloat();
     }
 
     @Override
@@ -180,6 +263,13 @@
         return this.kmer.compareTo(other.kmer);
     }
     
+    public class SortByCoverage implements Comparator<NodeWritable> {
+        @Override
+        public int compare(NodeWritable left, NodeWritable right) {
+            return Float.compare(left.averageCoverage, right.averageCoverage);
+        }
+    }
+    
     @Override
     public int hashCode() {
         return this.kmer.hashCode();
@@ -211,15 +301,15 @@
         return sbuilder.toString();
     }
 
-    public void mergeForwardNext(NodeWritable nextNode, int initialKmerSize) {
-        this.forwardForwardList.set(nextNode.forwardForwardList);
-        this.forwardReverseList.set(nextNode.forwardReverseList);
+    public void mergeForwardNext(final NodeWritable nextNode, int initialKmerSize) {
+        this.forwardForwardList.setCopy(nextNode.forwardForwardList);
+        this.forwardReverseList.setCopy(nextNode.forwardReverseList);
         kmer.mergeWithFFKmer(initialKmerSize, nextNode.getKmer());
     }
 
-    public void mergeForwardPre(NodeWritable preNode, int initialKmerSize) {
-        this.reverseForwardList.set(preNode.reverseForwardList);
-        this.reverseReverseList.set(preNode.reverseReverseList);
+    public void mergeForwardPre(final NodeWritable preNode, int initialKmerSize) {
+        this.reverseForwardList.setCopy(preNode.reverseForwardList);
+        this.reverseReverseList.setCopy(preNode.reverseReverseList);
         kmer.mergeWithRRKmer(initialKmerSize, preNode.getKmer());
     }
     
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
index f135292..8de4b0e 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
@@ -4,6 +4,7 @@
 import java.io.DataOutput;
 import java.io.IOException;
 import java.io.Serializable;
+import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 
@@ -12,129 +13,160 @@
 import edu.uci.ics.genomix.data.Marshal;
 import edu.uci.ics.genomix.type.PositionWritable;
 
-public class PositionListWritable implements Writable, Iterable<PositionWritable>, Serializable{
+public class PositionListWritable implements Writable, Iterable<PositionWritable>, Serializable {
     private static final long serialVersionUID = 1L;
+    protected static final byte[] EMPTY_BYTES = {0,0,0,0};
+    protected static final int HEADER_SIZE = 4;
+    
     protected byte[] storage;
     protected int offset;
     protected int valueCount;
-    protected static final byte[] EMPTY = {};
-    
+    protected int maxStorageSize;
+
+
     protected PositionWritable posIter = new PositionWritable();
-    
+
     public PositionListWritable() {
-        this.storage = EMPTY;
-        this.valueCount = 0;
-        this.offset = 0;
+        storage = EMPTY_BYTES;
+        valueCount = 0;
+        offset = 0;
+        maxStorageSize = storage.length; 
     }
-    
-    public PositionListWritable(int count, byte[] data, int offset) {
-        setNewReference(count, data, offset);
+
+    public PositionListWritable(byte[] data, int offset) {
+        setNewReference(data, offset);
     }
-    
+
     public PositionListWritable(List<PositionWritable> posns) {
         this();
-        setSize(posns.size());  // reserve space for all elements
+        setSize(posns.size() * PositionWritable.LENGTH + HEADER_SIZE); // reserve space for all elements
         for (PositionWritable p : posns) {
             append(p);
         }
     }
-    
-    public void setNewReference(int count, byte[] data, int offset) {
-        this.valueCount = count;
+  
+    public void setNewReference(byte[] data, int offset) {
+        this.valueCount = Marshal.getInt(data, offset);
         this.storage = data;
         this.offset = offset;
+        maxStorageSize = valueCount * PositionWritable.LENGTH + HEADER_SIZE;
     }
-    
+
     public void append(long uuid) {
-        setSize((1 + valueCount) * PositionWritable.LENGTH);
-        Marshal.putLong(uuid, storage, offset + valueCount * PositionWritable.LENGTH);
+        setSize((1 + valueCount) * PositionWritable.LENGTH + HEADER_SIZE);
+        Marshal.putLong(uuid, storage, offset + valueCount * PositionWritable.LENGTH + HEADER_SIZE);
         valueCount += 1;
+        Marshal.putInt(valueCount, storage, offset);
     }
-    
-    public void append(byte mateId, long readId, int posId){
+
+    public void append(byte mateId, long readId, int posId) {
         append(PositionWritable.makeUUID(mateId, readId, posId));
     }
-    
+
     public void append(PositionWritable pos) {
-        if(pos != null)
+        if (pos != null)
             append(pos.getUUID());
         else
             throw new RuntimeException("This position is null pointer!");
     }
-    
+
     /*
      * Append the otherList to the end of myList
      */
     public void appendList(PositionListWritable otherList) {
         if (otherList.valueCount > 0) {
-            setSize((valueCount + otherList.valueCount) * PositionWritable.LENGTH);
+            setSize((valueCount + otherList.valueCount) * PositionWritable.LENGTH + HEADER_SIZE);
             // copy contents of otherList into the end of my storage
-            System.arraycopy(otherList.storage, otherList.offset,
-                    storage, offset + valueCount * PositionWritable.LENGTH, 
-                    otherList.valueCount * PositionWritable.LENGTH);
+            System.arraycopy(otherList.storage, otherList.offset + HEADER_SIZE, storage, offset + valueCount
+                    * PositionWritable.LENGTH + HEADER_SIZE, otherList.valueCount * PositionWritable.LENGTH);
             valueCount += otherList.valueCount;
+            Marshal.putInt(valueCount, storage, offset);
         }
     }
-    
+
+    /**
+     * Save the union of my list and otherList. Uses a temporary HashSet for
+     * uniquefication
+     */
+    public void unionUpdate(PositionListWritable otherList) {
+        int newSize = valueCount + otherList.valueCount;
+        HashSet<PositionWritable> uniqueElements = new HashSet<PositionWritable>(newSize);
+        for (PositionWritable pos : this) {
+            uniqueElements.add(pos);
+        }
+        for (PositionWritable pos : otherList) {
+            uniqueElements.add(pos);
+        }
+        valueCount = 0;
+        setSize(newSize * PositionWritable.LENGTH + HEADER_SIZE);
+        for (PositionWritable pos : uniqueElements) {
+            append(pos);
+        }
+    }
+
     public static int getCountByDataLength(int length) {
         if (length % PositionWritable.LENGTH != 0) {
             throw new IllegalArgumentException("Length of positionlist is invalid");
         }
         return length / PositionWritable.LENGTH;
     }
-    
+
     public void set(PositionListWritable otherList) {
-        set(otherList.valueCount, otherList.storage, otherList.offset);
+        set(otherList.storage, otherList.offset);
     }
 
-    public void set(int valueCount, byte[] newData, int offset) {
-        this.valueCount = valueCount;
-        setSize(valueCount * PositionWritable.LENGTH);
-        if (valueCount > 0) {
-            System.arraycopy(newData, offset, storage, this.offset, valueCount * PositionWritable.LENGTH);
+    public void set(byte[] newData, int newOffset) {
+        int newValueCount = Marshal.getInt(newData, newOffset);
+        setSize(newValueCount * PositionWritable.LENGTH + HEADER_SIZE);
+        if (newValueCount > 0) {
+            System.arraycopy(newData, newOffset + HEADER_SIZE, storage, this.offset + HEADER_SIZE, newValueCount * PositionWritable.LENGTH);
         }
+        valueCount = newValueCount;
+        Marshal.putInt(valueCount, storage, this.offset);
     }
 
     public void reset() {
         valueCount = 0;
+        Marshal.putInt(valueCount, storage, offset);
     }
-    
+
     protected void setSize(int size) {
         if (size > getCapacity()) {
             setCapacity((size * 3 / 2));
         }
     }
-    
+
     protected int getCapacity() {
-        return storage.length - offset;
+        return maxStorageSize - offset;
     }
 
     protected void setCapacity(int new_cap) {
         if (new_cap > getCapacity()) {
             byte[] new_data = new byte[new_cap];
-            if (storage.length - offset > 0) {
-                System.arraycopy(storage, offset, new_data, 0, storage.length - offset);
+            if (valueCount > 0) {
+                System.arraycopy(storage, offset, new_data, 0, valueCount * PositionWritable.LENGTH + HEADER_SIZE);
             }
             storage = new_data;
             offset = 0;
+            maxStorageSize = storage.length;
         }
     }
-    
+
     public PositionWritable getPosition(int i) {
         if (i >= valueCount) {
             throw new ArrayIndexOutOfBoundsException("No such positions");
         }
-        posIter.setNewReference(storage, offset + i * PositionWritable.LENGTH);
+        posIter.setNewReference(storage, offset + i * PositionWritable.LENGTH + HEADER_SIZE);
         return posIter;
     }
-    
+
     public void resetPosition(int i, long uuid) {
         if (i >= valueCount) {
             throw new ArrayIndexOutOfBoundsException("No such positions");
         }
-        Marshal.putLong(uuid, storage, offset + i * PositionWritable.LENGTH);
+        Marshal.putLong(uuid, storage, offset + i * PositionWritable.LENGTH + HEADER_SIZE);
     }
-    
+
     public int getCountOfPosition() {
         return valueCount;
     }
@@ -148,9 +180,9 @@
     }
 
     public int getLength() {
-        return valueCount * PositionWritable.LENGTH;
+        return valueCount * PositionWritable.LENGTH + HEADER_SIZE;
     }
-    
+
     @Override
     public Iterator<PositionWritable> iterator() {
         Iterator<PositionWritable> it = new Iterator<PositionWritable>() {
@@ -169,50 +201,54 @@
 
             @Override
             public void remove() {
-                if(currentIndex < valueCount)
-                    System.arraycopy(storage, offset + currentIndex * PositionWritable.LENGTH, 
-                          storage, offset + (currentIndex - 1) * PositionWritable.LENGTH, 
-                          (valueCount - currentIndex) * PositionWritable.LENGTH);
+                if (currentIndex < valueCount)
+                    System.arraycopy(storage, offset + currentIndex * PositionWritable.LENGTH + HEADER_SIZE, storage, offset
+                            + (currentIndex - 1) * PositionWritable.LENGTH + HEADER_SIZE, (valueCount - currentIndex)
+                            * PositionWritable.LENGTH);
                 valueCount--;
                 currentIndex--;
+                Marshal.putInt(valueCount, storage, offset);
             }
         };
         return it;
     }
-    
+
     /*
      * remove the first instance of @toRemove. Uses a linear scan.  Throws an exception if not in this list.
      */
     public void remove(PositionWritable toRemove, boolean ignoreMissing) {
         Iterator<PositionWritable> posIterator = this.iterator();
         while (posIterator.hasNext()) {
-            if(toRemove.equals(posIterator.next())) {
+            if (toRemove.equals(posIterator.next())) {
                 posIterator.remove();
-                return;
+                return;  // found it. return early. 
             }
         }
+        // element not found.
         if (!ignoreMissing) {
-        	throw new ArrayIndexOutOfBoundsException("the PositionWritable `" + toRemove.toString() + "` was not found in this list.");
+            throw new ArrayIndexOutOfBoundsException("the PositionWritable `" + toRemove.toString()
+                    + "` was not found in this list.");
         }
     }
-    
+
     public void remove(PositionWritable toRemove) {
-    	remove(toRemove, false);
+        remove(toRemove, false);
     }
-    
+
     @Override
     public void write(DataOutput out) throws IOException {
         out.writeInt(valueCount);
-        out.write(storage, offset, valueCount * PositionWritable.LENGTH);
+        out.write(storage, offset + HEADER_SIZE, valueCount * PositionWritable.LENGTH);
     }
-    
+
     @Override
     public void readFields(DataInput in) throws IOException {
         this.valueCount = in.readInt();
-        setSize(valueCount * PositionWritable.LENGTH);
-        in.readFully(storage, offset, valueCount * PositionWritable.LENGTH);
+        setSize(valueCount * PositionWritable.LENGTH + HEADER_SIZE);
+        in.readFully(storage, offset + HEADER_SIZE, valueCount * PositionWritable.LENGTH);
+        Marshal.putInt(valueCount, storage, offset);
     }
-    
+
     @Override
     public String toString() {
         StringBuilder sbuilder = new StringBuilder();
@@ -228,12 +264,12 @@
         }
         return sbuilder.toString();
     }
-    
+
     @Override
     public int hashCode() {
         return Marshal.hashBytes(getByteArray(), getStartOffset(), getLength());
     }
-    
+
     @Override
     public boolean equals(Object o) {
         if (!(o instanceof PositionListWritable))
@@ -241,9 +277,9 @@
         PositionListWritable other = (PositionListWritable) o;
         if (this.valueCount != other.valueCount)
             return false;
-        for (int i=0; i < this.valueCount; i++) {
-                if (!this.getPosition(i).equals(other.getPosition(i)))
-                    return false;
+        for (int i = 0; i < this.valueCount; i++) {
+            if (!this.getPosition(i).equals(other.getPosition(i)))
+                return false;
         }
         return true;
     }
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
index 1079677..03d66a6 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
@@ -119,10 +119,10 @@
     }
     
     /*
-     * String of form "(readId-posID_mate)" where mate is _1 or _2
+     * String of form "(readId-posID_mate)" where mate is _0 or _1
      */
     @Override
     public String toString() {
-        return "(" + this.getReadId() + "-" + this.getPosId() + "_" + (this.getMateId() + 1) + ")";
+        return "(" + this.getReadId() + "-" + this.getPosId() + "_" + (this.getMateId()) + ")";
     }
 }
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
new file mode 100644
index 0000000..4f34542
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
@@ -0,0 +1,668 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.type;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+import java.io.Serializable;
+
+import org.apache.hadoop.io.BinaryComparable;
+import org.apache.hadoop.io.WritableComparable;
+import org.apache.hadoop.io.WritableComparator;
+
+import edu.uci.ics.genomix.data.KmerUtil;
+import edu.uci.ics.genomix.data.Marshal;
+import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
+
+
+/**
+ * Variable-length kmer which stores its length internally.
+ * Note: `offset` as used in this class is the offset at which the *kmer*
+ * begins. There is a {@value HEADER_SIZE}-byte header preceding the kmer
+ */
+public class VKmerBytesWritable extends BinaryComparable implements Serializable, WritableComparable<BinaryComparable> {
+    private static final long serialVersionUID = 1L;
+    protected static final byte[] EMPTY_BYTES = { 0, 0, 0, 0 }; // int indicating 0 length
+    protected static final int HEADER_SIZE = 4; // number of bytes for header info
+
+    protected int lettersInKmer;
+    protected int bytesUsed;
+    protected byte[] bytes;
+    protected int kmerStartOffset;
+    protected int storageMaxSize;  // since we may be a reference inside a larger datablock, we must track our maximum size
+
+    /**
+     * Initialize as empty kmer
+     */
+    public VKmerBytesWritable() {
+        this(EMPTY_BYTES, 0);
+    }
+
+    /**
+     * Copy contents of kmer string
+     */
+    public VKmerBytesWritable(String kmer) {
+        bytes = new byte[HEADER_SIZE + KmerUtil.getByteNumFromK(kmer.length())];
+        kmerStartOffset = HEADER_SIZE;
+        storageMaxSize = bytes.length;
+        setAsCopy(kmer);
+    }
+
+    /**
+     * Set as reference to given data
+     * 
+     * @param storage
+     *            : byte array with header
+     * @param offset
+     */
+    public VKmerBytesWritable(byte[] storage, int offset) {
+        setAsReference(storage, offset);
+    }
+
+    /**
+     * Reserve space for k letters
+     */
+    public VKmerBytesWritable(int k) {
+        if (k > 0) {
+            bytes = new byte[HEADER_SIZE + KmerUtil.getByteNumFromK(k)];
+        } else if (k == 0) {
+            bytes = EMPTY_BYTES;
+        } else {
+            throw new IllegalArgumentException("Invalid K (" + k + ").");
+        }
+        kmerStartOffset = HEADER_SIZE;
+        storageMaxSize = bytes.length;
+        setKmerLength(k);
+    }
+
+    /**
+     * deep copy of kmer in other
+     * 
+     * @param other
+     */
+    public VKmerBytesWritable(VKmerBytesWritable other) {
+        this(other.lettersInKmer);
+        setAsCopy(other);
+    }
+    
+    /**
+     * deep copy of kmer in other
+     * 
+     * @param other
+     */
+    public VKmerBytesWritable(KmerBytesWritable other) {
+        this(other.lettersInKmer);
+        setAsCopy(other);
+    }
+
+    /**
+     * Deep copy of the given kmer
+     * 
+     * @param other
+     */
+    public void setAsCopy(VKmerBytesWritable other) {
+        reset(other.lettersInKmer);
+        if (lettersInKmer > 0) {
+            System.arraycopy(other.bytes, other.kmerStartOffset, bytes, this.kmerStartOffset, bytesUsed);
+        }
+    }
+    
+    /**
+     * Deep copy of the given kmer
+     * 
+     * @param other
+     */
+    public void setAsCopy(KmerBytesWritable other) {
+        reset(other.lettersInKmer);
+        if (lettersInKmer > 0) {
+            System.arraycopy(other.bytes, other.offset, bytes, this.kmerStartOffset, bytesUsed);
+        }
+    }
+
+    /**
+     * set from String kmer
+     */
+    public void setAsCopy(String kmer) {
+        int k = kmer.length();
+        reset(k);
+        System.arraycopy(kmer.getBytes(), 0, bytes, kmerStartOffset, bytesUsed);
+    }
+
+    /**
+     * Deep copy of the given bytes data
+     * 
+     * @param newData
+     *            : byte array to copy (should have a header)
+     * @param offset
+     */
+    public void setAsCopy(byte[] newData, int offset) {
+        int k = Marshal.getInt(newData, offset);
+        reset(k);
+        System.arraycopy(newData, offset + HEADER_SIZE, bytes, this.kmerStartOffset, bytesUsed);
+    }
+
+    /**
+     * Point this datablock to the given bytes array It works like the pointer
+     * to new datablock.
+     * 
+     * @param newData
+     *            : byte array to copy (should have a header)
+     * @param blockOffset
+     */
+    public void setAsReference(byte[] newData, int blockOffset) {
+        bytes = newData;
+        kmerStartOffset = blockOffset + HEADER_SIZE;
+        int kRequested = Marshal.getInt(newData, blockOffset);
+        int bytesRequested = KmerUtil.getByteNumFromK(kRequested) + HEADER_SIZE;
+        if (newData.length - blockOffset < bytesRequested) {
+            throw new IllegalArgumentException("Requested " + bytesRequested + " bytes (k=" + kRequested
+                    + ") but buffer has only " + (newData.length - blockOffset) + " bytes");
+        }
+        storageMaxSize = bytesRequested;  // since we are a reference, store our max capacity
+        setKmerLength(kRequested);
+    }
+
+    /**
+     * Reset array by kmerlength
+     * 
+     * @param k
+     */
+    public void reset(int k) {
+        int newByteLength = KmerUtil.getByteNumFromK(k);
+        if (bytesUsed < newByteLength) {
+            bytes = new byte[newByteLength + HEADER_SIZE];
+            kmerStartOffset = HEADER_SIZE;
+            storageMaxSize = bytes.length;
+        }
+        setKmerLength(k);
+    }
+
+    protected void clearLeadBit() {
+        if (lettersInKmer % 4 != 0) {
+            bytes[kmerStartOffset] &= (1 << ((lettersInKmer % 4) << 1)) - 1;
+        }
+    }
+
+    /**
+     * Get one genecode (A|G|C|T) from the given kmer index e.g. Get the 4th
+     * gene of the kmer ACGTA will return T
+     * 
+     * @param pos
+     * @return
+     */
+    public byte getGeneCodeAtPosition(int pos) {
+        if (pos >= lettersInKmer || pos < 0) {
+            throw new ArrayIndexOutOfBoundsException("Gene position (" + pos + ") out of bounds for k=" + lettersInKmer);
+        }
+        return geneCodeAtPosition(pos);
+    }
+
+    /**
+     * unchecked version of getGeneCodeAtPosition. Used when kmerlength is
+     * inaccurate (mid-merge)
+     */
+    private byte geneCodeAtPosition(int pos) {
+        int posByte = pos / 4;
+        int shift = (pos % 4) << 1;
+        return (byte) ((bytes[kmerStartOffset + bytesUsed - 1 - posByte] >> shift) & 0x3);
+    }
+
+    /**
+     * Shift Kmer to accept new char input
+     * 
+     * @param c
+     *            Input new gene character
+     * @return the shift out gene, in gene code format
+     */
+    public byte shiftKmerWithNextChar(byte c) {
+        return shiftKmerWithNextCode(GeneCode.getCodeFromSymbol(c));
+    }
+
+    /**
+     * Shift Kmer to accept new gene code
+     * 
+     * @param c
+     *            Input new gene code
+     * @return the shift out gene, in gene code format
+     */
+    public byte shiftKmerWithNextCode(byte c) {
+        byte output = (byte) (bytes[kmerStartOffset + bytesUsed - 1] & 0x03);
+        for (int i = bytesUsed - 1; i > 0; i--) {
+            byte in = (byte) (bytes[kmerStartOffset + i - 1] & 0x03);
+            bytes[kmerStartOffset + i] = (byte) (((bytes[kmerStartOffset + i] >>> 2) & 0x3f) | (in << 6));
+        }
+        int pos = ((lettersInKmer - 1) % 4) << 1;
+        byte code = (byte) (c << pos);
+        bytes[kmerStartOffset] = (byte) (((bytes[kmerStartOffset] >>> 2) & 0x3f) | code);
+        clearLeadBit();
+        return output;
+    }
+
+    /**
+     * Shift Kmer to accept new input char
+     * 
+     * @param c
+     *            Input new gene character
+     * @return the shiftout gene, in gene code format
+     */
+    public byte shiftKmerWithPreChar(byte c) {
+        return shiftKmerWithPreCode(GeneCode.getCodeFromSymbol(c));
+    }
+
+    /**
+     * Shift Kmer to accept new gene code
+     * 
+     * @param c
+     *            Input new gene code
+     * @return the shiftout gene, in gene code format
+     */
+    public byte shiftKmerWithPreCode(byte c) {
+        int pos = ((lettersInKmer - 1) % 4) << 1;
+        byte output = (byte) ((bytes[kmerStartOffset] >> pos) & 0x03);
+        for (int i = 0; i < bytesUsed - 1; i++) {
+            byte in = (byte) ((bytes[kmerStartOffset + i + 1] >> 6) & 0x03);
+            bytes[kmerStartOffset + i] = (byte) ((bytes[kmerStartOffset + i] << 2) | in);
+        }
+        bytes[kmerStartOffset + bytesUsed - 1] = (byte) ((bytes[kmerStartOffset + bytesUsed - 1] << 2) | c);
+        clearLeadBit();
+        return output;
+    }
+
+    public int getKmerLetterLength() {
+        return lettersInKmer;
+    }
+
+    @Override
+    public byte[] getBytes() {
+        return bytes;
+    }
+
+    /**
+     * Return the (hyracks-specific) data block offset. This includes the header.
+     */
+    public int getBlockOffset() {
+        return kmerStartOffset - HEADER_SIZE;
+    }
+
+    /**
+     * Return the data block offset where the kmer data begins. This excludes the header.
+     */
+    public int getKmerOffset() {
+        return kmerStartOffset;
+    }
+
+    /**
+     * Return the number of bytes used by both header and kmer chain
+     */
+    @Override
+    public int getLength() {
+        return bytesUsed + HEADER_SIZE;
+    }
+    
+    /**
+     * Return the number of bytes used by the kmer chain
+     */
+    public int getKmerByteLength() {
+        return bytesUsed;
+    }
+    
+
+    public void setKmerLength(int k) {
+        this.bytesUsed = KmerUtil.getByteNumFromK(k);
+        this.lettersInKmer = k;
+        saveHeader(k);
+    }
+
+    protected int getKmerByteCapacity() {
+        return storageMaxSize  - HEADER_SIZE;
+    }
+
+    protected void setKmerByteCapacity(int new_cap) {
+        if (new_cap != getKmerByteCapacity()) {
+            byte[] new_data = new byte[new_cap + HEADER_SIZE];
+            if (new_cap < bytesUsed) {
+                bytesUsed = new_cap;
+            }
+            if (bytesUsed != 0) {
+                System.arraycopy(bytes, kmerStartOffset, new_data, HEADER_SIZE, bytesUsed);
+            }
+            bytes = new_data;
+            kmerStartOffset = HEADER_SIZE;
+            storageMaxSize = bytes.length;
+        }
+    }
+
+    private void saveHeader(int length) {
+        Marshal.putInt(length, bytes, kmerStartOffset - HEADER_SIZE);
+    }
+
+    @Override
+    public void readFields(DataInput in) throws IOException {
+        lettersInKmer = in.readInt();
+        bytesUsed = KmerUtil.getByteNumFromK(lettersInKmer);
+        if (lettersInKmer > 0) {
+            if (getKmerByteCapacity() < this.bytesUsed) {
+                this.bytes = new byte[this.bytesUsed + HEADER_SIZE];
+                this.kmerStartOffset = HEADER_SIZE;
+                storageMaxSize = bytes.length;
+            }
+            in.readFully(bytes, kmerStartOffset, bytesUsed);
+        }
+    }
+
+    /**
+     * write the entire byte array including the header
+     */
+    @Override
+    public void write(DataOutput out) throws IOException {
+        out.write(bytes, kmerStartOffset - HEADER_SIZE, bytesUsed + HEADER_SIZE);
+    }
+
+    @Override
+    public int hashCode() {
+        return Marshal.hashBytes(bytes, kmerStartOffset - HEADER_SIZE, bytesUsed + HEADER_SIZE);
+    }
+
+    @Override
+    public boolean equals(Object right_obj) {
+        if (right_obj instanceof VKmerBytesWritable) {
+            // since these may be backed by storage of different sizes, we have to manually check each byte, including the header
+            VKmerBytesWritable right = (VKmerBytesWritable) right_obj;
+            for (int i = -HEADER_SIZE; i < bytesUsed; i++) {
+                if (bytes[kmerStartOffset + i] != right.bytes[right.kmerStartOffset + i]) {
+                    return false;
+                }
+            }
+            return true;
+        }
+        return false;
+    }
+
+    @Override
+    public String toString() {
+        return KmerUtil.recoverKmerFrom(this.lettersInKmer, bytes, kmerStartOffset, bytesUsed);
+    }
+
+    public static class Comparator extends WritableComparator {
+
+        public Comparator() {
+            super(VKmerBytesWritable.class);
+        }
+
+        public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) {
+            int kmerlength1 = Marshal.getInt(b1, s1);
+            int kmerlength2 = Marshal.getInt(b2, s2);
+            if (kmerlength1 == kmerlength2) {
+                return compareBytes(b1, s1 + HEADER_SIZE, l1 - HEADER_SIZE, b2, s2 + HEADER_SIZE, l2 - HEADER_SIZE);
+            }
+            return kmerlength1 - kmerlength2;
+        }
+    }
+
+    static { // register this comparator
+        WritableComparator.define(VKmerBytesWritable.class, new Comparator());
+    }
+
+    /**
+     * Ensures that there is space for at least `size` bytes of kmer (not
+     * including any header)
+     */
+    protected void setSize(int size) {
+        if (size > getKmerByteCapacity()) {
+            setKmerByteCapacity((size * 3 / 2));
+        }
+        this.bytesUsed = size;
+    }
+
+    public void setByRead(int k, byte[] stringBytes, int start) {
+        reset(k);
+        setByRead(stringBytes, start);
+    }
+
+    /**
+     * Read Kmer from read text into bytes array e.g. AATAG will compress as
+     * [0x000G, 0xATAA]
+     * 
+     * @param stringBytes
+     * @param start
+     */
+    public void setByRead(byte[] stringBytes, int start) {
+        byte l = 0;
+        int bytecount = 0;
+        int bcount = this.bytesUsed - 1;
+        for (int i = start; i < start + lettersInKmer && i < stringBytes.length; i++) {
+            byte code = GeneCode.getCodeFromSymbol(stringBytes[i]);
+            l |= (byte) (code << bytecount);
+            bytecount += 2;
+            if (bytecount == 8) {
+                bytes[kmerStartOffset + bcount--] = l;
+                l = 0;
+                bytecount = 0;
+            }
+        }
+        if (bcount >= 0) {
+            bytes[kmerStartOffset] = l;
+        }
+    }
+
+    public void setByReadReverse(int k, byte[] stringBytes, int start) {
+        reset(k);
+        setByReadReverse(stringBytes, start);
+    }
+
+    /**
+     * Compress Reversed read into bytes array e.g. AATAG will paired to CTATT,
+     * and then compress as [0x000T,0xTATC]
+     * 
+     * @param input
+     *            array
+     * @param start
+     *            position
+     */
+    public void setByReadReverse(byte[] array, int start) {
+        byte l = 0;
+        int bytecount = 0;
+        int bcount = bytesUsed - 1;
+        // for (int i = start + kmerlength - 1; i >= 0 && i < array.length; i--)
+        // {
+        for (int i = start + lettersInKmer - 1; i >= start && i < array.length; i--) {
+            byte code = GeneCode.getPairedCodeFromSymbol(array[i]);
+            l |= (byte) (code << bytecount);
+            bytecount += 2;
+            if (bytecount == 8) {
+                bytes[kmerStartOffset + bcount--] = l;
+                l = 0;
+                bytecount = 0;
+            }
+        }
+        if (bcount >= 0) {
+            bytes[kmerStartOffset] = l;
+        }
+    }
+
+    /**
+     * Merge Kmer with the next connected Kmer e.g. AAGCTAA merge with AACAACC,
+     * if the initial kmerSize = 3 then it will return AAGCTAACAACC
+     * 
+     * @param initialKmerSize
+     *            : the initial kmerSize
+     * @param kmer
+     *            : the next kmer
+     */
+    public void mergeWithFFKmer(int initialKmerSize, VKmerBytesWritable kmer) {
+        int preKmerLength = lettersInKmer;
+        int preSize = bytesUsed;
+        lettersInKmer += kmer.lettersInKmer - initialKmerSize + 1;
+        setSize(KmerUtil.getByteNumFromK(lettersInKmer));
+        for (int i = 1; i <= preSize; i++) {
+            bytes[kmerStartOffset + bytesUsed - i] = bytes[kmerStartOffset + preSize - i];
+        }
+        for (int k = initialKmerSize - 1; k < kmer.getKmerLetterLength(); k += 4) {
+            byte onebyte = KmerBytesWritable.getOneByteFromKmerAtPosition(k, kmer.bytes, kmer.kmerStartOffset,
+                    kmer.bytesUsed);
+            KmerBytesWritable.appendOneByteAtPosition(preKmerLength + k - initialKmerSize + 1, onebyte, bytes,
+                    kmerStartOffset, bytesUsed);
+        }
+        clearLeadBit();
+        saveHeader(lettersInKmer);
+    }
+    
+    public void mergeWithFFKmer(int kmerSize, KmerBytesWritable kmer) {
+        // TODO make this more efficient
+        mergeWithFFKmer(kmerSize, new VKmerBytesWritable(kmer.toString()));
+    }
+
+    /**
+     * Merge Kmer with the next connected Kmer, when that Kmer needs to be
+     * reverse-complemented e.g. AAGCTAA merge with GGTTGTT, if the initial
+     * kmerSize = 3 then it will return AAGCTAACAACC A merge B => A B~
+     * 
+     * @param initialKmerSize
+     *            : the initial kmerSize
+     * @param kmer
+     *            : the next kmer
+     */
+    public void mergeWithFRKmer(int initialKmerSize, VKmerBytesWritable kmer) {
+        int preSize = bytesUsed;
+        int preKmerLength = lettersInKmer;
+        lettersInKmer += kmer.lettersInKmer - initialKmerSize + 1;
+        setSize(KmerUtil.getByteNumFromK(lettersInKmer));
+        // copy prefix into right-side of buffer
+        for (int i = 1; i <= preSize; i++) {
+            bytes[kmerStartOffset + bytesUsed - i] = bytes[kmerStartOffset + preSize - i];
+        }
+
+        int bytecount = (preKmerLength % 4) * 2;
+        int bcount = bytesUsed - preSize - bytecount / 8; // may overlap
+                                                          // previous kmer
+        byte l = bcount == bytesUsed - preSize ? bytes[kmerStartOffset + bcount] : 0x00;
+        bytecount %= 8;
+        for (int i = kmer.lettersInKmer - initialKmerSize; i >= 0; i--) {
+            byte code = GeneCode.getPairedGeneCode(kmer.getGeneCodeAtPosition(i));
+            l |= (byte) (code << bytecount);
+            bytecount += 2;
+            if (bytecount == 8) {
+                bytes[kmerStartOffset + bcount--] = l;
+                l = 0;
+                bytecount = 0;
+            }
+        }
+        if (bcount >= 0) {
+            bytes[kmerStartOffset] = l;
+        }
+        saveHeader(lettersInKmer);
+    }
+    
+    public void mergeWithFRKmer(int kmerSize, KmerBytesWritable kmer) {
+        // TODO make this more efficient
+        mergeWithFRKmer(kmerSize, new VKmerBytesWritable(kmer.toString()));
+    }
+
+    /**
+     * Merge Kmer with the previous connected Kmer, when that kmer needs to be
+     * reverse-complemented e.g. AACAACC merge with TTCTGCC, if the initial
+     * kmerSize = 3 then it will return GGCAGAACAACC
+     * 
+     * @param initialKmerSize
+     *            : the initial kmerSize
+     * @param preKmer
+     *            : the previous kmer
+     */
+    public void mergeWithRFKmer(int initialKmerSize, VKmerBytesWritable preKmer) {
+        // TODO make this more efficient
+        VKmerBytesWritable reversed = new VKmerBytesWritable(preKmer.lettersInKmer);
+        reversed.setByReadReverse(preKmer.toString().getBytes(), 0);
+        mergeWithRRKmer(initialKmerSize, reversed);
+    }
+    
+    public void mergeWithRFKmer(int kmerSize, KmerBytesWritable kmer) {
+        // TODO make this more efficient
+        mergeWithRFKmer(kmerSize, new VKmerBytesWritable(kmer.toString()));
+    }
+
+    /**
+     * Merge Kmer with the previous connected Kmer e.g. AACAACC merge with
+     * AAGCTAA, if the initial kmerSize = 3 then it will return AAGCTAACAACC
+     * 
+     * @param initialKmerSize
+     *            : the initial kmerSize
+     * @param preKmer
+     *            : the previous kmer
+     */
+    public void mergeWithRRKmer(int initialKmerSize, VKmerBytesWritable preKmer) {
+        int preKmerLength = lettersInKmer;
+        int preSize = bytesUsed;
+        lettersInKmer += preKmer.lettersInKmer - initialKmerSize + 1;
+        setSize(KmerUtil.getByteNumFromK(lettersInKmer));
+        byte cacheByte = KmerBytesWritable.getOneByteFromKmerAtPosition(0, bytes, kmerStartOffset, preSize);
+
+        // copy prekmer
+        for (int k = 0; k < preKmer.lettersInKmer - initialKmerSize + 1; k += 4) {
+            byte onebyte = KmerBytesWritable.getOneByteFromKmerAtPosition(k, preKmer.bytes, preKmer.kmerStartOffset,
+                    preKmer.bytesUsed);
+            KmerBytesWritable.appendOneByteAtPosition(k, onebyte, bytes, kmerStartOffset, bytesUsed);
+        }
+
+        // copy current kmer
+        int k = 4;
+        for (; k < preKmerLength; k += 4) {
+            byte onebyte = KmerBytesWritable.getOneByteFromKmerAtPosition(k, bytes, kmerStartOffset, preSize);
+            KmerBytesWritable.appendOneByteAtPosition(preKmer.lettersInKmer - initialKmerSize + k - 4 + 1, cacheByte,
+                    bytes, kmerStartOffset, bytesUsed);
+            cacheByte = onebyte;
+        }
+        KmerBytesWritable.appendOneByteAtPosition(preKmer.lettersInKmer - initialKmerSize + k - 4 + 1, cacheByte,
+                bytes, kmerStartOffset, bytesUsed);
+        clearLeadBit();
+    }
+    
+    public void mergeWithRRKmer(int kmerSize, KmerBytesWritable kmer) {
+        // TODO make this more efficient
+        mergeWithRRKmer(kmerSize, new VKmerBytesWritable(kmer.toString()));
+    }
+
+    public void mergeWithKmerInDir(byte dir, int initialKmerSize, VKmerBytesWritable kmer) {
+        switch (dir & DirectionFlag.DIR_MASK) {
+            case DirectionFlag.DIR_FF:
+                mergeWithFFKmer(initialKmerSize, kmer);
+                break;
+            case DirectionFlag.DIR_FR:
+                mergeWithFRKmer(initialKmerSize, kmer);
+                break;
+            case DirectionFlag.DIR_RF:
+                mergeWithRFKmer(initialKmerSize, kmer);
+                break;
+            case DirectionFlag.DIR_RR:
+                mergeWithRRKmer(initialKmerSize, kmer);
+                break;
+            default:
+                throw new RuntimeException("Direction not recognized: " + dir);
+        }
+    }
+    public void mergeWithKmerInDir(byte dir, int initialKmerSize, KmerBytesWritable kmer) {
+        // TODO make this more efficient
+        mergeWithKmerInDir(dir, initialKmerSize, new VKmerBytesWritable(kmer.toString()));
+    }
+
+    public KmerBytesWritable asFixedLengthKmer() {
+        if (lettersInKmer != KmerBytesWritable.getKmerLength()) {
+            throw new IllegalArgumentException("VKmer " + this.toString() + " is not of the same length as the fixed length Kmer (" + KmerBytesWritable.getKmerLength() + " )!");
+        }
+        return new KmerBytesWritable(bytes, kmerStartOffset);
+    }
+
+}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerListWritable.java
new file mode 100644
index 0000000..abd46ef
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerListWritable.java
@@ -0,0 +1,321 @@
+package edu.uci.ics.genomix.type;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.hadoop.io.Writable;
+
+import edu.uci.ics.genomix.data.KmerUtil;
+import edu.uci.ics.genomix.data.Marshal;
+
+/**
+ * A list of fixed-length kmers. The length of this list is stored internally.
+ */
+public class VKmerListWritable implements Writable, Iterable<VKmerBytesWritable>, Serializable {
+    private static final long serialVersionUID = 1L;
+    protected static final byte[] EMPTY_BYTES = { 0, 0, 0, 0 };
+    protected static final int HEADER_SIZE = 4;
+
+    protected byte[] storage;
+    protected int offset;
+    protected int valueCount;
+    protected int storageMaxSize;  // since we may be a reference inside a larger datablock, we must track our maximum size
+
+    private VKmerBytesWritable posIter = new VKmerBytesWritable();
+
+    public VKmerListWritable() {
+        storage = EMPTY_BYTES;
+        valueCount = 0;
+        offset = 0;
+        storageMaxSize = storage.length; 
+    }
+
+    public VKmerListWritable(byte[] data, int offset) {
+        setNewReference(data, offset);
+    }
+
+    public VKmerListWritable(List<VKmerBytesWritable> kmers) {
+        this();
+        for (VKmerBytesWritable kmer : kmers) {
+            append(kmer);
+        }
+    }
+
+    public void setNewReference(byte[] data, int offset) {
+        valueCount = Marshal.getInt(data, offset);
+        this.storage = data;
+        this.offset = offset;
+        this.storageMaxSize = getLength();
+    }
+
+    public void append(VKmerBytesWritable kmer) {
+        setSize(getLength() + kmer.getLength());
+        System.arraycopy(kmer.getBytes(), kmer.kmerStartOffset - VKmerBytesWritable.HEADER_SIZE,
+                storage, offset + getLength(), 
+                kmer.getLength());
+        valueCount += 1;
+        Marshal.putInt(valueCount, storage, offset);
+    }
+    
+    public void append(KmerBytesWritable kmer) { // TODO optimize this into two separate containers...
+        setSize(getLength() + kmer.getLength() + VKmerBytesWritable.HEADER_SIZE);
+        int myLength = getLength();
+        Marshal.putInt(KmerBytesWritable.getKmerLength(), storage, offset + myLength); // write a new VKmer header
+        System.arraycopy(kmer.getBytes(), kmer.offset,
+                storage, offset + myLength + VKmerBytesWritable.HEADER_SIZE,
+                kmer.getLength());
+        valueCount += 1;
+        Marshal.putInt(valueCount, storage, offset);
+    }
+
+    /*
+     * Append the otherList to the end of myList
+     */
+    public void appendList(VKmerListWritable otherList) {
+        if (otherList.valueCount > 0) {
+            setSize(getLength() + otherList.getLength() - HEADER_SIZE); // one of the headers is redundant
+            
+            // copy contents of otherList into the end of my storage
+            System.arraycopy(otherList.storage, otherList.offset + HEADER_SIZE, // skip other header
+                    storage, offset + getLength(), // add to end
+                    otherList.getLength() - HEADER_SIZE);
+            valueCount += otherList.valueCount;
+            Marshal.putInt(valueCount, storage, offset);
+        }
+    }
+
+    /**
+     * Save the union of my list and otherList. Uses a temporary HashSet for
+     * uniquefication
+     */
+    public void unionUpdate(VKmerListWritable otherList) {
+        int newSize = valueCount + otherList.valueCount;
+        HashSet<VKmerBytesWritable> uniqueElements = new HashSet<VKmerBytesWritable>(newSize);
+        for (VKmerBytesWritable kmer : this) {
+            // have to make copies of my own kmers since I may overwrite them
+            uniqueElements.add(new VKmerBytesWritable(kmer));
+        }
+        for (VKmerBytesWritable kmer : otherList) {
+            uniqueElements.add(kmer); // references okay
+        }
+        setSize(getLength() + otherList.getLength());  // upper bound on memory usage
+        valueCount = 0;
+        for (VKmerBytesWritable kmer : uniqueElements) {
+            append(kmer);
+        }
+        Marshal.putInt(valueCount, storage, offset);
+    }
+
+    protected void setSize(int size) {
+        if (size > getCapacity()) {
+            setCapacity((size * 3 / 2));
+        }
+    }
+
+    protected int getCapacity() {
+        return storageMaxSize - offset;
+    }
+
+    protected void setCapacity(int new_cap) {
+        if (new_cap > getCapacity()) {
+            byte[] new_data = new byte[new_cap];
+            if (valueCount > 0) {
+                System.arraycopy(storage, offset, new_data, 0, getLength());
+            }
+            storage = new_data;
+            offset = 0;
+            storageMaxSize = storage.length;
+        }
+    }
+
+    public void reset() {
+        valueCount = 0;
+        Marshal.putInt(valueCount, storage, offset);
+    }
+
+    public VKmerBytesWritable getPosition(int i) {
+        posIter.setAsReference(storage, getOffsetOfKmer(i));
+        return posIter;
+    }
+    
+    /**
+     * Return the offset of the kmer at the i'th position 
+     */
+    public int getOffsetOfKmer(int i) {
+        if (i >= valueCount) {
+            throw new ArrayIndexOutOfBoundsException("No such position " + i + " in list " + toString());
+        }
+        // seek to the given position
+        int posOffset = offset + HEADER_SIZE;
+        for (int curIndex = 0; curIndex < i; curIndex++) {
+            posOffset += KmerUtil.getByteNumFromK(Marshal.getInt(storage, posOffset)) + VKmerBytesWritable.HEADER_SIZE;
+        }
+        return posOffset;
+    }
+
+    public void setCopy(VKmerListWritable otherList) {
+        setCopy(otherList.storage, otherList.offset);
+    }
+
+    /**
+     * read a KmerListWritable from newData, which should include the header
+     */
+    public void setCopy(byte[] newData, int newOffset) {
+        int newValueCount = Marshal.getInt(newData, newOffset);
+        int newLength = getLength(newData, newOffset);
+        setSize(newLength);
+        if (newValueCount > 0) {
+            System.arraycopy(newData, newOffset + HEADER_SIZE, 
+                    storage, this.offset + HEADER_SIZE,
+                    newLength - HEADER_SIZE);
+        }
+        valueCount = newValueCount;
+        Marshal.putInt(valueCount, storage, this.offset);
+    }
+
+    @Override
+    public Iterator<VKmerBytesWritable> iterator() {
+        Iterator<VKmerBytesWritable> it = new Iterator<VKmerBytesWritable>() {
+
+            private int currentIndex = 0;
+            private int currentOffset = offset + HEADER_SIZE; // init as offset of first kmer
+
+            @Override
+            public boolean hasNext() {
+                return currentIndex < valueCount;
+            }
+
+            @Override
+            public VKmerBytesWritable next() {
+                posIter.setAsReference(storage, currentOffset);
+                currentOffset += KmerUtil.getByteNumFromK(Marshal.getInt(storage, currentOffset)) + VKmerBytesWritable.HEADER_SIZE;
+                currentIndex++;
+                return posIter;
+            }
+
+            @Override
+            public void remove() {
+                if (currentOffset <= 0) {
+                    throw new IllegalStateException("You must advance the iterator using .next() before calling remove()!");
+                }
+                // we're removing the element at prevIndex
+                int prevIndex = currentIndex - 1;
+                int prevOffset = getOffsetOfKmer(prevIndex);
+                
+                if (currentIndex < valueCount) { // if it's the last element, don't have to do any copying
+                    System.arraycopy(storage, currentOffset, // from the "next" element
+                            storage, prevOffset, // to the one just returned (overwriting it)
+                            getLength() - currentOffset + offset);  // remaining bytes except current element
+                }
+                valueCount--;
+                currentIndex--;
+                Marshal.putInt(valueCount, storage, offset);
+                currentOffset = prevOffset;
+            }
+        };
+        return it;
+    }
+
+    /*
+     * remove the first instance of `toRemove`. Uses a linear scan. Throws an
+     * exception if not in this list.
+     */
+    public void remove(VKmerBytesWritable toRemove, boolean ignoreMissing) {
+        Iterator<VKmerBytesWritable> posIterator = this.iterator();
+        while (posIterator.hasNext()) {
+            if (toRemove.equals(posIterator.next())) {
+                posIterator.remove();
+                return;  // break as soon as the element is found 
+            }
+        }
+        // element was not found
+        if (!ignoreMissing) {
+            throw new ArrayIndexOutOfBoundsException("the KmerBytesWritable `" + toRemove.toString()
+                    + "` was not found in this list.");
+        }
+    }
+
+    public void remove(VKmerBytesWritable toRemove) {
+        remove(toRemove, false);
+    }
+
+    @Override
+    public void readFields(DataInput in) throws IOException {
+        reset();
+        valueCount = in.readInt();
+        Marshal.putInt(valueCount, storage, offset);
+        int curOffset = offset + HEADER_SIZE;
+        int elemBytes = 0;
+        int elemLetters = 0;
+        int curLength = getLength();
+        for (int i = 0; i < valueCount; i++) {
+            elemLetters = in.readInt();
+            elemBytes = KmerUtil.getByteNumFromK(elemLetters) + VKmerBytesWritable.HEADER_SIZE;
+            setSize(curLength + elemBytes); // make sure we have room for the new element
+            Marshal.putInt(elemLetters, storage, curOffset); // write header
+            in.readFully(storage, curOffset + VKmerBytesWritable.HEADER_SIZE, elemBytes - VKmerBytesWritable.HEADER_SIZE); // write kmer
+            curOffset += elemBytes;
+            curLength += elemBytes;
+        }
+    }
+
+    @Override
+    public void write(DataOutput out) throws IOException {
+        out.write(storage, offset, getLength());
+    }
+
+    public int getCountOfPosition() {
+        return valueCount;
+    }
+
+    public byte[] getByteArray() {
+        return storage;
+    }
+
+    public int getStartOffset() {
+        return offset;
+    }
+
+    public int getLength() {
+        int totalSize = HEADER_SIZE;
+        for (int curCount = 0; curCount < valueCount; curCount++) {
+            totalSize += KmerUtil.getByteNumFromK(Marshal.getInt(storage, offset + totalSize)) + VKmerBytesWritable.HEADER_SIZE;
+        }
+        return totalSize;
+    }
+    
+    public static int getLength(byte[] listStorage, int listOffset) {
+      int totalSize = HEADER_SIZE;
+      int listValueCount = Marshal.getInt(listStorage, listOffset);
+      for (int curCount = 0; curCount < listValueCount; curCount++) {
+          totalSize += KmerUtil.getByteNumFromK(Marshal.getInt(listStorage, listOffset + totalSize)) + VKmerBytesWritable.HEADER_SIZE;
+      }
+      return totalSize;
+  }
+
+    @Override
+    public String toString() {
+        StringBuilder sbuilder = new StringBuilder();
+        sbuilder.append('[');
+        for (int i = 0; i < valueCount; i++) {
+            sbuilder.append(getPosition(i).toString());
+            sbuilder.append(',');
+        }
+        if (valueCount > 0) {
+            sbuilder.setCharAt(sbuilder.length() - 1, ']');
+        } else {
+            sbuilder.append(']');
+        }
+        return sbuilder.toString();
+    }
+
+    @Override
+    public int hashCode() {
+        return Marshal.hashBytes(getByteArray(), getStartOffset(), getLength());
+    }
+}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/GeneCode.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/GeneCode.java
new file mode 100644
index 0000000..c3d8a98
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/GeneCode.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.velvet.oldtype;
+
+public class GeneCode {
+    public final static byte[] GENE_SYMBOL = { 'A', 'C', 'G', 'T' };
+    /**
+     * make sure this 4 ids equal to the sequence id of char in {@GENE_SYMBOL
+	 * }
+     */
+    public static final byte A = 0;
+    public static final byte C = 1;
+    public static final byte G = 2;
+    public static final byte T = 3;
+
+    public static byte getCodeFromSymbol(byte ch) {
+        byte r = 0;
+        switch (ch) {
+            case 'A':
+            case 'a':
+                r = A;
+                break;
+            case 'C':
+            case 'c':
+                r = C;
+                break;
+            case 'G':
+            case 'g':
+                r = G;
+                break;
+            case 'T':
+            case 't':
+                r = T;
+                break;
+        }
+        return r;
+    }
+    
+    public static byte getPairedGeneCode(byte genecode){
+        if ( genecode < 0 || genecode > 3){
+            throw new IllegalArgumentException("Invalid genecode");
+        }
+        return (byte) (3- genecode);
+    }
+    
+    public static byte getPairedCodeFromSymbol(byte ch){
+        return getPairedGeneCode(getCodeFromSymbol(ch));
+    }
+
+    public static byte getSymbolFromCode(byte code) {
+        if (code > 3 || code < 0 ) {
+            throw new IllegalArgumentException("Invalid genecode");
+        }
+        return GENE_SYMBOL[code];
+    }
+}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/KmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/KmerBytesWritable.java
new file mode 100644
index 0000000..630dbad
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/KmerBytesWritable.java
@@ -0,0 +1,502 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.velvet.oldtype;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+import java.io.Serializable;
+
+import org.apache.hadoop.io.BinaryComparable;
+import org.apache.hadoop.io.WritableComparable;
+import org.apache.hadoop.io.WritableComparator;
+
+import edu.uci.ics.genomix.data.KmerUtil;
+
+/**
+ * Variable kmer length byteswritable
+ * It was used to generate the graph in which phase the kmer length doesn't change.
+ * Thus the size of bytes doesn't change either.
+ */
+public class KmerBytesWritable extends BinaryComparable implements Serializable, WritableComparable<BinaryComparable> {
+    /**
+	 * 
+	 */
+    private static final long serialVersionUID = 1L;
+    private static final byte[] EMPTY_BYTES = {};
+
+    protected int size;
+    protected byte[] bytes;
+    protected int offset;
+    protected int kmerlength;
+
+    public KmerBytesWritable() {
+        this(0, EMPTY_BYTES, 0);
+    }
+
+    public KmerBytesWritable(int k, byte[] storage, int offset) {
+        setNewReference(k, storage, offset);
+    }
+    
+    public KmerBytesWritable(int k, String kmer) {
+        setNewReference(kmer.length(), kmer.getBytes(), 0);
+    }
+
+    /**
+     * Initial Kmer space by kmerlength
+     * 
+     * @param k
+     *            kmerlength
+     */
+    public KmerBytesWritable(int k) {
+        this.kmerlength = k;
+        this.size = KmerUtil.getByteNumFromK(kmerlength);
+        if (k > 0) {
+            this.bytes = new byte[this.size];
+        } else {
+            this.bytes = EMPTY_BYTES;
+        }
+        this.offset = 0;
+    }
+
+    public KmerBytesWritable(KmerBytesWritable right) {
+        this(right.kmerlength);
+        set(right);
+    }
+
+    /**
+     * Deep copy of the given kmer
+     * 
+     * @param newData
+     */
+    public void set(KmerBytesWritable newData) {
+        if (newData == null) {
+            this.set(0, EMPTY_BYTES, 0);
+        } else {
+            this.set(newData.kmerlength, newData.bytes, newData.getOffset());
+        }
+    }
+
+    /**
+     * Deep copy of the given bytes data
+     * It will not change the kmerlength
+     * 
+     * @param newData
+     * @param offset
+     */
+    public void set(byte[] newData, int offset) {
+        if (kmerlength > 0) {
+            System.arraycopy(newData, offset, bytes, this.offset, size);
+        }
+    }
+
+    /**
+     * Deep copy of the given data, and also set to new kmerlength
+     * 
+     * @param k
+     *            : new kmer length
+     * @param newData
+     *            : data storage
+     * @param offset
+     *            : start offset
+     */
+    public void set(int k, byte[] newData, int offset) {
+        reset(k);
+        if (k > 0) {
+            System.arraycopy(newData, offset, bytes, this.offset, size);
+        }
+    }
+
+    /**
+     * Reset array by kmerlength
+     * 
+     * @param k
+     */
+    public void reset(int k) {
+        this.kmerlength = k;
+        setSize(KmerUtil.getByteNumFromK(k));
+        clearLeadBit();
+    }
+
+    /**
+     * Point this datablock to the given bytes array
+     * It works like the pointer to new datablock.
+     * kmerlength will not change
+     * 
+     * @param newData
+     * @param offset
+     */
+    public void setNewReference(byte[] newData, int offset) {
+        this.bytes = newData;
+        this.offset = offset;
+        if (newData.length - offset < size) {
+            throw new IllegalArgumentException("Not given enough space");
+        }
+    }
+
+    /**
+     * Point this datablock to the given bytes array
+     * It works like the pointer to new datablock.
+     * It also set the new kmerlength
+     * 
+     * @param k
+     * @param newData
+     * @param offset
+     */
+    public void setNewReference(int k, byte[] newData, int offset) {
+        this.kmerlength = k;
+        this.size = KmerUtil.getByteNumFromK(k);
+        setNewReference(newData, offset);
+    }
+
+    protected void setSize(int size) {
+        if (size > getCapacity()) {
+            setCapacity((size * 3 / 2));
+        }
+        this.size = size;
+    }
+
+    protected int getCapacity() {
+        return bytes.length;
+    }
+
+    protected void setCapacity(int new_cap) {
+        if (new_cap != getCapacity()) {
+            byte[] new_data = new byte[new_cap];
+            if (new_cap < size) {
+                size = new_cap;
+            }
+            if (size != 0) {
+                System.arraycopy(bytes, offset, new_data, 0, size);
+            }
+            bytes = new_data;
+            offset = 0;
+        }
+    }
+
+    /**
+     * Get one genecode (A|G|C|T) from the given kmer index
+     * e.g. Get the 4th gene of the kmer ACGTA will return T
+     * 
+     * @param pos
+     * @return
+     */
+    public byte getGeneCodeAtPosition(int pos) {
+        if (pos >= kmerlength) {
+            throw new IllegalArgumentException("gene position out of bound");
+        }
+        int posByte = pos / 4;
+        int shift = (pos % 4) << 1;
+        return (byte) ((bytes[offset + size - 1 - posByte] >> shift) & 0x3);
+    }
+
+    public int getKmerLength() {
+        return this.kmerlength;
+    }
+
+    @Override
+    public byte[] getBytes() {
+        return bytes;
+    }
+
+    public int getOffset() {
+        return offset;
+    }
+
+    @Override
+    public int getLength() {
+        return size;
+    }
+
+    /**
+     * Read Kmer from read text into bytes array e.g. AATAG will compress as
+     * [0x000G, 0xATAA]
+     * 
+     * @param k
+     * @param array
+     * @param start
+     */
+    public void setByRead(byte[] array, int start) {
+        byte l = 0;
+        int bytecount = 0;
+        int bcount = this.size - 1;
+        for (int i = start; i < start + kmerlength && i < array.length; i++) {
+            byte code = GeneCode.getCodeFromSymbol(array[i]);
+            l |= (byte) (code << bytecount);
+            bytecount += 2;
+            if (bytecount == 8) {
+                bytes[offset + bcount--] = l;
+                l = 0;
+                bytecount = 0;
+            }
+        }
+        if (bcount >= 0) {
+            bytes[offset] = l;
+        }
+    }
+
+    public void setByRead(int k, byte[] array, int start) {
+        reset(k);
+        setByRead(array, start);
+    }
+
+    /**
+     * Compress Reversed read into bytes array
+     * e.g. AATAG will paired to CTATT, and then compress as
+     * [0x000T,0xTATC]
+     * 
+     * @param input
+     *            array
+     * @param start
+     *            position
+     */
+    public void setByReadReverse(byte[] array, int start) {
+        byte l = 0;
+        int bytecount = 0;
+        int bcount = size - 1;
+        for (int i = start + kmerlength - 1; i >= 0 && i < array.length; i--) {
+            byte code = GeneCode.getPairedCodeFromSymbol(array[i]);
+            l |= (byte) (code << bytecount);
+            bytecount += 2;
+            if (bytecount == 8) {
+                bytes[offset + bcount--] = l;
+                l = 0;
+                bytecount = 0;
+            }
+        }
+        if (bcount >= 0) {
+            bytes[offset] = l;
+        }
+    }
+
+    public void setByReadReverse(int k, byte[] array, int start) {
+        reset(k);
+        setByReadReverse(array, start);
+    }
+
+    /**
+     * Shift Kmer to accept new char input
+     * 
+     * @param c
+     *            Input new gene character
+     * @return the shift out gene, in gene code format
+     */
+    public byte shiftKmerWithNextChar(byte c) {
+        return shiftKmerWithNextCode(GeneCode.getCodeFromSymbol(c));
+    }
+
+    /**
+     * Shift Kmer to accept new gene code
+     * 
+     * @param c
+     *            Input new gene code
+     * @return the shift out gene, in gene code format
+     */
+    public byte shiftKmerWithNextCode(byte c) {
+        byte output = (byte) (bytes[offset + size - 1] & 0x03);
+        for (int i = size - 1; i > 0; i--) {
+            byte in = (byte) (bytes[offset + i - 1] & 0x03);
+            bytes[offset + i] = (byte) (((bytes[offset + i] >>> 2) & 0x3f) | (in << 6));
+        }
+        int pos = ((kmerlength - 1) % 4) << 1;
+        byte code = (byte) (c << pos);
+        bytes[offset] = (byte) (((bytes[offset] >>> 2) & 0x3f) | code);
+        clearLeadBit();
+        return output;
+    }
+
+    /**
+     * Shift Kmer to accept new input char
+     * 
+     * @param c
+     *            Input new gene character
+     * @return the shiftout gene, in gene code format
+     */
+    public byte shiftKmerWithPreChar(byte c) {
+        return shiftKmerWithPreCode(GeneCode.getCodeFromSymbol(c));
+    }
+
+    /**
+     * Shift Kmer to accept new gene code
+     * 
+     * @param c
+     *            Input new gene code
+     * @return the shiftout gene, in gene code format
+     */
+    public byte shiftKmerWithPreCode(byte c) {
+        int pos = ((kmerlength - 1) % 4) << 1;
+        byte output = (byte) ((bytes[offset] >> pos) & 0x03);
+        for (int i = 0; i < size - 1; i++) {
+            byte in = (byte) ((bytes[offset + i + 1] >> 6) & 0x03);
+            bytes[offset + i] = (byte) ((bytes[offset + i] << 2) | in);
+        }
+        bytes[offset + size - 1] = (byte) ((bytes[offset + size - 1] << 2) | c);
+        clearLeadBit();
+        return output;
+    }
+
+    /**
+     * Merge Kmer with the next connected Kmer
+     * e.g. AAGCTAA merge with AACAACC, if the initial kmerSize = 3
+     * then it will return AAGCTAACAACC
+     * 
+     * @param initialKmerSize
+     *            : the initial kmerSize
+     * @param kmer
+     *            : the next kmer
+     */
+    public void mergeNextKmer(int initialKmerSize, KmerBytesWritable kmer) {
+        int preKmerLength = kmerlength;
+        int preSize = size;
+        this.kmerlength += kmer.kmerlength - initialKmerSize + 1;
+        setSize(KmerUtil.getByteNumFromK(kmerlength));
+        for (int i = 1; i <= preSize; i++) {
+            bytes[offset + size - i] = bytes[offset + preSize - i];
+        }
+        for (int k = initialKmerSize - 1; k < kmer.getKmerLength(); k += 4) {
+            byte onebyte = getOneByteFromKmerAtPosition(k, kmer.getBytes(), kmer.getOffset(), kmer.getLength());
+            appendOneByteAtPosition(preKmerLength + k - initialKmerSize + 1, onebyte, bytes, offset, size);
+        }
+        clearLeadBit();
+    }
+
+    /**
+     * Merge Kmer with the previous connected Kmer
+     * e.g. AACAACC merge with AAGCTAA, if the initial kmerSize = 3
+     * then it will return AAGCTAACAACC
+     * 
+     * @param initialKmerSize
+     *            : the initial kmerSize
+     * @param preKmer
+     *            : the previous kmer
+     */
+    public void mergePreKmer(int initialKmerSize, KmerBytesWritable preKmer) {
+        int preKmerLength = kmerlength;
+        int preSize = size;
+        this.kmerlength += preKmer.kmerlength - initialKmerSize + 1;
+        setSize(KmerUtil.getByteNumFromK(kmerlength));
+        byte cacheByte = getOneByteFromKmerAtPosition(0, bytes, offset, preSize);
+
+        // copy prekmer
+        for (int k = 0; k < preKmer.kmerlength - initialKmerSize + 1; k += 4) {
+            byte onebyte = getOneByteFromKmerAtPosition(k, preKmer.bytes, preKmer.offset, preKmer.size);
+            appendOneByteAtPosition(k, onebyte, bytes, offset, size);
+        }
+
+        // copy current kmer
+        int k = 4;
+        for (; k < preKmerLength; k += 4) {
+            byte onebyte = getOneByteFromKmerAtPosition(k, bytes, offset, preSize);
+            appendOneByteAtPosition(preKmer.kmerlength - initialKmerSize + k - 4 + 1, cacheByte, bytes, offset, size);
+            cacheByte = onebyte;
+        }
+        appendOneByteAtPosition(preKmer.kmerlength - initialKmerSize + k - 4 + 1, cacheByte, bytes, offset, size);
+        clearLeadBit();
+    }
+
+    public static void appendOneByteAtPosition(int k, byte onebyte, byte[] buffer, int start, int length) {
+        int position = start + length - 1 - k / 4;
+        if (position < start) {
+            throw new IllegalArgumentException("Buffer for kmer storage is invalid");
+        }
+        int shift = ((k) % 4) << 1;
+        int mask = shift == 0 ? 0 : ((1 << shift) - 1);
+
+        buffer[position] = (byte) ((buffer[position] & mask) | ((0xff & onebyte) << shift));
+        if (position > start && shift != 0) {
+            buffer[position - 1] = (byte) ((buffer[position - 1] & (0xff - mask)) | ((byte) ((0xff & onebyte) >> (8 - shift))));
+        }
+    }
+
+    public static byte getOneByteFromKmerAtPosition(int k, byte[] buffer, int start, int length) {
+        int position = start + length - 1 - k / 4;
+        if (position < start) {
+            throw new IllegalArgumentException("Buffer of kmer storage is invalid");
+        }
+        int shift = (k % 4) << 1;
+        byte data = (byte) (((0xff) & buffer[position]) >> shift);
+        if (shift != 0 && position > start) {
+            data |= 0xff & (buffer[position - 1] << (8 - shift));
+        }
+        return data;
+    }
+
+    protected void clearLeadBit() {
+        if (kmerlength % 4 != 0) {
+            bytes[offset] &= (1 << ((kmerlength % 4) << 1)) - 1;
+        }
+    }
+
+    @Override
+    public void readFields(DataInput in) throws IOException {
+        this.kmerlength = in.readInt();
+        this.size = KmerUtil.getByteNumFromK(kmerlength);
+        if (this.kmerlength > 0) {
+            if (this.bytes.length < this.size) {
+                this.bytes = new byte[this.size];
+                this.offset = 0;
+            }
+            in.readFully(bytes, offset, size);
+        }
+    }
+
+    @Override
+    public void write(DataOutput out) throws IOException {
+        out.writeInt(kmerlength);
+        if (kmerlength > 0) {
+            out.write(bytes, offset, size);
+        }
+    }
+
+    @Override
+    public int hashCode() {
+        return super.hashCode() * 31 + this.kmerlength;
+    }
+
+    @Override
+    public boolean equals(Object right_obj) {
+        if (right_obj instanceof KmerBytesWritable)
+            return this.kmerlength == ((KmerBytesWritable) right_obj).kmerlength && super.equals(right_obj);
+        return false;
+    }
+
+    @Override
+    public String toString() {
+        return KmerUtil.recoverKmerFrom(this.kmerlength, this.getBytes(), offset, this.getLength());
+    }
+
+    public static class Comparator extends WritableComparator {
+        public final int LEAD_BYTES = 4;
+
+        public Comparator() {
+            super(KmerBytesWritable.class);
+        }
+
+        public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) {
+            int kmerlength1 = readInt(b1, s1);
+            int kmerlength2 = readInt(b2, s2);
+            if (kmerlength1 == kmerlength2) {
+                return compareBytes(b1, s1 + LEAD_BYTES, l1 - LEAD_BYTES, b2, s2 + LEAD_BYTES, l2 - LEAD_BYTES);
+            }
+            return kmerlength1 - kmerlength2;
+        }
+    }
+
+    static { // register this comparator
+        WritableComparator.define(KmerBytesWritable.class, new Comparator());
+    }
+
+}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/KmerBytesWritableFactory.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/KmerBytesWritableFactory.java
new file mode 100644
index 0000000..b0aaebc
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/KmerBytesWritableFactory.java
@@ -0,0 +1,313 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.velvet.oldtype;
+
+public class KmerBytesWritableFactory {
+    private KmerBytesWritable kmer;
+
+    public KmerBytesWritableFactory(int k) {
+        kmer = new KmerBytesWritable(k);
+    }
+
+    /**
+     * Read Kmer from read text into bytes array e.g. AATAG will compress as
+     * [0x000G, 0xATAA]
+     * 
+     * @param k
+     * @param array
+     * @param start
+     */
+    public KmerBytesWritable getKmerByRead(int k, byte[] array, int start) {
+        kmer.reset(k);
+        kmer.setByRead(array, start);
+        return kmer;
+    }
+
+    /**
+     * Compress Reversed Kmer into bytes array AATAG will compress as
+     * [0x000A,0xATAG]
+     * 
+     * @param array
+     * @param start
+     */
+    public KmerBytesWritable getKmerByReadReverse(int k, byte[] array, int start) {
+        kmer.reset(k);
+        kmer.setByReadReverse(array, start);
+        return kmer;
+    }
+
+    /**
+     * Get last kmer from kmer-chain.
+     * e.g. kmerChain is AAGCTA, if k =5, it will
+     * return AGCTA
+     * 
+     * @param k
+     * @param kInChain
+     * @param kmerChain
+     * @return LastKmer bytes array
+     */
+    public KmerBytesWritable getLastKmerFromChain(int lastK, final KmerBytesWritable kmerChain) {
+        if (lastK > kmerChain.getKmerLength()) {
+            return null;
+        }
+        if (lastK == kmerChain.getKmerLength()) {
+            kmer.set(kmerChain);
+            return kmer;
+        }
+        kmer.reset(lastK);
+
+        /** from end to start */
+        int byteInChain = kmerChain.getLength() - 1 - (kmerChain.getKmerLength() - lastK) / 4;
+        int posInByteOfChain = ((kmerChain.getKmerLength() - lastK) % 4) << 1; // *2
+        int byteInKmer = kmer.getLength() - 1;
+        for (; byteInKmer >= 0 && byteInChain > 0; byteInKmer--, byteInChain--) {
+            kmer.getBytes()[byteInKmer] = (byte) ((0xff & kmerChain.getBytes()[byteInChain]) >> posInByteOfChain);
+            kmer.getBytes()[byteInKmer] |= ((kmerChain.getBytes()[byteInChain - 1] << (8 - posInByteOfChain)));
+        }
+
+        /** last kmer byte */
+        if (byteInKmer == 0) {
+            kmer.getBytes()[0] = (byte) ((kmerChain.getBytes()[0] & 0xff) >> posInByteOfChain);
+        }
+        kmer.clearLeadBit();
+        return kmer;
+    }
+
+    /**
+     * Get first kmer from kmer-chain e.g. kmerChain is AAGCTA, if k=5, it will
+     * return AAGCT
+     * 
+     * @param k
+     * @param kInChain
+     * @param kmerChain
+     * @return FirstKmer bytes array
+     */
+    public KmerBytesWritable getFirstKmerFromChain(int firstK, final KmerBytesWritable kmerChain) {
+        if (firstK > kmerChain.getKmerLength()) {
+            return null;
+        }
+        if (firstK == kmerChain.getKmerLength()) {
+            kmer.set(kmerChain);
+            return kmer;
+        }
+        kmer.reset(firstK);
+
+        int i = 1;
+        for (; i < kmer.getLength(); i++) {
+            kmer.getBytes()[kmer.getLength() - i] = kmerChain.getBytes()[kmerChain.getLength() - i];
+        }
+        int posInByteOfChain = (firstK % 4) << 1; // *2
+        if (posInByteOfChain == 0) {
+            kmer.getBytes()[0] = kmerChain.getBytes()[kmerChain.getLength() - i];
+        } else {
+            kmer.getBytes()[0] = (byte) (kmerChain.getBytes()[kmerChain.getLength() - i] & ((1 << posInByteOfChain) - 1));
+        }
+        kmer.clearLeadBit();
+        return kmer;
+    }
+
+    public KmerBytesWritable getSubKmerFromChain(int startK, int kSize, final KmerBytesWritable kmerChain) {
+        if (startK + kSize > kmerChain.getKmerLength()) {
+            return null;
+        }
+        if (startK == 0 && kSize == kmerChain.getKmerLength()) {
+            kmer.set(kmerChain);
+            return kmer;
+        }
+        kmer.reset(kSize);
+
+        /** from end to start */
+        int byteInChain = kmerChain.getLength() - 1 - startK / 4;
+        int posInByteOfChain = startK % 4 << 1; // *2
+        int byteInKmer = kmer.getLength() - 1;
+        for (; byteInKmer >= 0 && byteInChain > 0; byteInKmer--, byteInChain--) {
+            kmer.getBytes()[byteInKmer] = (byte) ((0xff & kmerChain.getBytes()[byteInChain]) >> posInByteOfChain);
+            kmer.getBytes()[byteInKmer] |= ((kmerChain.getBytes()[byteInChain - 1] << (8 - posInByteOfChain)));
+        }
+
+        /** last kmer byte */
+        if (byteInKmer == 0) {
+            kmer.getBytes()[0] = (byte) ((kmerChain.getBytes()[0] & 0xff) >> posInByteOfChain);
+        }
+        kmer.clearLeadBit();
+        return kmer;
+    }
+
+    /**
+     * Merge kmer with next neighbor in gene-code format.
+     * The k of new kmer will increase by 1
+     * e.g. AAGCT merge with A => AAGCTA
+     * 
+     * @param k
+     *            :input k of kmer
+     * @param kmer
+     *            : input bytes of kmer
+     * @param nextCode
+     *            : next neighbor in gene-code format
+     * @return the merged Kmer, this K of this Kmer is k+1
+     */
+    public KmerBytesWritable mergeKmerWithNextCode(final KmerBytesWritable kmer, byte nextCode) {
+        this.kmer.reset(kmer.getKmerLength() + 1);
+        for (int i = 1; i <= kmer.getLength(); i++) {
+            this.kmer.getBytes()[this.kmer.getLength() - i] = kmer.getBytes()[kmer.getLength() - i];
+        }
+        if (this.kmer.getLength() > kmer.getLength()) {
+            this.kmer.getBytes()[0] = (byte) (nextCode & 0x3);
+        } else {
+            this.kmer.getBytes()[0] = (byte) (kmer.getBytes()[0] | ((nextCode & 0x3) << ((kmer.getKmerLength() % 4) << 1)));
+        }
+        this.kmer.clearLeadBit();
+        return this.kmer;
+    }
+
+    /**
+     * Merge kmer with previous neighbor in gene-code format.
+     * The k of new kmer will increase by 1
+     * e.g. AAGCT merge with A => AAAGCT
+     * 
+     * @param k
+     *            :input k of kmer
+     * @param kmer
+     *            : input bytes of kmer
+     * @param preCode
+     *            : next neighbor in gene-code format
+     * @return the merged Kmer,this K of this Kmer is k+1
+     */
+    public KmerBytesWritable mergeKmerWithPreCode(final KmerBytesWritable kmer, byte preCode) {
+        this.kmer.reset(kmer.getKmerLength() + 1);
+        int byteInMergedKmer = 0;
+        if (kmer.getKmerLength() % 4 == 0) {
+            this.kmer.getBytes()[0] = (byte) ((kmer.getBytes()[0] >> 6) & 0x3);
+            byteInMergedKmer++;
+        }
+        for (int i = 0; i < kmer.getLength() - 1; i++, byteInMergedKmer++) {
+            this.kmer.getBytes()[byteInMergedKmer] = (byte) ((kmer.getBytes()[i] << 2) | ((kmer.getBytes()[i + 1] >> 6) & 0x3));
+        }
+        this.kmer.getBytes()[byteInMergedKmer] = (byte) ((kmer.getBytes()[kmer.getLength() - 1] << 2) | (preCode & 0x3));
+        this.kmer.clearLeadBit();
+        return this.kmer;
+    }
+
+    /**
+     * Merge two kmer to one kmer
+     * e.g. ACTA + ACCGT => ACTAACCGT
+     * 
+     * @param preK
+     *            : previous k of kmer
+     * @param kmerPre
+     *            : bytes array of previous kmer
+     * @param nextK
+     *            : next k of kmer
+     * @param kmerNext
+     *            : bytes array of next kmer
+     * @return merged kmer, the new k is @preK + @nextK
+     */
+    public KmerBytesWritable mergeTwoKmer(final KmerBytesWritable preKmer, final KmerBytesWritable nextKmer) {
+        kmer.reset(preKmer.getKmerLength() + nextKmer.getKmerLength());
+        int i = 1;
+        for (; i <= preKmer.getLength(); i++) {
+            kmer.getBytes()[kmer.getLength() - i] = preKmer.getBytes()[preKmer.getLength() - i];
+        }
+        if (i > 1) {
+            i--;
+        }
+        if (preKmer.getKmerLength() % 4 == 0) {
+            for (int j = 1; j <= nextKmer.getLength(); j++) {
+                kmer.getBytes()[kmer.getLength() - i - j] = nextKmer.getBytes()[nextKmer.getLength() - j];
+            }
+        } else {
+            int posNeedToMove = ((preKmer.getKmerLength() % 4) << 1);
+            kmer.getBytes()[kmer.getLength() - i] |= nextKmer.getBytes()[nextKmer.getLength() - 1] << posNeedToMove;
+            for (int j = 1; j < nextKmer.getLength(); j++) {
+                kmer.getBytes()[kmer.getLength() - i - j] = (byte) (((nextKmer.getBytes()[nextKmer.getLength() - j] & 0xff) >> (8 - posNeedToMove)) | (nextKmer
+                        .getBytes()[nextKmer.getLength() - j - 1] << posNeedToMove));
+            }
+            if (nextKmer.getKmerLength() % 4 == 0 || (nextKmer.getKmerLength() % 4) * 2 + posNeedToMove > 8) {
+                kmer.getBytes()[0] = (byte) ((0xff & nextKmer.getBytes()[0]) >> (8 - posNeedToMove));
+            }
+        }
+        kmer.clearLeadBit();
+        return kmer;
+    }
+
+    /**
+     * Safely shifted the kmer forward without change the input kmer
+     * e.g. AGCGC shift with T => GCGCT
+     * 
+     * @param k
+     *            : kmer length
+     * @param kmer
+     *            : input kmer
+     * @param afterCode
+     *            : input genecode
+     * @return new created kmer that shifted by afterCode, the K will not change
+     */
+    public KmerBytesWritable shiftKmerWithNextCode(final KmerBytesWritable kmer, byte afterCode) {
+        this.kmer.set(kmer);
+        this.kmer.shiftKmerWithNextCode(afterCode);
+        return this.kmer;
+    }
+
+    /**
+     * Safely shifted the kmer backward without change the input kmer
+     * e.g. AGCGC shift with T => TAGCG
+     * 
+     * @param k
+     *            : kmer length
+     * @param kmer
+     *            : input kmer
+     * @param preCode
+     *            : input genecode
+     * @return new created kmer that shifted by preCode, the K will not change
+     */
+    public KmerBytesWritable shiftKmerWithPreCode(final KmerBytesWritable kmer, byte preCode) {
+        this.kmer.set(kmer);
+        this.kmer.shiftKmerWithPreCode(preCode);
+        return this.kmer;
+    }
+
+    /**
+     * get the reverse sequence of given kmer
+     * 
+     * @param kmer
+     */
+    public KmerBytesWritable reverse(final KmerBytesWritable kmer) {
+        this.kmer.reset(kmer.getKmerLength());
+
+        int curPosAtKmer = ((kmer.getKmerLength() - 1) % 4) << 1;
+        int curByteAtKmer = 0;
+
+        int curPosAtReverse = 0;
+        int curByteAtReverse = this.kmer.getLength() - 1;
+        this.kmer.getBytes()[curByteAtReverse] = 0;
+        for (int i = 0; i < kmer.getKmerLength(); i++) {
+            byte gene = (byte) ((kmer.getBytes()[curByteAtKmer] >> curPosAtKmer) & 0x03);
+            this.kmer.getBytes()[curByteAtReverse] |= gene << curPosAtReverse;
+            curPosAtReverse += 2;
+            if (curPosAtReverse >= 8) {
+                curPosAtReverse = 0;
+                this.kmer.getBytes()[--curByteAtReverse] = 0;
+            }
+            curPosAtKmer -= 2;
+            if (curPosAtKmer < 0) {
+                curPosAtKmer = 6;
+                curByteAtKmer++;
+            }
+        }
+        this.kmer.clearLeadBit();
+        return this.kmer;
+    }
+}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/NodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/NodeWritable.java
similarity index 77%
rename from genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/NodeWritable.java
rename to genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/NodeWritable.java
index 9fc1829..128bf9f 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/NodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/NodeWritable.java
@@ -13,7 +13,7 @@
  * limitations under the License.
  */
 
-package edu.uci.ics.genomix.oldtype;
+package edu.uci.ics.genomix.velvet.oldtype;
 
 import java.io.DataInput;
 import java.io.DataOutput;
@@ -22,24 +22,11 @@
 
 import org.apache.hadoop.io.WritableComparable;
 
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-
 public class NodeWritable implements WritableComparable<NodeWritable>, Serializable {
     /**
      * 
      */
     private static final long serialVersionUID = 1L;
-    public static final NodeWritable EMPTY_NODE = new NodeWritable(0);
-
-    // merge/update directions
-    public static class DirectionFlag {
-        public static final byte DIR_FF = 0b00 << 0;
-        public static final byte DIR_FR = 0b01 << 0;
-        public static final byte DIR_RF = 0b10 << 0;
-        public static final byte DIR_RR = 0b11 << 0;
-        public static final byte DIR_MASK = 0b11 << 0;
-    }
-
     private PositionWritable nodeID;
     private PositionListWritable forwardForwardList;
     private PositionListWritable forwardReverseList;
@@ -71,16 +58,6 @@
         kmer.set(kmer);
     }
 
-    public void set(PositionWritable nodeID, PositionListWritable FFList, PositionListWritable FRList,
-            PositionListWritable RFList, PositionListWritable RRList, KmerBytesWritable kmer) {
-        this.nodeID.set(nodeID);
-        this.forwardForwardList.set(FFList);
-        this.forwardReverseList.set(FRList);
-        this.reverseForwardList.set(RFList);
-        this.reverseReverseList.set(RRList);
-        this.kmer.set(kmer);
-    }
-
     public void setNodeID(PositionWritable ref) {
         this.setNodeID(ref.getReadID(), ref.getPosInRead());
     }
@@ -118,21 +95,6 @@
         return reverseReverseList;
     }
 
-    public PositionListWritable getListFromDir(byte dir) {
-        switch (dir & DirectionFlag.DIR_MASK) {
-            case DirectionFlag.DIR_FF:
-                return getFFList();
-            case DirectionFlag.DIR_FR:
-                return getFRList();
-            case DirectionFlag.DIR_RF:
-                return getRFList();
-            case DirectionFlag.DIR_RR:
-                return getRRList();
-            default:
-                throw new RuntimeException("Unrecognized direction in getListFromDir: " + dir);
-        }
-    }
-
     public PositionWritable getNodeID() {
         return nodeID;
     }
@@ -148,13 +110,13 @@
     public void mergeForwardNext(NodeWritable nextNode, int initialKmerSize) {
         this.forwardForwardList.set(nextNode.forwardForwardList);
         this.forwardReverseList.set(nextNode.forwardReverseList);
-        kmer.mergeWithFFKmer(initialKmerSize, nextNode.getKmer());
+        kmer.mergeNextKmer(initialKmerSize, nextNode.getKmer());
     }
 
     public void mergeForwardPre(NodeWritable preNode, int initialKmerSize) {
         this.reverseForwardList.set(preNode.reverseForwardList);
         this.reverseReverseList.set(preNode.reverseReverseList);
-        kmer.mergeWithRRKmer(initialKmerSize, preNode.getKmer());
+        kmer.mergePreKmer(initialKmerSize, preNode.getKmer());
     }
 
     public void set(NodeWritable node) {
@@ -211,13 +173,13 @@
     @Override
     public String toString() {
         StringBuilder sbuilder = new StringBuilder();
-        sbuilder.append('{');
+        sbuilder.append('(');
         sbuilder.append(nodeID.toString()).append('\t');
         sbuilder.append(forwardForwardList.toString()).append('\t');
         sbuilder.append(forwardReverseList.toString()).append('\t');
         sbuilder.append(reverseForwardList.toString()).append('\t');
         sbuilder.append(reverseReverseList.toString()).append('\t');
-        sbuilder.append(kmer.toString()).append('}');
+        sbuilder.append(kmer.toString()).append(')');
         return sbuilder.toString();
     }
 
@@ -236,8 +198,4 @@
         return inDegree() == 1 && outDegree() == 1;
     }
 
-    public boolean isSimpleOrTerminalPath() {
-        return isPathNode() || (inDegree() == 0 && outDegree() == 1) || (inDegree() == 1 && outDegree() == 0);
-    }
-
 }
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/PositionListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/PositionListWritable.java
new file mode 100644
index 0000000..b6c42c2
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/PositionListWritable.java
@@ -0,0 +1,229 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.velvet.oldtype;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.hadoop.io.Writable;
+
+import edu.uci.ics.genomix.data.Marshal;
+
+public class PositionListWritable implements Writable, Iterable<PositionWritable>, Serializable {
+    /**
+     * 
+     */
+    private static final long serialVersionUID = 1L;
+    protected byte[] storage;
+    protected int offset;
+    protected int valueCount;
+    protected static final byte[] EMPTY = {};
+    public static final int INTBYTES = 4;
+    
+    protected PositionWritable posIter = new PositionWritable();
+
+    public PositionListWritable() {
+        this.storage = EMPTY;
+        this.valueCount = 0;
+        this.offset = 0;
+    }
+
+    public PositionListWritable(int count, byte[] data, int offset) {
+        setNewReference(count, data, offset);
+    }
+    
+    public PositionListWritable(List<PositionWritable> posns) {
+        this();
+        for (PositionWritable p : posns) {
+            append(p);
+        }
+    }
+
+    public void setNewReference(int count, byte[] data, int offset) {
+        this.valueCount = count;
+        this.storage = data;
+        this.offset = offset;
+    }
+
+    protected void setSize(int size) {
+        if (size > getCapacity()) {
+            setCapacity((size * 3 / 2));
+        }
+    }
+
+    protected int getCapacity() {
+        return storage.length - offset;
+    }
+
+    protected void setCapacity(int new_cap) {
+        if (new_cap > getCapacity()) {
+            byte[] new_data = new byte[new_cap];
+            if (storage.length - offset > 0) {
+                System.arraycopy(storage, offset, new_data, 0, storage.length - offset);
+            }
+            storage = new_data;
+            offset = 0;
+        }
+    }
+
+    public PositionWritable getPosition(int i) {
+        if (i >= valueCount) {
+            throw new ArrayIndexOutOfBoundsException("No such positions");
+        }
+        posIter.setNewReference(storage, offset + i * PositionWritable.LENGTH);
+        return posIter;
+    }
+
+    public void resetPosition(int i, int readID, byte posInRead) {
+        if (i >= valueCount) {
+            throw new ArrayIndexOutOfBoundsException("No such positions");
+        }
+        Marshal.putInt(readID, storage, offset + i * PositionWritable.LENGTH);
+        storage[offset + INTBYTES] = posInRead;
+    }
+    
+    @Override
+    public Iterator<PositionWritable> iterator() {
+        Iterator<PositionWritable> it = new Iterator<PositionWritable>() {
+
+            private int currentIndex = 0;
+
+            @Override
+            public boolean hasNext() {
+                return currentIndex < valueCount;
+            }
+
+            @Override
+            public PositionWritable next() {
+                return getPosition(currentIndex++);
+            }
+
+            @Override
+            public void remove() {
+            }
+        };
+        return it;
+    }
+
+    public void set(PositionListWritable list2) {
+        set(list2.valueCount, list2.storage, list2.offset);
+    }
+
+    public void set(int valueCount, byte[] newData, int offset) {
+        this.valueCount = valueCount;
+        setSize(valueCount * PositionWritable.LENGTH);
+        if (valueCount > 0) {
+            System.arraycopy(newData, offset, storage, this.offset, valueCount * PositionWritable.LENGTH);
+        }
+    }
+
+    public void reset() {
+        valueCount = 0;
+    }
+
+    public void append(PositionWritable pos) {
+        setSize((1 + valueCount) * PositionWritable.LENGTH);
+        System.arraycopy(pos.getByteArray(), pos.getStartOffset(), storage, offset + valueCount
+                * PositionWritable.LENGTH, pos.getLength());
+        valueCount += 1;
+    }
+
+    public void append(int readID, byte posInRead) {
+        setSize((1 + valueCount) * PositionWritable.LENGTH);
+        Marshal.putInt(readID, storage, offset + valueCount * PositionWritable.LENGTH);
+        storage[offset + valueCount * PositionWritable.LENGTH + PositionWritable.INTBYTES] = posInRead;
+        valueCount += 1;
+    }
+    
+    public static int getCountByDataLength(int length) {
+        if (length % PositionWritable.LENGTH != 0) {
+            for (StackTraceElement ste : Thread.currentThread().getStackTrace()) {
+                System.out.println(ste);
+            }
+            throw new IllegalArgumentException("Length of positionlist is invalid");
+        }
+        return length / PositionWritable.LENGTH;
+    }
+
+    public int getCountOfPosition() {
+        return valueCount;
+    }
+
+    public byte[] getByteArray() {
+        return storage;
+    }
+
+    public int getStartOffset() {
+        return offset;
+    }
+
+    public int getLength() {
+        return valueCount * PositionWritable.LENGTH;
+    }
+
+    @Override
+    public void readFields(DataInput in) throws IOException {
+        this.valueCount = in.readInt();
+        setSize(valueCount * PositionWritable.LENGTH);
+        in.readFully(storage, offset, valueCount * PositionWritable.LENGTH);
+    }
+
+    @Override
+    public void write(DataOutput out) throws IOException {
+        out.writeInt(valueCount);
+        out.write(storage, offset, valueCount * PositionWritable.LENGTH);
+    }
+
+    @Override
+    public String toString() {
+        StringBuilder sbuilder = new StringBuilder();
+        sbuilder.append('[');
+        for (PositionWritable pos : this) {
+            sbuilder.append(pos.toString());
+            sbuilder.append(',');
+        }
+        if (valueCount > 0) {
+            sbuilder.setCharAt(sbuilder.length() - 1, ']');
+        } else {
+            sbuilder.append(']');
+        }
+        return sbuilder.toString();
+    }
+    
+    @Override
+    public int hashCode() {
+        return Marshal.hashBytes(getByteArray(), getStartOffset(), getLength());
+    }
+    
+    @Override
+    public boolean equals(Object o) {
+        if (!(o instanceof PositionListWritable))
+            return false;
+        PositionListWritable other = (PositionListWritable) o;
+        if (this.valueCount != other.valueCount)
+            return false;
+        for (int i=0; i < this.valueCount; i++) {
+                if (!this.getPosition(i).equals(other.getPosition(i)))
+                    return false;
+        }
+        return true;
+    }
+}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/PositionWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/PositionWritable.java
new file mode 100644
index 0000000..1d509bb
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/velvet/oldtype/PositionWritable.java
@@ -0,0 +1,170 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.velvet.oldtype;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+import java.io.Serializable;
+
+import org.apache.hadoop.io.RawComparator;
+import org.apache.hadoop.io.WritableComparable;
+import org.apache.hadoop.io.WritableComparator;
+
+import edu.uci.ics.genomix.data.Marshal;
+
+public class PositionWritable implements WritableComparable<PositionWritable>, Serializable {
+    /**
+     * 
+     */
+    private static final long serialVersionUID = 1L;
+    protected byte[] storage;
+    protected int offset;
+    public static final int LENGTH = 5;
+    public static final int INTBYTES = 4;
+
+    public PositionWritable() {
+        storage = new byte[LENGTH];
+        offset = 0;
+    }
+
+    public PositionWritable(int readID, byte posInRead) {
+        this();
+        set(readID, posInRead);
+    }
+
+    public PositionWritable(byte[] storage, int offset) {
+        setNewReference(storage, offset);
+    }
+
+    public void setNewReference(byte[] storage, int offset) {
+        this.storage = storage;
+        this.offset = offset;
+    }
+
+    public void set(PositionWritable pos) {
+        set(pos.getReadID(), pos.getPosInRead());
+    }
+
+    public void set(int readID, byte posInRead) {
+        Marshal.putInt(readID, storage, offset);
+        storage[offset + INTBYTES] = posInRead;
+    }
+
+    public int getReadID() {
+        return Marshal.getInt(storage, offset);
+    }
+
+    public byte getPosInRead() {
+        return storage[offset + INTBYTES];
+    }
+
+    public byte[] getByteArray() {
+        return storage;
+    }
+
+    public int getStartOffset() {
+        return offset;
+    }
+
+    public int getLength() {
+        return LENGTH;
+    }
+
+    public boolean isSameReadID(PositionWritable other) {
+        return getReadID() == other.getReadID();
+    }
+
+    @Override
+    public void readFields(DataInput in) throws IOException {
+        in.readFully(storage, offset, LENGTH);
+    }
+
+    @Override
+    public void write(DataOutput out) throws IOException {
+        out.write(storage, offset, LENGTH);
+    }
+
+    @Override
+    public int hashCode() {
+        return Marshal.hashBytes(getByteArray(), getStartOffset(), getLength());
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (!(o instanceof PositionWritable))
+            return false;
+        PositionWritable other = (PositionWritable) o;
+        return this.getReadID() == other.getReadID() && this.getPosInRead() == other.getPosInRead();
+    }
+
+    @Override
+    public int compareTo(PositionWritable other) {
+        int diff1 = this.getReadID() - other.getReadID();
+        if (diff1 == 0) {
+            int diff2 = Math.abs((int) this.getPosInRead()) - Math.abs((int) other.getPosInRead());
+            if (diff2 == 0) {
+                return this.getPosInRead() - other.getPosInRead();
+            }
+            return diff2;
+        }
+        return diff1;
+    }
+
+    @Override
+    public String toString() {
+        return "(" + Integer.toString(getReadID()) + "," + Integer.toString((int) getPosInRead()) + ")";
+    }
+
+    /** A Comparator optimized for IntWritable. */
+    public static class Comparator extends WritableComparator {
+        public Comparator() {
+            super(PositionWritable.class);
+        }
+
+        public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) {
+            int thisValue = Marshal.getInt(b1, s1);
+            int thatValue = Marshal.getInt(b2, s2);
+            int diff1 = thisValue - thatValue;
+            if (diff1 == 0) {
+                int diff2 = Math.abs((int) b1[s1 + INTBYTES]) - Math.abs((int) b2[s2 + INTBYTES]);
+                if (diff2 == 0) {
+                    return b1[s1 + INTBYTES] - b2[s2 + INTBYTES];
+                }
+                return diff2;
+            }
+            return diff1;
+        }
+    }
+
+    public static class FirstComparator implements RawComparator<PositionWritable> {
+        @Override
+        public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) {
+            return WritableComparator.compareBytes(b1, s1, l1 - 1, b2, s2, l2 - 1);
+        }
+
+        @Override
+        public int compare(PositionWritable o1, PositionWritable o2) {
+            int l = o1.getReadID();
+            int r = o2.getReadID();
+            return l == r ? 0 : (l < r ? -1 : 1);
+        }
+    }
+
+    static { // register this comparator
+        WritableComparator.define(PositionWritable.class, new Comparator());
+    }
+}
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableFactoryTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableFactoryTest.java
index 486e13b..7808719 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableFactoryTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableFactoryTest.java
@@ -19,8 +19,8 @@
 import org.junit.Test;
 
 import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.KmerBytesWritableFactory;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 public class KmerBytesWritableFactoryTest {
     static byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
@@ -29,17 +29,17 @@
 
     @Test
     public void TestGetLastKmer() {
-        KmerBytesWritable kmer = new KmerBytesWritable(9);
+        VKmerBytesWritable kmer = new VKmerBytesWritable(9);
         kmer.setByRead(array, 0);
         Assert.assertEquals("AGCTGACCG", kmer.toString());
-        KmerBytesWritable lastKmer;
+        VKmerBytesWritable lastKmer;
         for (int i = 8; i > 0; i--) {
             lastKmer = kmerFactory.getLastKmerFromChain(i, kmer);
             Assert.assertEquals("AGCTGACCG".substring(9 - i), lastKmer.toString());
             lastKmer = kmerFactory.getSubKmerFromChain(9 - i, i, kmer);
             Assert.assertEquals("AGCTGACCG".substring(9 - i), lastKmer.toString());
         }
-        KmerBytesWritable vlastKmer;
+        VKmerBytesWritable vlastKmer;
         for (int i = 8; i > 0; i--) {
             vlastKmer = kmerFactory.getLastKmerFromChain(i, kmer);
             Assert.assertEquals("AGCTGACCG".substring(9 - i), vlastKmer.toString());
@@ -50,17 +50,17 @@
 
     @Test
     public void TestGetFirstKmer() {
-        KmerBytesWritable kmer = new KmerBytesWritable(9);
+        VKmerBytesWritable kmer = new VKmerBytesWritable(9);
         kmer.setByRead(array, 0);
         Assert.assertEquals("AGCTGACCG", kmer.toString());
-        KmerBytesWritable firstKmer;
+        VKmerBytesWritable firstKmer;
         for (int i = 8; i > 0; i--) {
             firstKmer = kmerFactory.getFirstKmerFromChain(i, kmer);
             Assert.assertEquals("AGCTGACCG".substring(0, i), firstKmer.toString());
             firstKmer = kmerFactory.getSubKmerFromChain(0, i, kmer);
             Assert.assertEquals("AGCTGACCG".substring(0, i), firstKmer.toString());
         }
-        KmerBytesWritable vfirstKmer;
+        VKmerBytesWritable vfirstKmer;
         for (int i = 8; i > 0; i--) {
             vfirstKmer = kmerFactory.getFirstKmerFromChain(i, kmer);
             Assert.assertEquals("AGCTGACCG".substring(0, i), vfirstKmer.toString());
@@ -71,12 +71,12 @@
 
     @Test
     public void TestGetSubKmer() {
-        KmerBytesWritable kmer = new KmerBytesWritable(9);
+        VKmerBytesWritable kmer = new VKmerBytesWritable(9);
         kmer.setByRead(array, 0);
         Assert.assertEquals("AGCTGACCG", kmer.toString());
-        KmerBytesWritable subKmer;
-        for (int istart = 0; istart < kmer.getKmerLength() - 1; istart++) {
-            for (int isize = 1; isize + istart <= kmer.getKmerLength(); isize++) {
+        VKmerBytesWritable subKmer;
+        for (int istart = 0; istart < kmer.getKmerLetterLength() - 1; istart++) {
+            for (int isize = 1; isize + istart <= kmer.getKmerLetterLength(); isize++) {
                 subKmer = kmerFactory.getSubKmerFromChain(istart, isize, kmer);
                 Assert.assertEquals("AGCTGACCG".substring(istart, istart + isize), subKmer.toString());
             }
@@ -85,60 +85,60 @@
 
     @Test
     public void TestMergeNext() {
-        KmerBytesWritable kmer = new KmerBytesWritable(9);
+        VKmerBytesWritable kmer = new VKmerBytesWritable(9);
         kmer.setByRead(array, 0);
         Assert.assertEquals("AGCTGACCG", kmer.toString());
 
         String text = "AGCTGACCG";
         for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
-            KmerBytesWritable newkmer = kmerFactory.mergeKmerWithNextCode(kmer, x);
+            VKmerBytesWritable newkmer = kmerFactory.mergeKmerWithNextCode(kmer, x);
             text = text + (char) GeneCode.GENE_SYMBOL[x];
             Assert.assertEquals(text, newkmer.toString());
-            kmer = new KmerBytesWritable(newkmer);
+            kmer = new VKmerBytesWritable(newkmer);
         }
         for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
-            KmerBytesWritable newkmer = kmerFactory.mergeKmerWithNextCode(kmer, x);
+            VKmerBytesWritable newkmer = kmerFactory.mergeKmerWithNextCode(kmer, x);
             text = text + (char) GeneCode.GENE_SYMBOL[x];
             Assert.assertEquals(text, newkmer.toString());
-            kmer = new KmerBytesWritable(newkmer);
+            kmer = new VKmerBytesWritable(newkmer);
         }
     }
 
     @Test
     public void TestMergePre() {
-        KmerBytesWritable kmer = new KmerBytesWritable(9);
+        VKmerBytesWritable kmer = new VKmerBytesWritable(9);
         kmer.setByRead(array, 0);
         Assert.assertEquals("AGCTGACCG", kmer.toString());
         String text = "AGCTGACCG";
         for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
-            KmerBytesWritable newkmer = kmerFactory.mergeKmerWithPreCode(kmer, x);
+            VKmerBytesWritable newkmer = kmerFactory.mergeKmerWithPreCode(kmer, x);
             text = (char) GeneCode.GENE_SYMBOL[x] + text;
             Assert.assertEquals(text, newkmer.toString());
-            kmer = new KmerBytesWritable(newkmer);
+            kmer = new VKmerBytesWritable(newkmer);
         }
         for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
-            KmerBytesWritable newkmer = kmerFactory.mergeKmerWithPreCode(kmer, x);
+            VKmerBytesWritable newkmer = kmerFactory.mergeKmerWithPreCode(kmer, x);
             text = (char) GeneCode.GENE_SYMBOL[x] + text;
             Assert.assertEquals(text, newkmer.toString());
-            kmer = new KmerBytesWritable(newkmer);
+            kmer = new VKmerBytesWritable(newkmer);
         }
     }
 
     @Test
     public void TestMergeTwoKmer() {
-        KmerBytesWritable kmer1 = new KmerBytesWritable(9);
+        VKmerBytesWritable kmer1 = new VKmerBytesWritable(9);
         kmer1.setByRead(array, 0);
         String text1 = "AGCTGACCG";
-        KmerBytesWritable kmer2 = new KmerBytesWritable(9);
+        VKmerBytesWritable kmer2 = new VKmerBytesWritable(9);
         kmer2.setByRead(array, 1);
         String text2 = "GCTGACCGT";
         Assert.assertEquals(text1, kmer1.toString());
         Assert.assertEquals(text2, kmer2.toString());
 
-        KmerBytesWritable merged = kmerFactory.mergeTwoKmer(kmer1, kmer2);
+        VKmerBytesWritable merged = kmerFactory.mergeTwoKmer(kmer1, kmer2);
         Assert.assertEquals(text1 + text2, merged.toString());
 
-        KmerBytesWritable kmer3 = new KmerBytesWritable(3);
+        VKmerBytesWritable kmer3 = new VKmerBytesWritable(3);
         kmer3.setByRead(array, 1);
         String text3 = "GCT";
         Assert.assertEquals(text3, kmer3.toString());
@@ -148,17 +148,17 @@
         merged = kmerFactory.mergeTwoKmer(kmer3, kmer1);
         Assert.assertEquals(text3 + text1, merged.toString());
 
-        KmerBytesWritable kmer4 = new KmerBytesWritable(8);
+        VKmerBytesWritable kmer4 = new VKmerBytesWritable(8);
         kmer4.setByRead(array, 0);
         String text4 = "AGCTGACC";
         Assert.assertEquals(text4, kmer4.toString());
         merged = kmerFactory.mergeTwoKmer(kmer4, kmer3);
         Assert.assertEquals(text4 + text3, merged.toString());
 
-        KmerBytesWritable kmer5 = new KmerBytesWritable(7);
+        VKmerBytesWritable kmer5 = new VKmerBytesWritable(7);
         kmer5.setByRead(array, 0);
         String text5 = "AGCTGAC";
-        KmerBytesWritable kmer6 = new KmerBytesWritable(9);
+        VKmerBytesWritable kmer6 = new VKmerBytesWritable(9);
         kmer6.setByRead(9, array, 1);
         String text6 = "GCTGACCGT";
         merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
@@ -173,19 +173,18 @@
         String text8 = "GCTG";
         merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
         Assert.assertEquals(text5 + text8, merged.toString());
-
     }
 
     @Test
     public void TestShift() {
-        KmerBytesWritable kmer = new KmerBytesWritable(kmerFactory.getKmerByRead(9, array, 0));
+        VKmerBytesWritable kmer = new VKmerBytesWritable(kmerFactory.getKmerByRead(9, array, 0));
         String text = "AGCTGACCG";
         Assert.assertEquals(text, kmer.toString());
 
-        KmerBytesWritable kmerForward = kmerFactory.shiftKmerWithNextCode(kmer, GeneCode.A);
+        VKmerBytesWritable kmerForward = kmerFactory.shiftKmerWithNextCode(kmer, GeneCode.A);
         Assert.assertEquals(text, kmer.toString());
         Assert.assertEquals("GCTGACCGA", kmerForward.toString());
-        KmerBytesWritable kmerBackward = kmerFactory.shiftKmerWithPreCode(kmer, GeneCode.C);
+        VKmerBytesWritable kmerBackward = kmerFactory.shiftKmerWithPreCode(kmer, GeneCode.C);
         Assert.assertEquals(text, kmer.toString());
         Assert.assertEquals("CAGCTGACC", kmerBackward.toString());
 
@@ -193,10 +192,10 @@
 
     @Test
     public void TestReverseKmer() {
-        KmerBytesWritable kmer = new KmerBytesWritable(7);
+        VKmerBytesWritable kmer = new VKmerBytesWritable(7);
         kmer.setByRead(array, 0);
         Assert.assertEquals(kmer.toString(), "AGCTGAC");
-        KmerBytesWritable reversed = kmerFactory.reverse(kmer);
+        VKmerBytesWritable reversed = kmerFactory.reverse(kmer);
         Assert.assertEquals(reversed.toString(), "CAGTCGA");
         
         kmer.reset(8);
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
index fa5725b..4f7b90e 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
@@ -15,18 +15,12 @@
 
 package edu.uci.ics.genomix.data.test;
 
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
 import junit.framework.Assert;
 
 import org.junit.Test;
 
 import edu.uci.ics.genomix.type.GeneCode;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
 
 public class KmerBytesWritableTest {
     static byte[] array = { 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'G' };
@@ -34,7 +28,8 @@
 
     @Test
     public void TestCompressKmer() {
-        KmerBytesWritable kmer = new KmerBytesWritable(k);
+        KmerBytesWritable.setGlobalKmerLength(k);
+        KmerBytesWritable kmer = new KmerBytesWritable();
         kmer.setByRead(array, 0);
         Assert.assertEquals(kmer.toString(), "AATAGAA");
 
@@ -44,7 +39,8 @@
 
     @Test
     public void TestMoveKmer() {
-        KmerBytesWritable kmer = new KmerBytesWritable(k);
+        KmerBytesWritable.setGlobalKmerLength(k);
+        KmerBytesWritable kmer = new KmerBytesWritable();
         kmer.setByRead(array, 0);
         Assert.assertEquals(kmer.toString(), "AATAGAA");
 
@@ -60,7 +56,8 @@
 
     @Test
     public void TestCompressKmerReverse() {
-        KmerBytesWritable kmer = new KmerBytesWritable(k);
+        KmerBytesWritable.setGlobalKmerLength(k);
+        KmerBytesWritable kmer = new KmerBytesWritable();
         kmer.setByRead(array, 0);
         Assert.assertEquals(kmer.toString(), "AATAGAA");
 
@@ -70,7 +67,8 @@
 
     @Test
     public void TestMoveKmerReverse() {
-        KmerBytesWritable kmer = new KmerBytesWritable(k);
+        KmerBytesWritable.setGlobalKmerLength(k);
+        KmerBytesWritable kmer = new KmerBytesWritable();
         kmer.setByRead(array, 0);
         Assert.assertEquals(kmer.toString(), "AATAGAA");
 
@@ -86,7 +84,8 @@
 
     @Test
     public void TestGetGene() {
-        KmerBytesWritable kmer = new KmerBytesWritable(9);
+        KmerBytesWritable.setGlobalKmerLength(9);
+        KmerBytesWritable kmer = new KmerBytesWritable();
         String text = "AGCTGACCG";
         byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G' };
         kmer.setByRead(array, 0);
@@ -101,8 +100,9 @@
         byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
         String string = "AGCTGACCGT";
         for (int k = 3; k <= 10; k++) {
-            KmerBytesWritable kmer = new KmerBytesWritable(k);
-            KmerBytesWritable kmerAppend = new KmerBytesWritable(k);
+            KmerBytesWritable.setGlobalKmerLength(k);
+            KmerBytesWritable kmer = new KmerBytesWritable();
+            KmerBytesWritable kmerAppend = new KmerBytesWritable();
             kmer.setByRead(array, 0);
             Assert.assertEquals(string.substring(0, k), kmer.toString());
             for (int b = 0; b < k; b++) {
@@ -118,312 +118,5 @@
             }
             Assert.assertEquals(kmer.toString(), kmerAppend.toString());
         }
-    }
-
-    @Test
-    public void TestMergeFFKmer() {
-        byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
-        String text = "AGCTGACCGT";
-        KmerBytesWritable kmer1 = new KmerBytesWritable(8);
-        kmer1.setByRead(array, 0);
-        String text1 = "AGCTGACC";
-        KmerBytesWritable kmer2 = new KmerBytesWritable(8);
-        kmer2.setByRead(array, 1);
-        String text2 = "GCTGACCG";
-        Assert.assertEquals(text2, kmer2.toString());
-        KmerBytesWritable merge = new KmerBytesWritable(kmer1);
-        int kmerSize = 8;
-        merge.mergeWithFFKmer(kmerSize, kmer2);
-        Assert.assertEquals(text1 + text2.substring(kmerSize - 1), merge.toString());
-
-        for (int i = 1; i < 8; i++) {
-            merge.set(kmer1);
-            merge.mergeWithFFKmer(i, kmer2);
-            Assert.assertEquals(text1 + text2.substring(i - 1), merge.toString());
-        }
-
-        for (int ik = 1; ik <= 10; ik++) {
-            for (int jk = 1; jk <= 10; jk++) {
-                kmer1 = new KmerBytesWritable(ik);
-                kmer2 = new KmerBytesWritable(jk);
-                kmer1.setByRead(array, 0);
-                kmer2.setByRead(array, 0);
-                text1 = text.substring(0, ik);
-                text2 = text.substring(0, jk);
-                Assert.assertEquals(text1, kmer1.toString());
-                Assert.assertEquals(text2, kmer2.toString());
-                for (int x = 1; x < jk; x++) {
-                    merge.set(kmer1);
-                    merge.mergeWithFFKmer(x, kmer2);
-                    Assert.assertEquals(text1 + text2.substring(x - 1), merge.toString());
-                }
-            }
-        }
-    }
-    
-    @Test
-    public void TestMergeFRKmer() {
-        int kmerSize = 3;
-        String result = "AAGCTAACAACC";
-        byte[] resultArray = result.getBytes();
-        
-        String text1 = "AAGCTAA";
-        KmerBytesWritable kmer1 = new KmerBytesWritable(text1.length());
-        kmer1.setByRead(resultArray, 0);
-        Assert.assertEquals(text1, kmer1.toString());
-        
-        // kmer2 is the rc of the end of the read
-        String text2 = "GGTTGTT";
-        KmerBytesWritable kmer2 = new KmerBytesWritable(text2.length());
-        kmer2.setByReadReverse(resultArray, result.length() - text2.length());
-        Assert.assertEquals(text2, kmer2.toString());
-        
-        KmerBytesWritable merge = new KmerBytesWritable(kmer1);
-        merge.mergeWithFRKmer(kmerSize, kmer2);
-        Assert.assertEquals(result, merge.toString());
-        
-        int i = 1;
-        merge.set(kmer1);
-        merge.mergeWithFRKmer(i, kmer2);
-        Assert.assertEquals("AAGCTAAAACAACC", merge.toString());
-        
-        i = 2;
-        merge.set(kmer1);
-        merge.mergeWithFRKmer(i, kmer2);
-        Assert.assertEquals("AAGCTAAACAACC", merge.toString());
-        
-        i = 3;
-        merge.set(kmer1);
-        merge.mergeWithFRKmer(i, kmer2);
-        Assert.assertEquals("AAGCTAACAACC", merge.toString());
-    }
-    
-    
-    @Test
-    public void TestMergeRFKmer() {
-        int kmerSize = 3;
-        String result = "GGCACAACAACCC";
-        byte[] resultArray = result.getBytes();
-        
-        String text1 = "AACAACCC";
-        KmerBytesWritable kmer1 = new KmerBytesWritable(text1.length());
-        kmer1.setByRead(resultArray, 5);
-        Assert.assertEquals(text1, kmer1.toString());
-        
-        // kmer2 is the rc of the end of the read
-        String text2 = "TTGTGCC";
-        KmerBytesWritable kmer2 = new KmerBytesWritable(text2.length());
-        kmer2.setByReadReverse(resultArray, 0);
-        Assert.assertEquals(text2, kmer2.toString());
-        
-        KmerBytesWritable merge = new KmerBytesWritable(kmer1);
-        merge.mergeWithRFKmer(kmerSize, kmer2);
-        Assert.assertEquals(result, merge.toString());
-        
-        int i = 1;
-        merge.set(kmer1);
-        merge.mergeWithRFKmer(i, kmer2);
-        Assert.assertEquals("GGCACAAAACAACCC", merge.toString());
-        
-        i = 2;
-        merge.set(kmer1);
-        merge.mergeWithRFKmer(i, kmer2);
-        Assert.assertEquals("GGCACAAACAACCC", merge.toString());
-        
-        i = 3;
-        merge.set(kmer1);
-        merge.mergeWithRFKmer(i, kmer2);
-        Assert.assertEquals("GGCACAACAACCC", merge.toString());
-        
-        String test1;
-        String test2;
-        test1 = "CTA";
-        test2 = "AGA";
-        KmerBytesWritable k1 = new KmerBytesWritable(3);
-        KmerBytesWritable k2 = new KmerBytesWritable(3);
-        k1.setByRead(test1.getBytes(), 0);
-        k2.setByRead(test2.getBytes(), 0);
-        k1.mergeWithRFKmer(3, k2);
-        Assert.assertEquals("TCTA", k1.toString());
-        
-        test1 = "CTA";
-        test2 = "ATA"; //TAT
-        k1 = new KmerBytesWritable(3);
-        k2 = new KmerBytesWritable(3);
-        k1.setByRead(test1.getBytes(), 0);
-        k2.setByRead(test2.getBytes(), 0);
-        k1.mergeWithFRKmer(3, k2);
-        Assert.assertEquals("CTAT", k1.toString());
-        
-        test1 = "ATA";
-        test2 = "CTA"; //TAT
-        k1 = new KmerBytesWritable(3);
-        k2 = new KmerBytesWritable(3);
-        k1.setByRead(test1.getBytes(), 0);
-        k2.setByRead(test2.getBytes(), 0);
-        k1.mergeWithFRKmer(3, k2);
-        Assert.assertEquals("ATAG", k1.toString());
-        
-        test1 = "TCTAT";
-        test2 = "GAAC";
-        k1 = new KmerBytesWritable(5);
-        k2 = new KmerBytesWritable(4);
-        k1.setByRead(test1.getBytes(), 0);
-        k2.setByRead(test2.getBytes(), 0);
-        k1.mergeWithRFKmer(3, k2);
-        Assert.assertEquals("GTTCTAT", k1.toString());
-    }
-    
-    
-
-    @Test
-    public void TestMergeRRKmer() {
-        byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
-        String text = "AGCTGACCGT";
-        KmerBytesWritable kmer1 = new KmerBytesWritable(8);
-        kmer1.setByRead(array, 0);
-        String text1 = "AGCTGACC";
-        KmerBytesWritable kmer2 = new KmerBytesWritable(8);
-        kmer2.setByRead(array, 1);
-        String text2 = "GCTGACCG";
-        Assert.assertEquals(text2, kmer2.toString());
-        KmerBytesWritable merge = new KmerBytesWritable(kmer2);
-        int kmerSize = 8;
-        merge.mergeWithRRKmer(kmerSize, kmer1);
-        Assert.assertEquals(text1 + text2.substring(kmerSize - 1), merge.toString());
-
-        for (int i = 1; i < 8; i++) {
-            merge.set(kmer2);
-            merge.mergeWithRRKmer(i, kmer1);
-            Assert.assertEquals(text1.substring(0, text1.length() - i + 1) + text2, merge.toString());
-        }
-
-        for (int ik = 1; ik <= 10; ik++) {
-            for (int jk = 1; jk <= 10; jk++) {
-                kmer1 = new KmerBytesWritable(ik);
-                kmer2 = new KmerBytesWritable(jk);
-                kmer1.setByRead(array, 0);
-                kmer2.setByRead(array, 0);
-                text1 = text.substring(0, ik);
-                text2 = text.substring(0, jk);
-                Assert.assertEquals(text1, kmer1.toString());
-                Assert.assertEquals(text2, kmer2.toString());
-                for (int x = 1; x < ik; x++) {
-                    merge.set(kmer2);
-                    merge.mergeWithRRKmer(x, kmer1);
-                    Assert.assertEquals(text1.substring(0, text1.length() - x + 1) + text2, merge.toString());
-                }
-            }
-        }
-    }
-    
-    @Test
-    public void TestFinalMerge() {
-        String selfString;
-        String match;
-        String msgString;
-        int index;
-        KmerBytesWritable kmer = new KmerBytesWritable();
-        int kmerSize = 3;
-        
-        String F1 = "AATAG";
-        String F2 = "TAGAA";
-        String R1 = "CTATT";
-        String R2 = "TTCTA";
-        
-        //FF test
-        selfString = F1;
-        match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
-        msgString = F2;
-        index = msgString.indexOf(match);
-        kmer.reset(msgString.length() - index);
-        kmer.setByRead(msgString.substring(index).getBytes(), 0);
-        System.out.println(kmer.toString());
-        
-        //FR test
-        selfString = F1;
-        match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
-        msgString = GeneCode.reverseComplement(R2);
-        index = msgString.indexOf(match);
-        kmer.reset(msgString.length() - index);
-        kmer.setByRead(msgString.substring(index).getBytes(), 0);
-        System.out.println(kmer.toString());
-        
-        //RF test
-        selfString = R1;
-        match = selfString.substring(0,kmerSize - 1); 
-        msgString = GeneCode.reverseComplement(F2);
-        index = msgString.lastIndexOf(match) + kmerSize - 2;
-        kmer.reset(index + 1);
-        kmer.setByReadReverse(msgString.substring(0, index + 1).getBytes(), 0);
-        System.out.println(kmer.toString());
-        
-        //RR test
-        selfString = R1;
-        match = selfString.substring(0,kmerSize - 1); 
-        msgString = R2;
-        index = msgString.lastIndexOf(match) + kmerSize - 2;
-        kmer.reset(index + 1);
-        kmer.setByRead(msgString.substring(0, index + 1).getBytes(), 0);
-        System.out.println(kmer.toString());
-        
-        String[][] connectedTable = new String[][]{
-                {"FF", "RF"},
-                {"FF", "RR"},
-                {"FR", "RF"},
-                {"FR", "RR"}
-        };
-        System.out.println(connectedTable[0][1]);
-        
-        Set<Long> s1 = new HashSet<Long>();
-        Set<Long> s2 = new HashSet<Long>();
-        s1.add((long) 1);
-        s1.add((long) 2);
-        s2.add((long) 2);
-        s2.add((long) 3);
-        Set<Long> intersection = new HashSet<Long>();
-        intersection.addAll(s1);
-        intersection.retainAll(s2);
-        System.out.println(intersection.toString());
-        Set<Long> difference = new HashSet<Long>();
-        difference.addAll(s1);
-        difference.removeAll(s2);
-        System.out.println(difference.toString());
-        
-        Map<KmerBytesWritable, Set<Long>> map = new HashMap<KmerBytesWritable, Set<Long>>();
-        KmerBytesWritable k1 = new KmerBytesWritable(3);
-        Set<Long> set1 = new HashSet<Long>();
-        k1.setByRead(("CTA").getBytes(), 0);
-        set1.add((long)1);
-        map.put(k1, set1);
-        KmerBytesWritable k2 = new KmerBytesWritable(3);
-        k2.setByRead(("GTA").getBytes(), 0);
-        Set<Long> set2 = new HashSet<Long>();
-        set2.add((long) 2);
-        map.put(k2, set2);
-        KmerBytesWritable k3 = new KmerBytesWritable(3);
-        k3.setByRead(("ATG").getBytes(), 0);
-        Set<Long> set3 = new HashSet<Long>();
-        set3.add((long) 2);
-        map.put(k3, set3);
-        KmerBytesWritable k4 = new KmerBytesWritable(3);
-        k4.setByRead(("AAT").getBytes(), 0);
-        Set<Long> set4 = new HashSet<Long>();
-        set4.add((long) 1);
-        map.put(k4, set4);
-        KmerListWritable kmerList = new KmerListWritable(3);
-        kmerList.append(k1);
-        kmerList.append(k2);
-        System.out.println("CTA = " + map.get(k1).toString());
-        System.out.println("GTA = " + map.get(k2).toString());
-        System.out.println("ATG = " + map.get(k3).toString());
-        System.out.println("AAT = " + map.get(k4).toString());
-        System.out.println(k1.compareTo(k2));
-        System.out.println(k2.compareTo(k1));
-        
-        System.out.println("CTA = " + kmerList.getPosition(0).toString());
-        System.out.println("GTA = " + kmerList.getPosition(1).toString());
-        System.out.println("CTA = " + map.get(kmerList.getPosition(0)).toString());
-        System.out.println("GTA = " + map.get(kmerList.getPosition(1)).toString());
-    }
+    }    
 }
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java.orig b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java.orig
new file mode 100644
index 0000000..8a0cb6d
--- /dev/null
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java.orig
@@ -0,0 +1,427 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.data.test;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import junit.framework.Assert;
+
+import org.junit.Test;
+
+import edu.uci.ics.genomix.type.GeneCode;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+
+public class KmerBytesWritableTest {
+    static byte[] array = { 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'G' };
+    static int k = 7;
+
+    @Test
+    public void TestCompressKmer() {
+        KmerBytesWritable.setGlobalKmerLength(k);
+        KmerBytesWritable kmer = new KmerBytesWritable();
+        kmer.setByRead(array, 0);
+        Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+        kmer.setByRead(array, 1);
+        Assert.assertEquals(kmer.toString(), "ATAGAAG");
+    }
+
+    @Test
+    public void TestMoveKmer() {
+        KmerBytesWritable.setGlobalKmerLength(k);
+        KmerBytesWritable kmer = new KmerBytesWritable();
+        kmer.setByRead(array, 0);
+        Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+        for (int i = k; i < array.length - 1; i++) {
+            kmer.shiftKmerWithNextCode(array[i]);
+            Assert.assertTrue(false);
+        }
+
+        byte out = kmer.shiftKmerWithNextChar(array[array.length - 1]);
+        Assert.assertEquals(out, GeneCode.getCodeFromSymbol((byte) 'A'));
+        Assert.assertEquals(kmer.toString(), "ATAGAAG");
+    }
+
+    @Test
+    public void TestCompressKmerReverse() {
+        KmerBytesWritable.setGlobalKmerLength(k);
+        KmerBytesWritable kmer = new KmerBytesWritable();
+        kmer.setByRead(array, 0);
+        Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+        kmer.setByReadReverse(array, 1);
+        Assert.assertEquals(kmer.toString(), "CTTCTAT");
+    }
+
+    @Test
+    public void TestMoveKmerReverse() {
+        KmerBytesWritable.setGlobalKmerLength(k);
+        KmerBytesWritable kmer = new KmerBytesWritable();
+        kmer.setByRead(array, 0);
+        Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+        for (int i = k; i < array.length - 1; i++) {
+            kmer.shiftKmerWithPreChar(array[i]);
+            Assert.assertTrue(false);
+        }
+
+        byte out = kmer.shiftKmerWithPreChar(array[array.length - 1]);
+        Assert.assertEquals(out, GeneCode.getCodeFromSymbol((byte) 'A'));
+        Assert.assertEquals(kmer.toString(), "GAATAGA");
+    }
+
+    @Test
+    public void TestGetGene() {
+        KmerBytesWritable.setGlobalKmerLength(9);
+        KmerBytesWritable kmer = new KmerBytesWritable();
+        String text = "AGCTGACCG";
+        byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G' };
+        kmer.setByRead(array, 0);
+
+        for (int i = 0; i < 9; i++) {
+            Assert.assertEquals(text.charAt(i), (char) (GeneCode.getSymbolFromCode(kmer.getGeneCodeAtPosition(i))));
+        }
+    }
+
+    @Test
+    public void TestGetOneByteFromKmer() {
+        byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
+        String string = "AGCTGACCGT";
+        for (int k = 3; k <= 10; k++) {
+            KmerBytesWritable.setGlobalKmerLength(k);
+            KmerBytesWritable kmer = new KmerBytesWritable();
+            KmerBytesWritable kmerAppend = new KmerBytesWritable();
+            kmer.setByRead(array, 0);
+            Assert.assertEquals(string.substring(0, k), kmer.toString());
+            for (int b = 0; b < k; b++) {
+                byte byteActual = KmerBytesWritable.getOneByteFromKmerAtPosition(b, kmer.getBytes(), kmer.getOffset(),
+                        kmer.getLength());
+                byte byteExpect = GeneCode.getCodeFromSymbol(array[b]);
+                for (int i = 1; i < 4 && b + i < k; i++) {
+                    byteExpect += GeneCode.getCodeFromSymbol(array[b + i]) << (i * 2);
+                }
+                Assert.assertEquals(byteActual, byteExpect);
+                KmerBytesWritable.appendOneByteAtPosition(b, byteActual, kmerAppend.getBytes(), kmerAppend.getOffset(),
+                        kmerAppend.getLength());
+            }
+            Assert.assertEquals(kmer.toString(), kmerAppend.toString());
+        }
+    }
+<<<<<<< HEAD
+=======
+
+    @Test
+    public void TestMergeFFKmer() {
+        byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
+        String text = "AGCTGACCGT";
+        KmerBytesWritable kmer1 = new KmerBytesWritable(8);
+        kmer1.setByRead(array, 0);
+        String text1 = "AGCTGACC";
+        KmerBytesWritable kmer2 = new KmerBytesWritable(8);
+        kmer2.setByRead(array, 1);
+        String text2 = "GCTGACCG";
+        Assert.assertEquals(text2, kmer2.toString());
+        KmerBytesWritable merge = new KmerBytesWritable(kmer1);
+        int kmerSize = 8;
+        merge.mergeWithFFKmer(kmerSize, kmer2);
+        Assert.assertEquals(text1 + text2.substring(kmerSize - 1), merge.toString());
+
+        for (int i = 1; i < 8; i++) {
+            merge.set(kmer1);
+            merge.mergeWithFFKmer(i, kmer2);
+            Assert.assertEquals(text1 + text2.substring(i - 1), merge.toString());
+        }
+
+        for (int ik = 1; ik <= 10; ik++) {
+            for (int jk = 1; jk <= 10; jk++) {
+                kmer1 = new KmerBytesWritable(ik);
+                kmer2 = new KmerBytesWritable(jk);
+                kmer1.setByRead(array, 0);
+                kmer2.setByRead(array, 0);
+                text1 = text.substring(0, ik);
+                text2 = text.substring(0, jk);
+                Assert.assertEquals(text1, kmer1.toString());
+                Assert.assertEquals(text2, kmer2.toString());
+                for (int x = 1; x < jk; x++) {
+                    merge.set(kmer1);
+                    merge.mergeWithFFKmer(x, kmer2);
+                    Assert.assertEquals(text1 + text2.substring(x - 1), merge.toString());
+                }
+            }
+        }
+    }
+    
+    @Test
+    public void TestMergeFRKmer() {
+        int kmerSize = 3;
+        String result = "AAGCTAACAACC";
+        byte[] resultArray = result.getBytes();
+        
+        String text1 = "AAGCTAA";
+        KmerBytesWritable kmer1 = new KmerBytesWritable(text1.length());
+        kmer1.setByRead(resultArray, 0);
+        Assert.assertEquals(text1, kmer1.toString());
+        
+        // kmer2 is the rc of the end of the read
+        String text2 = "GGTTGTT";
+        KmerBytesWritable kmer2 = new KmerBytesWritable(text2.length());
+        kmer2.setByReadReverse(resultArray, result.length() - text2.length());
+        Assert.assertEquals(text2, kmer2.toString());
+        
+        KmerBytesWritable merge = new KmerBytesWritable(kmer1);
+        merge.mergeWithFRKmer(kmerSize, kmer2);
+        Assert.assertEquals(result, merge.toString());
+        
+        int i = 1;
+        merge.set(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAAAACAACC", merge.toString());
+        
+        i = 2;
+        merge.set(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAAACAACC", merge.toString());
+        
+        i = 3;
+        merge.set(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAACAACC", merge.toString());
+    }
+    
+    
+    @Test
+    public void TestMergeRFKmer() {
+        int kmerSize = 3;
+        String result = "GGCACAACAACCC";
+        byte[] resultArray = result.getBytes();
+        
+        String text1 = "AACAACCC";
+        KmerBytesWritable kmer1 = new KmerBytesWritable(text1.length());
+        kmer1.setByRead(resultArray, 5);
+        Assert.assertEquals(text1, kmer1.toString());
+        
+        // kmer2 is the rc of the end of the read
+        String text2 = "TTGTGCC";
+        KmerBytesWritable kmer2 = new KmerBytesWritable(text2.length());
+        kmer2.setByReadReverse(resultArray, 0);
+        Assert.assertEquals(text2, kmer2.toString());
+        
+        KmerBytesWritable merge = new KmerBytesWritable(kmer1);
+        merge.mergeWithRFKmer(kmerSize, kmer2);
+        Assert.assertEquals(result, merge.toString());
+        
+        int i = 1;
+        merge.set(kmer1);
+        merge.mergeWithRFKmer(i, kmer2);
+        Assert.assertEquals("GGCACAAAACAACCC", merge.toString());
+        
+        i = 2;
+        merge.set(kmer1);
+        merge.mergeWithRFKmer(i, kmer2);
+        Assert.assertEquals("GGCACAAACAACCC", merge.toString());
+        
+        i = 3;
+        merge.set(kmer1);
+        merge.mergeWithRFKmer(i, kmer2);
+        Assert.assertEquals("GGCACAACAACCC", merge.toString());
+        
+        String test1;
+        String test2;
+        test1 = "CTA";
+        test2 = "AGA";
+        KmerBytesWritable k1 = new KmerBytesWritable(3);
+        KmerBytesWritable k2 = new KmerBytesWritable(3);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k1.mergeWithRFKmer(3, k2);
+        Assert.assertEquals("TCTA", k1.toString());
+        
+        test1 = "CTA";
+        test2 = "ATA"; //TAT
+        k1 = new KmerBytesWritable(3);
+        k2 = new KmerBytesWritable(3);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k1.mergeWithFRKmer(3, k2);
+        Assert.assertEquals("CTAT", k1.toString());
+        
+        test1 = "ATA";
+        test2 = "CTA"; //TAT
+        k1 = new KmerBytesWritable(3);
+        k2 = new KmerBytesWritable(3);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k1.mergeWithFRKmer(3, k2);
+        Assert.assertEquals("ATAG", k1.toString());
+        
+        test1 = "TCTAT";
+        test2 = "GAAC";
+        k1 = new KmerBytesWritable(5);
+        k2 = new KmerBytesWritable(4);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k1.mergeWithRFKmer(3, k2);
+        Assert.assertEquals("GTTCTAT", k1.toString());
+    }
+    
+    
+
+    @Test
+    public void TestMergeRRKmer() {
+        byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
+        String text = "AGCTGACCGT";
+        KmerBytesWritable kmer1 = new KmerBytesWritable(8);
+        kmer1.setByRead(array, 0);
+        String text1 = "AGCTGACC";
+        KmerBytesWritable kmer2 = new KmerBytesWritable(8);
+        kmer2.setByRead(array, 1);
+        String text2 = "GCTGACCG";
+        Assert.assertEquals(text2, kmer2.toString());
+        KmerBytesWritable merge = new KmerBytesWritable(kmer2);
+        int kmerSize = 8;
+        merge.mergeWithRRKmer(kmerSize, kmer1);
+        Assert.assertEquals(text1 + text2.substring(kmerSize - 1), merge.toString());
+
+        for (int i = 1; i < 8; i++) {
+            merge.set(kmer2);
+            merge.mergeWithRRKmer(i, kmer1);
+            Assert.assertEquals(text1.substring(0, text1.length() - i + 1) + text2, merge.toString());
+        }
+
+        for (int ik = 1; ik <= 10; ik++) {
+            for (int jk = 1; jk <= 10; jk++) {
+                kmer1 = new KmerBytesWritable(ik);
+                kmer2 = new KmerBytesWritable(jk);
+                kmer1.setByRead(array, 0);
+                kmer2.setByRead(array, 0);
+                text1 = text.substring(0, ik);
+                text2 = text.substring(0, jk);
+                Assert.assertEquals(text1, kmer1.toString());
+                Assert.assertEquals(text2, kmer2.toString());
+                for (int x = 1; x < ik; x++) {
+                    merge.set(kmer2);
+                    merge.mergeWithRRKmer(x, kmer1);
+                    Assert.assertEquals(text1.substring(0, text1.length() - x + 1) + text2, merge.toString());
+                }
+            }
+        }
+    }
+    
+    @Test
+    public void TestFinalMerge() {
+        String selfString;
+        String match;
+        String msgString;
+        int index;
+        KmerBytesWritable kmer = new KmerBytesWritable();
+        int kmerSize = 3;
+        
+        String F1 = "AATAG";
+        String F2 = "TAGAA";
+        String R1 = "CTATT";
+        String R2 = "TTCTA";
+        
+        //FF test
+        selfString = F1;
+        match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
+        msgString = F2;
+        index = msgString.indexOf(match);
+        kmer.reset(msgString.length() - index);
+        kmer.setByRead(msgString.substring(index).getBytes(), 0);
+        System.out.println(kmer.toString());
+        
+        //FR test
+        selfString = F1;
+        match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
+        msgString = GeneCode.reverseComplement(R2);
+        index = msgString.indexOf(match);
+        kmer.reset(msgString.length() - index);
+        kmer.setByRead(msgString.substring(index).getBytes(), 0);
+        System.out.println(kmer.toString());
+        
+        //RF test
+        selfString = R1;
+        match = selfString.substring(0,kmerSize - 1); 
+        msgString = GeneCode.reverseComplement(F2);
+        index = msgString.lastIndexOf(match) + kmerSize - 2;
+        kmer.reset(index + 1);
+        kmer.setByReadReverse(msgString.substring(0, index + 1).getBytes(), 0);
+        System.out.println(kmer.toString());
+        
+        //RR test
+        selfString = R1;
+        match = selfString.substring(0,kmerSize - 1); 
+        msgString = R2;
+        index = msgString.lastIndexOf(match) + kmerSize - 2;
+        kmer.reset(index + 1);
+        kmer.setByRead(msgString.substring(0, index + 1).getBytes(), 0);
+        System.out.println(kmer.toString());
+        
+        String[][] connectedTable = new String[][]{
+                {"FF", "RF"},
+                {"FF", "RR"},
+                {"FR", "RF"},
+                {"FR", "RR"}
+        };
+        System.out.println(connectedTable[0][1]);
+        
+        Set<Long> s1 = new HashSet<Long>();
+        Set<Long> s2 = new HashSet<Long>();
+        s1.add((long) 1);
+        s1.add((long) 2);
+        s2.add((long) 2);
+        s2.add((long) 3);
+        Set<Long> intersection = new HashSet<Long>();
+        intersection.addAll(s1);
+        intersection.retainAll(s2);
+        System.out.println(intersection.toString());
+        Set<Long> difference = new HashSet<Long>();
+        difference.addAll(s1);
+        difference.removeAll(s2);
+        System.out.println(difference.toString());
+        
+        Map<KmerBytesWritable, Set<Long>> map = new HashMap<KmerBytesWritable, Set<Long>>();
+        KmerBytesWritable k1 = new KmerBytesWritable(3);
+        Set<Long> set1 = new HashSet<Long>();
+        k1.setByRead(("CTA").getBytes(), 0);
+        set1.add((long)1);
+        map.put(k1, set1);
+        KmerBytesWritable k2 = new KmerBytesWritable(3);
+        k2.setByRead(("GTA").getBytes(), 0);
+        Set<Long> set2 = new HashSet<Long>();
+        set2.add((long) 2);
+        map.put(k2, set2);
+        KmerBytesWritable k3 = new KmerBytesWritable(3);
+        k3.setByRead(("ATG").getBytes(), 0);
+        Set<Long> set3 = new HashSet<Long>();
+        set3.add((long) 3);
+        map.put(k3, set3);
+        KmerBytesWritable k4 = new KmerBytesWritable(3);
+        k4.setByRead(("AAT").getBytes(), 0);
+        Set<Long> set4 = new HashSet<Long>();
+        set4.add((long) 4);
+        map.put(k4, set4);
+        System.out.println("CTA = " + map.get(k1).toString());
+        System.out.println("GTA = " + map.get(k2).toString());
+        System.out.println("ATG = " + map.get(k3).toString());
+        System.out.println("AAT = " + map.get(k4).toString());
+    }
+>>>>>>> 94e075b5c3db9aa613ef61c2581430a143b17bc8
+}
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
index 3c1428a..9ca4488 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
@@ -7,33 +7,33 @@
 
 import org.junit.Test;
 
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
 
 public class KmerListWritableTest {
 
     @Test
     public void TestInitial() {
-        KmerListWritable kmerList = new KmerListWritable();
+        VKmerListWritable kmerList = new VKmerListWritable();
         Assert.assertEquals(kmerList.getCountOfPosition(), 0);
         
         //one kmer in list and reset each time
-        KmerBytesWritable kmer;
+        VKmerBytesWritable kmer;
         for (int i = 1; i < 200; i++) {
-            kmer = new KmerBytesWritable(i);
+            kmer = new VKmerBytesWritable(i);
             String randomString = generaterRandomString(i);
             byte[] array = randomString.getBytes();
             kmer.setByRead(array, 0);
-            kmerList.reset(kmer.getKmerLength());
+            kmerList.reset();
             kmerList.append(kmer);
-            Assert.assertEquals(kmerList.getPosition(0).toString(), randomString);
+            Assert.assertEquals(randomString, kmerList.getPosition(0).toString());
             Assert.assertEquals(1, kmerList.getCountOfPosition());
         }
         
-        kmerList.reset(0);
+        kmerList.reset();
         //add one more kmer each time and fix kmerSize
         for (int i = 0; i < 200; i++) {
-            kmer = new KmerBytesWritable(5);
+            kmer = new VKmerBytesWritable(5);
             String randomString = generaterRandomString(5);
             byte[] array = randomString.getBytes();
             kmer.setByRead(array, 0);
@@ -44,8 +44,8 @@
         
         byte [] another = new byte [kmerList.getLength()*2];
         int start = 20;
-        System.arraycopy(kmerList.getByteArray(), 0, another, start, kmerList.getLength());
-        KmerListWritable plist2 = new KmerListWritable(kmerList.kmerlength, kmerList.getCountOfPosition(),another,start);
+        System.arraycopy(kmerList.getByteArray(), kmerList.getStartOffset(), another, start, kmerList.getLength());
+        VKmerListWritable plist2 = new VKmerListWritable(another, start);
         for(int i = 0; i < plist2.getCountOfPosition(); i++){
             Assert.assertEquals(kmerList.getPosition(i).toString(), plist2.getPosition(i).toString());
         }
@@ -53,39 +53,42 @@
     
     @Test
     public void TestRemove() {
-        KmerListWritable kmerList = new KmerListWritable();
+        VKmerListWritable kmerList = new VKmerListWritable();
         Assert.assertEquals(kmerList.getCountOfPosition(), 0);
         
         int i;
-        KmerBytesWritable kmer;
+        VKmerBytesWritable kmer;
         for (i = 0; i < 200; i++) {
-            kmer = new KmerBytesWritable(5);
+            kmer = new VKmerBytesWritable(5);
             String randomString = generaterRandomString(5);
             byte[] array = randomString.getBytes();
             kmer.setByRead(array, 0);
             kmerList.append(kmer);
-            Assert.assertEquals(kmerList.getPosition(i).toString(), randomString);
+            Assert.assertEquals(randomString, kmerList.getPosition(i).toString());
             Assert.assertEquals(i + 1, kmerList.getCountOfPosition());
         }
         
         //delete one element each time
-        KmerBytesWritable tmpKmer = new KmerBytesWritable();
+        VKmerBytesWritable tmpKmer = new VKmerBytesWritable(5);
         i = 0;
-        KmerListWritable copyList = new KmerListWritable();
-        copyList.set(kmerList);
-        Iterator<KmerBytesWritable> iterator;
+        VKmerListWritable copyList = new VKmerListWritable();
+        copyList.setCopy(kmerList);
+        Iterator<VKmerBytesWritable> iterator;
         for(int j = 0; j < 5; j++){
             iterator = copyList.iterator();
             byte[] array = kmerList.getPosition(j).toString().getBytes();
-            KmerBytesWritable deletePos = new KmerBytesWritable(5);
+            VKmerBytesWritable deletePos = new VKmerBytesWritable(5);
             deletePos.setByRead(array, 0);
+            boolean removed = false;
             while(iterator.hasNext()){
                 tmpKmer = iterator.next();
                 if(tmpKmer.equals(deletePos)){
                     iterator.remove();
+                    removed = true;
                     break;
                 }
             }
+            Assert.assertTrue(removed);
             Assert.assertEquals(200 - 1 - j, copyList.getCountOfPosition());
             while(iterator.hasNext()){
                 tmpKmer = iterator.next();
@@ -104,13 +107,13 @@
         
         Assert.assertEquals(0, kmerList.getCountOfPosition());
         
-        KmerListWritable edgeList = new KmerListWritable(3);
-        KmerBytesWritable k = new KmerBytesWritable(3);
+        VKmerListWritable edgeList = new VKmerListWritable();
+        VKmerBytesWritable k = new VKmerBytesWritable(3);
         k.setByRead(("AAA").getBytes(), 0);
         edgeList.append(k);
         k.setByRead(("CCC").getBytes(), 0);
         edgeList.append(k);
-        for(KmerBytesWritable edge : edgeList){
+        for(VKmerBytesWritable edge : edgeList){
         	System.out.println(edge.toString());
         }
     }
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionListWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionListWritableTest.java
index fea658d..ac7322e 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionListWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionListWritableTest.java
@@ -41,7 +41,7 @@
         byte [] another = new byte [plist.getLength()*2];
         int start = 20;
         System.arraycopy(plist.getByteArray(), 0, another, start, plist.getLength());
-        PositionListWritable plist2 = new PositionListWritable(plist.getCountOfPosition(),another,start);
+        PositionListWritable plist2 = new PositionListWritable(another,start);
         for( i = 0; i < plist2.getCountOfPosition(); i++){
             Assert.assertEquals(plist.getPosition(i), plist2.getPosition(i));
         }
@@ -84,19 +84,22 @@
             iterator = copyList.iterator();
             PositionWritable deletePos = new PositionWritable();
             deletePos.set((byte)1, (long)j, j);
+            boolean removed = false;
             while(iterator.hasNext()){
                 pos = iterator.next();
                 if(pos.equals(deletePos)){
                     iterator.remove();
+                    removed = true;
                     break;
                 }
             }
+            Assert.assertTrue(removed);
             Assert.assertEquals(5 - 1 - j, copyList.getCountOfPosition());
             while(iterator.hasNext()){
                 pos = iterator.next();
-                Assert.assertTrue(pos.getUUID() != deletePos.getUUID());
-                Assert.assertTrue(pos.getReadId() != deletePos.getReadId());
-                Assert.assertTrue(pos.getPosId() != deletePos.getPosId());
+                Assert.assertTrue(! (pos.getUUID() == deletePos.getUUID() && 
+                                  pos.getReadId() == deletePos.getReadId() && 
+                                  pos.getPosId() == deletePos.getPosId()));
                 i++;
             }
         }
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/VKmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/VKmerBytesWritableTest.java
new file mode 100644
index 0000000..2493b7e
--- /dev/null
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/VKmerBytesWritableTest.java
@@ -0,0 +1,558 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.data.test;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import junit.framework.Assert;
+
+import org.junit.Test;
+
+import edu.uci.ics.genomix.type.GeneCode;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
+
+
+public class VKmerBytesWritableTest {
+    static byte[] array = { 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'G' };
+    static int k = 7;
+
+    @Test
+    public void TestCompressKmer() {
+        VKmerBytesWritable kmer = new VKmerBytesWritable(k);
+        kmer.setByRead(array, 0);
+        Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+        kmer.setByRead(array, 1);
+        Assert.assertEquals(kmer.toString(), "ATAGAAG");
+    }
+
+    @Test
+    public void TestMoveKmer() {
+        VKmerBytesWritable kmer = new VKmerBytesWritable(k);
+        kmer.setByRead(array, 0);
+        Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+        for (int i = k; i < array.length - 1; i++) {
+            kmer.shiftKmerWithNextCode(array[i]);
+            Assert.assertTrue(false);
+        }
+
+        byte out = kmer.shiftKmerWithNextChar(array[array.length - 1]);
+        Assert.assertEquals(out, GeneCode.getCodeFromSymbol((byte) 'A'));
+        Assert.assertEquals(kmer.toString(), "ATAGAAG");
+    }
+
+    @Test
+    public void TestCompressKmerReverse() {
+        VKmerBytesWritable kmer = new VKmerBytesWritable(k);
+        kmer.setByRead(array, 0);
+        Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+        kmer.setByReadReverse(array, 1);
+        Assert.assertEquals(kmer.toString(), "CTTCTAT");
+    }
+
+    @Test
+    public void TestMoveKmerReverse() {
+        VKmerBytesWritable kmer = new VKmerBytesWritable(k);
+        kmer.setByRead(array, 0);
+        Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+        for (int i = k; i < array.length - 1; i++) {
+            kmer.shiftKmerWithPreChar(array[i]);
+            Assert.assertTrue(false);
+        }
+
+        byte out = kmer.shiftKmerWithPreChar(array[array.length - 1]);
+        Assert.assertEquals(out, GeneCode.getCodeFromSymbol((byte) 'A'));
+        Assert.assertEquals(kmer.toString(), "GAATAGA");
+    }
+
+    @Test
+    public void TestGetGene() {
+        VKmerBytesWritable kmer = new VKmerBytesWritable(9);
+        String text = "AGCTGACCG";
+        byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G' };
+        kmer.setByRead(array, 0);
+
+        for (int i = 0; i < 9; i++) {
+            Assert.assertEquals(text.charAt(i), (char) (GeneCode.getSymbolFromCode(kmer.getGeneCodeAtPosition(i))));
+        }
+    }
+
+    @Test
+    public void TestGetOneByteFromKmer() {
+        byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
+        String string = "AGCTGACCGT";
+        for (int k = 3; k <= 10; k++) {
+            VKmerBytesWritable kmer = new VKmerBytesWritable(k);
+            VKmerBytesWritable kmerAppend = new VKmerBytesWritable(k);
+            kmer.setByRead(array, 0);
+            Assert.assertEquals(string.substring(0, k), kmer.toString());
+            for (int b = 0; b < k; b++) {
+                byte byteActual = KmerBytesWritable.getOneByteFromKmerAtPosition(b, kmer.getBytes(),
+                        kmer.getKmerOffset(), kmer.getKmerByteLength());
+                byte byteExpect = GeneCode.getCodeFromSymbol(array[b]);
+                for (int i = 1; i < 4 && b + i < k; i++) {
+                    byteExpect += GeneCode.getCodeFromSymbol(array[b + i]) << (i * 2);
+                }
+                Assert.assertEquals(byteActual, byteExpect);
+                KmerBytesWritable.appendOneByteAtPosition(b, byteActual, kmerAppend.getBytes(),
+                        kmerAppend.getKmerOffset(), kmerAppend.getKmerByteLength());
+            }
+            Assert.assertEquals(kmer.toString(), kmerAppend.toString());
+        }
+    }
+
+    @Test
+    public void TestMergeFFKmer() {
+        byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
+        String text = "AGCTGACCGT";
+        VKmerBytesWritable kmer1 = new VKmerBytesWritable(8);
+        kmer1.setByRead(array, 0);
+        String text1 = "AGCTGACC";
+        Assert.assertEquals(text1, kmer1.toString());
+
+        VKmerBytesWritable kmer2 = new VKmerBytesWritable(8);
+        kmer2.setByRead(array, 1);
+        String text2 = "GCTGACCG";
+        Assert.assertEquals(text2, kmer2.toString());
+
+        VKmerBytesWritable merge = new VKmerBytesWritable(kmer1);
+        int kmerSize = 8;
+        merge.mergeWithFFKmer(kmerSize, kmer2);
+        Assert.assertEquals(text1 + text2.substring(kmerSize - 1), merge.toString());
+
+        for (int i = 1; i < 8; i++) {
+            merge.setAsCopy(kmer1);
+            merge.mergeWithFFKmer(i, kmer2);
+            Assert.assertEquals(text1 + text2.substring(i - 1), merge.toString());
+        }
+
+        for (int ik = 1; ik <= 10; ik++) {
+            for (int jk = 1; jk <= 10; jk++) {
+                kmer1 = new VKmerBytesWritable(ik);
+                kmer2 = new VKmerBytesWritable(jk);
+                kmer1.setByRead(array, 0);
+                kmer2.setByRead(array, 0);
+                text1 = text.substring(0, ik);
+                text2 = text.substring(0, jk);
+                Assert.assertEquals(text1, kmer1.toString());
+                Assert.assertEquals(text2, kmer2.toString());
+                for (int x = 1; x < jk; x++) {
+                    merge.setAsCopy(kmer1);
+                    merge.mergeWithFFKmer(x, kmer2);
+                    Assert.assertEquals(text1 + text2.substring(x - 1), merge.toString());
+                }
+            }
+        }
+    }
+
+    @Test
+    public void TestMergeFRKmer() {
+        int kmerSize = 3;
+        String result = "AAGCTAACAACC";
+        byte[] resultArray = result.getBytes();
+
+        String text1 = "AAGCTAA";
+        VKmerBytesWritable kmer1 = new VKmerBytesWritable(text1.length());
+        kmer1.setByRead(resultArray, 0);
+        Assert.assertEquals(text1, kmer1.toString());
+
+        // kmer2 is the rc of the end of the read
+        String text2 = "GGTTGTT";
+        VKmerBytesWritable kmer2 = new VKmerBytesWritable(text2.length());
+        kmer2.setByReadReverse(resultArray, result.length() - text2.length());
+        Assert.assertEquals(text2, kmer2.toString());
+
+        VKmerBytesWritable merge = new VKmerBytesWritable(kmer1);
+        merge.mergeWithFRKmer(kmerSize, kmer2);
+        Assert.assertEquals(result, merge.toString());
+
+        int i = 1;
+        merge.setAsCopy(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAAAACAACC", merge.toString());
+
+        i = 2;
+        merge.setAsCopy(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAAACAACC", merge.toString());
+
+        i = 3;
+        merge.setAsCopy(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAACAACC", merge.toString());
+    }
+
+    @Test
+    public void TestMergeRFKmer() {
+        int kmerSize = 3;
+        String result = "GGCACAACAACCC";
+        byte[] resultArray = result.getBytes();
+
+        String text1 = "AACAACCC";
+        VKmerBytesWritable kmer1 = new VKmerBytesWritable(text1.length());
+        kmer1.setByRead(resultArray, 5);
+        Assert.assertEquals(text1, kmer1.toString());
+
+        // kmer2 is the rc of the end of the read
+        String text2 = "TTGTGCC";
+        VKmerBytesWritable kmer2 = new VKmerBytesWritable(text2.length());
+        kmer2.setByReadReverse(resultArray, 0);
+        Assert.assertEquals(text2, kmer2.toString());
+
+        VKmerBytesWritable merge = new VKmerBytesWritable(kmer1);
+        merge.mergeWithRFKmer(kmerSize, kmer2);
+        Assert.assertEquals(result, merge.toString());
+
+        int i = 1;
+        merge.setAsCopy(kmer1);
+        merge.mergeWithRFKmer(i, kmer2);
+        Assert.assertEquals("GGCACAAAACAACCC", merge.toString());
+
+        i = 2;
+        merge.setAsCopy(kmer1);
+        merge.mergeWithRFKmer(i, kmer2);
+        Assert.assertEquals("GGCACAAACAACCC", merge.toString());
+
+        i = 3;
+        merge.setAsCopy(kmer1);
+        merge.mergeWithRFKmer(i, kmer2);
+        Assert.assertEquals("GGCACAACAACCC", merge.toString());
+
+        // String test1 = "CTTAT";
+        // String test2 = "AGACC"; // rc = GGTCT
+        // VKmerBytesWritable k1 = new VKmerBytesWritable(5);
+        // VKmerBytesWritable k2 = new VKmerBytesWritable(5);
+        // k1.setByRead(test1.getBytes(), 0);
+        // k2.setByRead(test2.getBytes(), 0);
+        // k1.mergeWithRFKmer(3, k2);
+        // Assert.assertEquals("GGTCTTAT", k1.toString()); //GGTCGTCT ->
+        // AGACGACC ??
+
+        String test3 = "CTA";
+        String test4 = "AGA"; // rc = TCT
+        VKmerBytesWritable k3 = new VKmerBytesWritable(3);
+        VKmerBytesWritable k4 = new VKmerBytesWritable(3);
+        k3.setByRead(test3.getBytes(), 0);
+        k4.setByRead(test4.getBytes(), 0);
+        k3.mergeWithRFKmer(3, k4);
+        Assert.assertEquals("TCTA", k3.toString());
+        // Assert.assertEquals("CTAT", k3); // this is an incorrect test case--
+        // the merge always flips the passed-in kmer
+        
+        String test1;
+        String test2;
+        test1 = "CTA";
+        test2 = "AGA";
+        VKmerBytesWritable k1 = new VKmerBytesWritable(3);
+        VKmerBytesWritable k2 = new VKmerBytesWritable(3);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k1.mergeWithRFKmer(3, k2);
+        Assert.assertEquals("TCTA", k1.toString());
+        
+        
+        
+        test1 = "CTA";
+        test2 = "ATA"; //TAT
+        k1 = new VKmerBytesWritable(3);
+        k2 = new VKmerBytesWritable(3);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k1.mergeWithFRKmer(3, k2);
+        Assert.assertEquals("CTAT", k1.toString());
+        
+        test1 = "ATA";
+        test2 = "CTA"; //TAT
+        k1 = new VKmerBytesWritable(3);
+        k2 = new VKmerBytesWritable(3);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k1.mergeWithFRKmer(3, k2);
+        Assert.assertEquals("ATAG", k1.toString());
+        
+        test1 = "TCTAT";
+        test2 = "GAAC";
+        k1 = new VKmerBytesWritable(5);
+        k2 = new VKmerBytesWritable(4);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k1.mergeWithRFKmer(3, k2);
+        Assert.assertEquals("GTTCTAT", k1.toString());
+    }
+
+    @Test
+    public void TestMergeRRKmer() {
+        byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
+        String text = "AGCTGACCGT";
+        VKmerBytesWritable kmer1 = new VKmerBytesWritable(8);
+        kmer1.setByRead(array, 0);
+        String text1 = "AGCTGACC";
+        VKmerBytesWritable kmer2 = new VKmerBytesWritable(8);
+        kmer2.setByRead(array, 1);
+        String text2 = "GCTGACCG";
+        Assert.assertEquals(text2, kmer2.toString());
+        VKmerBytesWritable merge = new VKmerBytesWritable(kmer2);
+        int kmerSize = 8;
+        merge.mergeWithRRKmer(kmerSize, kmer1);
+        Assert.assertEquals(text1 + text2.substring(kmerSize - 1), merge.toString());
+
+        for (int i = 1; i < 8; i++) {
+            merge.setAsCopy(kmer2);
+            merge.mergeWithRRKmer(i, kmer1);
+            Assert.assertEquals(text1.substring(0, text1.length() - i + 1) + text2, merge.toString());
+        }
+
+        for (int ik = 1; ik <= 10; ik++) {
+            for (int jk = 1; jk <= 10; jk++) {
+                kmer1 = new VKmerBytesWritable(ik);
+                kmer2 = new VKmerBytesWritable(jk);
+                kmer1.setByRead(array, 0);
+                kmer2.setByRead(array, 0);
+                text1 = text.substring(0, ik);
+                text2 = text.substring(0, jk);
+                Assert.assertEquals(text1, kmer1.toString());
+                Assert.assertEquals(text2, kmer2.toString());
+                for (int x = 1; x < ik; x++) {
+                    merge.setAsCopy(kmer2);
+                    merge.mergeWithRRKmer(x, kmer1);
+                    Assert.assertEquals(text1.substring(0, text1.length() - x + 1) + text2, merge.toString());
+                }
+            }
+        }
+    }
+
+    @Test
+    public void TestMergeRFAndRRKmer() {
+        String test1 = "TAGAT";
+        String test2 = "TCTAG"; // rc = CTAGA
+        String test3 = "GCTAG";
+        VKmerBytesWritable k1 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k2 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k3 = new VKmerBytesWritable(5);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k3.setByRead(test3.getBytes(), 0);
+        k1.mergeWithRFKmer(5, k2);
+        Assert.assertEquals("CTAGAT", k1.toString());
+        k1.mergeWithRRKmer(5, k3);
+        Assert.assertEquals("GCTAGAT", k1.toString());
+    }
+
+    @Test
+    public void TestMergeRFAndRFKmer() {
+        String test1 = "TAGAT";
+        String test2 = "TCTAG"; // rc = CTAGA
+        String test3 = "CTAGC"; // rc = GCTAG
+        VKmerBytesWritable k1 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k2 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k3 = new VKmerBytesWritable(5);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k3.setByRead(test3.getBytes(), 0);
+        k1.mergeWithRFKmer(5, k2);
+        Assert.assertEquals("CTAGAT", k1.toString());
+        k1.mergeWithRFKmer(5, k3);
+        Assert.assertEquals("GCTAGAT", k1.toString());
+    }
+
+    @Test
+    public void TestMergeRFAndFRKmer() {
+        String test1 = "TAGAT"; // rc = ATCTA
+        String test2 = "TCTAG"; // rc = CTAGA
+        String test3 = "GCTAG"; // rc = CTAGC
+        VKmerBytesWritable k1 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k2 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k3 = new VKmerBytesWritable(5);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k3.setByRead(test3.getBytes(), 0);
+        k2.mergeWithRFKmer(5, k1);
+        Assert.assertEquals("ATCTAG", k2.toString());
+        k2.mergeWithFRKmer(5, k3);
+        Assert.assertEquals("ATCTAGC", k2.toString());
+    }
+
+    @Test
+    public void TestMergeRFAndFFKmer() {
+        String test1 = "TAGAT"; // rc = ATCTA
+        String test2 = "TCTAG"; // rc = CTAGA
+        String test3 = "CTAGC"; // rc = GCTAG
+        VKmerBytesWritable k1 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k2 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k3 = new VKmerBytesWritable(5);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k3.setByRead(test3.getBytes(), 0);
+        k2.mergeWithRFKmer(5, k1);
+        Assert.assertEquals("ATCTAG", k2.toString());
+        k2.mergeWithFFKmer(5, k3);
+        Assert.assertEquals("ATCTAGC", k2.toString());
+    }
+
+    @Test
+    public void TestMergeThreeVKmersRF_FF() {
+        String test1 = "TAGAT"; // rc = ATCTA
+        String test2 = "TCTAG"; // rc = CTAGA
+        String test3 = "CTAGC"; // rc = GCTAG
+        VKmerBytesWritable k1 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k2 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k3 = new VKmerBytesWritable(5);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k3.setByRead(test3.getBytes(), 0);
+        k2.mergeWithRFKmer(5, k1);
+        Assert.assertEquals("ATCTAG", k2.toString());
+        k2.mergeWithFFKmer(5, k3);
+        Assert.assertEquals("ATCTAGC", k2.toString());
+    }
+
+    @Test
+    public void TestMergeThreeVKmerRF_RF() {
+        String test1 = "TAGAT";
+        String test2 = "TCTAG"; // rc = CTAGA
+        String test3 = "CTAGC"; // rc = GCTAG
+        VKmerBytesWritable k1 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k2 = new VKmerBytesWritable(5);
+        VKmerBytesWritable k3 = new VKmerBytesWritable(5);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k3.setByRead(test3.getBytes(), 0);
+        k1.mergeWithRFKmer(5, k2);
+        Assert.assertEquals("CTAGAT", k1.toString());
+        k1.mergeWithRFKmer(5, k3);
+        Assert.assertEquals("GCTAGAT", k1.toString());
+    }
+    
+    @Test
+    public void TestFinalMerge() {
+        String selfString;
+        String match;
+        String msgString;
+        int index;
+        VKmerBytesWritable kmer = new VKmerBytesWritable();
+        int kmerSize = 3;
+        
+        String F1 = "AATAG";
+        String F2 = "TAGAA";
+        String R1 = "CTATT";
+        String R2 = "TTCTA";
+        
+        //FF test
+        selfString = F1;
+        match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
+        msgString = F2;
+        index = msgString.indexOf(match);
+        // does this test belong in VKmer so it can have variable-length kmers?
+//        kmer.reset(msgString.length() - index);
+        kmer.setByRead(msgString.substring(index).getBytes(), 0);
+        System.out.println(kmer.toString());
+        
+        //FR test
+        selfString = F1;
+        match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
+        msgString = GeneCode.reverseComplement(R2);
+        index = msgString.indexOf(match);
+        kmer.reset(msgString.length() - index);
+        kmer.setByRead(msgString.substring(index).getBytes(), 0);
+        System.out.println(kmer.toString());
+        
+        //RF test
+        selfString = R1;
+        match = selfString.substring(0,kmerSize - 1); 
+        msgString = GeneCode.reverseComplement(F2);
+        index = msgString.lastIndexOf(match) + kmerSize - 2;
+        kmer.reset(index + 1);
+        kmer.setByReadReverse(msgString.substring(0, index + 1).getBytes(), 0);
+        System.out.println(kmer.toString());
+        
+        //RR test
+        selfString = R1;
+        match = selfString.substring(0,kmerSize - 1); 
+        msgString = R2;
+        index = msgString.lastIndexOf(match) + kmerSize - 2;
+        kmer.reset(index + 1);
+        kmer.setByRead(msgString.substring(0, index + 1).getBytes(), 0);
+        System.out.println(kmer.toString());
+        
+        String[][] connectedTable = new String[][]{
+                {"FF", "RF"},
+                {"FF", "RR"},
+                {"FR", "RF"},
+                {"FR", "RR"}
+        };
+        System.out.println(connectedTable[0][1]);
+        
+        Set<Long> s1 = new HashSet<Long>();
+        Set<Long> s2 = new HashSet<Long>();
+        s1.add((long) 1);
+        s1.add((long) 2);
+        s2.add((long) 2);
+        s2.add((long) 3);
+        Set<Long> intersection = new HashSet<Long>();
+        intersection.addAll(s1);
+        intersection.retainAll(s2);
+        System.out.println(intersection.toString());
+        Set<Long> difference = new HashSet<Long>();
+        difference.addAll(s1);
+        difference.removeAll(s2);
+        System.out.println(difference.toString());
+        
+        Map<VKmerBytesWritable, Set<Long>> map = new HashMap<VKmerBytesWritable, Set<Long>>();
+        VKmerBytesWritable k1 = new VKmerBytesWritable(3);
+        Set<Long> set1 = new HashSet<Long>();
+        k1.setByRead(("CTA").getBytes(), 0);
+        set1.add((long)1);
+        map.put(k1, set1);
+        VKmerBytesWritable k2 = new VKmerBytesWritable(3);
+        k2.setByRead(("GTA").getBytes(), 0);
+        Set<Long> set2 = new HashSet<Long>();
+        set2.add((long) 2);
+        map.put(k2, set2);
+        VKmerBytesWritable k3 = new VKmerBytesWritable(3);
+        k3.setByRead(("ATG").getBytes(), 0);
+        Set<Long> set3 = new HashSet<Long>();
+        set3.add((long) 2);
+        map.put(k3, set3);
+        VKmerBytesWritable k4 = new VKmerBytesWritable(3);
+        k4.setByRead(("AAT").getBytes(), 0);
+        Set<Long> set4 = new HashSet<Long>();
+        set4.add((long) 1);
+        map.put(k4, set4);
+        VKmerListWritable kmerList = new VKmerListWritable();
+        kmerList.append(k1);
+        kmerList.append(k2);
+        System.out.println("CTA = " + map.get(k1).toString());
+        System.out.println("GTA = " + map.get(k2).toString());
+        System.out.println("ATG = " + map.get(k3).toString());
+        System.out.println("AAT = " + map.get(k4).toString());
+        System.out.println(k1.compareTo(k2));
+        System.out.println(k2.compareTo(k1));
+        
+        System.out.println("CTA = " + kmerList.getPosition(0).toString());
+        System.out.println("GTA = " + kmerList.getPosition(1).toString());
+        System.out.println("CTA = " + map.get(kmerList.getPosition(0)).toString());
+        System.out.println("GTA = " + map.get(kmerList.getPosition(1)).toString());
+    }
+
+}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
index 98f561f..0c7cc20 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
@@ -13,10 +13,11 @@
 import org.apache.hadoop.mapred.Reporter;
 
 import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
 import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 @SuppressWarnings("deprecation")
 public class GenomixMapper extends MapReduceBase implements
@@ -36,8 +37,8 @@
     private KmerBytesWritable nextReverseKmer;
     private PositionWritable nodeId;
     private PositionListWritable nodeIdList;
-    private KmerListWritable edgeListForPreKmer;
-    private KmerListWritable edgeListForNextKmer;
+    private VKmerListWritable edgeListForPreKmer;
+    private VKmerListWritable edgeListForNextKmer;
     private NodeWritable outputNode;
     
     private KmerDir preKmerDir;
@@ -49,17 +50,18 @@
     @Override
     public void configure(JobConf job) {
         KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
-        preForwardKmer = new KmerBytesWritable(KMER_SIZE);
-        preReverseKmer = new KmerBytesWritable(KMER_SIZE);
-        curForwardKmer = new KmerBytesWritable(KMER_SIZE);
-        curReverseKmer = new KmerBytesWritable(KMER_SIZE);
-        nextForwardKmer = new KmerBytesWritable(KMER_SIZE);
-        nextReverseKmer = new KmerBytesWritable(KMER_SIZE);
+        KmerBytesWritable.setGlobalKmerLength(KMER_SIZE);
+        preForwardKmer = new KmerBytesWritable();
+        preReverseKmer = new KmerBytesWritable();
+        curForwardKmer = new KmerBytesWritable();
+        curReverseKmer = new KmerBytesWritable();
+        nextForwardKmer = new KmerBytesWritable();
+        nextReverseKmer = new KmerBytesWritable();
         nodeId = new PositionWritable();
         nodeIdList = new PositionListWritable();
-        edgeListForPreKmer = new KmerListWritable(KMER_SIZE);
-        edgeListForNextKmer = new KmerListWritable(KMER_SIZE);
-        outputNode = new NodeWritable(KMER_SIZE);
+        edgeListForPreKmer = new VKmerListWritable();
+        edgeListForNextKmer = new VKmerListWritable();
+        outputNode = new NodeWritable();
         preKmerDir = KmerDir.FORWARD;
         curKmerDir = KmerDir.FORWARD;
         nextKmerDir = KmerDir.FORWARD;
@@ -86,7 +88,7 @@
             }
             
             /** first kmer **/
-            outputNode.reset(KMER_SIZE);
+            outputNode.reset();
             curForwardKmer.setByRead(array, 0);
             curReverseKmer.setByReadReverse(array, 0);
             curKmerDir = curForwardKmer.compareTo(curReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
@@ -100,7 +102,7 @@
             
             /** middle kmer **/
             for (int i = KMER_SIZE + 1; i < array.length; i++) {
-                outputNode.reset(KMER_SIZE);
+                outputNode.reset();
             	setPreKmerByOldCurKmer();
             	setCurKmerByOldNextKmer();
             	setNextKmer(array[i]);
@@ -114,7 +116,7 @@
             }
             
             /** last kmer **/
-            outputNode.reset(KMER_SIZE);
+            outputNode.reset();
         	setPreKmerByOldCurKmer();
         	setCurKmerByOldNextKmer();
         	//set value.nodeId
@@ -138,12 +140,12 @@
     		case FORWARD:
     			switch(preKmerDir){
     				case FORWARD:
-    				    edgeListForPreKmer.reset(KMER_SIZE);
+    				    edgeListForPreKmer.reset();
     				    edgeListForPreKmer.append(preForwardKmer);
     					outputNode.setRRList(edgeListForPreKmer);
     					break;
     				case REVERSE:
-    				    edgeListForPreKmer.reset(KMER_SIZE);
+    				    edgeListForPreKmer.reset();
     				    edgeListForPreKmer.append(preReverseKmer);
     					outputNode.setRFList(edgeListForPreKmer);
     					break;
@@ -152,12 +154,12 @@
     		case REVERSE:
     			switch(preKmerDir){
     				case FORWARD:
-    				    edgeListForPreKmer.reset(KMER_SIZE);
+    				    edgeListForPreKmer.reset();
     				    edgeListForPreKmer.append(preForwardKmer);
     					outputNode.setFRList(edgeListForPreKmer);
     					break;
     				case REVERSE:
-    				    edgeListForPreKmer.reset(KMER_SIZE);
+    				    edgeListForPreKmer.reset();
     				    edgeListForPreKmer.append(preReverseKmer);
     					outputNode.setFFList(edgeListForPreKmer);
     					break;
@@ -171,12 +173,12 @@
     		case FORWARD:
     			switch(nextKmerDir){
     				case FORWARD:
-    					edgeListForNextKmer.reset(KMER_SIZE);
+    					edgeListForNextKmer.reset();
     					edgeListForNextKmer.append(nextForwardKmer);
     					outputNode.setFFList(edgeListForNextKmer);
     					break;
     				case REVERSE:
-    					edgeListForNextKmer.reset(KMER_SIZE);
+    					edgeListForNextKmer.reset();
     					edgeListForNextKmer.append(nextReverseKmer);
     					outputNode.setFRList(edgeListForNextKmer);
     					break;
@@ -185,12 +187,12 @@
     		case REVERSE:
     			switch(nextKmerDir){
     				case FORWARD:
-    					edgeListForNextKmer.reset(KMER_SIZE);
+    					edgeListForNextKmer.reset();
     					edgeListForNextKmer.append(nextForwardKmer);
     					outputNode.setRFList(edgeListForNextKmer);
     					break;
     				case REVERSE:
-    					edgeListForNextKmer.reset(KMER_SIZE);
+    					edgeListForNextKmer.reset();
     					edgeListForNextKmer.append(nextReverseKmer);
     					outputNode.setRRList(edgeListForNextKmer);
     					break;
@@ -201,7 +203,7 @@
     
     //set preKmer by shifting curKmer with preChar
     public void setPreKmer(byte preChar){
-        preForwardKmer.set(curForwardKmer);
+        preForwardKmer.setAsCopy(curForwardKmer);
         preForwardKmer.shiftKmerWithPreChar(preChar);
         preReverseKmer.setByReadReverse(preForwardKmer.toString().getBytes(), preForwardKmer.getOffset());
         preKmerDir = preForwardKmer.compareTo(preReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
@@ -209,7 +211,7 @@
     
     //set nextKmer by shifting curKmer with nextChar
     public void setNextKmer(byte nextChar){
-        nextForwardKmer.set(curForwardKmer);
+        nextForwardKmer.setAsCopy(curForwardKmer);
         nextForwardKmer.shiftKmerWithNextChar(nextChar);
         nextReverseKmer.setByReadReverse(nextForwardKmer.toString().getBytes(), nextForwardKmer.getOffset());
         nextKmerDir = nextForwardKmer.compareTo(nextReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
@@ -218,15 +220,15 @@
     //old curKmer becomes current preKmer
     public void setPreKmerByOldCurKmer(){
     	preKmerDir = curKmerDir;
-    	preForwardKmer.set(curForwardKmer);
-    	preReverseKmer.set(curReverseKmer);
+    	preForwardKmer.setAsCopy(curForwardKmer);
+    	preReverseKmer.setAsCopy(curReverseKmer);
     }
     
     //old nextKmer becomes current curKmer
     public void setCurKmerByOldNextKmer(){
     	curKmerDir = nextKmerDir;
-    	curForwardKmer.set(nextForwardKmer);
-    	curReverseKmer.set(nextReverseKmer);
+    	curForwardKmer.setAsCopy(nextForwardKmer);
+    	curReverseKmer.setAsCopy(nextReverseKmer);
     }
     
     public void setMapperOutput(OutputCollector<KmerBytesWritable, NodeWritable> output) throws IOException{
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
index 687474b..a0eb7c8 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
@@ -23,15 +23,16 @@
     @Override
     public void configure(JobConf job) {
         KMER_SIZE = GenomixMapper.KMER_SIZE;
-        outputNode = new NodeWritable(KMER_SIZE);
-        tmpNode = new NodeWritable(KMER_SIZE);
+        KmerBytesWritable.setGlobalKmerLength(KMER_SIZE);
+        outputNode = new NodeWritable();
+        tmpNode = new NodeWritable();
     }
     
 	@Override
 	public void reduce(KmerBytesWritable key, Iterator<NodeWritable> values,
 			OutputCollector<KmerBytesWritable, NodeWritable> output,
 			Reporter reporter) throws IOException {
-		outputNode.reset(KMER_SIZE);
+		outputNode.reset();
 		
 		while (values.hasNext()) {
 		    tmpNode.set(values.next());
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
index 8736fe3..b28328f 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
@@ -27,6 +27,7 @@
 import edu.uci.ics.genomix.hadoop.pmcommon.PathNodeInitial.PathNodeFlag;
 import edu.uci.ics.genomix.oldtype.NodeWritable;
 import edu.uci.ics.genomix.oldtype.PositionWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 
 @SuppressWarnings("deprecation")
 public class MergePathsH3 extends Configured implements Tool {
@@ -58,12 +59,14 @@
         private boolean finalMerge;
 
         public void configure(JobConf conf) {
+            KMER_SIZE = conf.getInt("sizeKmer", 0);
+            KmerBytesWritable.setGlobalKmerLength(KMER_SIZE);
+            
             randSeed = conf.getLong("randomSeed", 0);
             randGenerator = new Random(randSeed);
             probBeingRandomHead = conf.getFloat("probBeingRandomHead", 0.5f);
             finalMerge = conf.getBoolean("finalMerge", false);
 
-            KMER_SIZE = conf.getInt("sizeKmer", 0);
             outputValue = new NodeWithFlagWritable(KMER_SIZE);
             outputKey = new PositionWritable();
             curNode = new NodeWritable(KMER_SIZE);
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java
index 83fe200..f1bfec6 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java
@@ -60,7 +60,7 @@
                 // kill this node by NOT mapping it.  Update my neighbors with a suicide note
                 //TODO: update neighbors by removing me from its list
             } else {
-                outputValue.set(MergeMessageFlag.MSG_SELF, curNode);
+                outputValue.setAsCopy(MergeMessageFlag.MSG_SELF, curNode);
                 output.collect(key, value);
             }
         }
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
index 943b505..550cc7c 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
@@ -54,12 +54,12 @@
     public void set(PositionListAndKmerWritable right) {
         this.countOfKmer = right.countOfKmer;
         this.vertexIDList.set(right.vertexIDList);
-        this.kmer.set(right.kmer);
+        this.kmer.setAsCopy(right.kmer);
     }
 
     public void set(PositionListWritable list, KmerBytesWritable kmer) {
         this.vertexIDList.set(list);
-        this.kmer.set(kmer);
+        this.kmer.setAsCopy(kmer);
     }
     
     @Override
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/NodeReference.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/NodeReference.java
index 8f7a69e..60c0682 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/NodeReference.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/NodeReference.java
@@ -15,7 +15,7 @@
 
 package edu.uci.ics.genomix.hyracks.data.primitive;
 
-import edu.uci.ics.genomix.oldtype.NodeWritable;
+import edu.uci.ics.genomix.velvet.oldtype.NodeWritable;
 
 public class NodeReference extends NodeWritable {
 
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
index 0f0aa29..1827651 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
@@ -19,9 +19,11 @@
 import java.nio.ByteBuffer;
 
 import edu.uci.ics.genomix.hyracks.data.primitive.NodeReference;
-import edu.uci.ics.genomix.oldtype.PositionListWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+
+import edu.uci.ics.genomix.velvet.oldtype.PositionListWritable;
+import edu.uci.ics.genomix.velvet.oldtype.PositionWritable;
+import edu.uci.ics.genomix.velvet.oldtype.KmerBytesWritable;
+
 import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
 import edu.uci.ics.hyracks.api.dataflow.IOperatorNodePushable;
 import edu.uci.ics.hyracks.api.dataflow.value.IRecordDescriptorProvider;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ReadsKeyValueParserFactory.java
index 9aea9ad..2134177 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ReadsKeyValueParserFactory.java
@@ -25,8 +25,8 @@
 import org.apache.hadoop.io.Text;
 
 import edu.uci.ics.genomix.hyracks.data.primitive.PositionReference;
-import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.velvet.oldtype.GeneCode;
+import edu.uci.ics.genomix.velvet.oldtype.KmerBytesWritable;
 import edu.uci.ics.hyracks.api.comm.IFrameWriter;
 import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
 import edu.uci.ics.hyracks.api.dataflow.value.ISerializerDeserializer;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java
index f6c2cf9..def046b 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java
@@ -25,9 +25,9 @@
 import org.apache.hadoop.mapred.JobConf;
 
 import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.oldtype.PositionListWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.velvet.oldtype.PositionListWritable;
+import edu.uci.ics.genomix.velvet.oldtype.PositionWritable;
+import edu.uci.ics.genomix.velvet.oldtype.KmerBytesWritable;
 import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
 import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
index e7526ed..652a6f2 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
@@ -17,9 +17,9 @@
 import java.io.DataOutput;
 import java.io.IOException;
 
-import edu.uci.ics.genomix.oldtype.PositionListWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.velvet.oldtype.PositionListWritable;
+import edu.uci.ics.genomix.velvet.oldtype.PositionWritable;
+import edu.uci.ics.genomix.velvet.oldtype.KmerBytesWritable;
 import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
 import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java
index 77efcf8..e116ab9 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java
@@ -27,8 +27,8 @@
 import edu.uci.ics.genomix.data.Marshal;
 import edu.uci.ics.genomix.hyracks.dataflow.MapReadToNodeOperator;
 import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.oldtype.NodeWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
+import edu.uci.ics.genomix.velvet.oldtype.NodeWritable;
+import edu.uci.ics.genomix.velvet.oldtype.PositionWritable;
 import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
 import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java
index dffd3a9..bc00aa5 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java
@@ -18,8 +18,8 @@
 import java.io.IOException;
 
 import edu.uci.ics.genomix.data.Marshal;
-import edu.uci.ics.genomix.oldtype.NodeWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
+import edu.uci.ics.genomix.velvet.oldtype.NodeWritable;
+import edu.uci.ics.genomix.velvet.oldtype.PositionWritable;
 import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
 import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
index c3ec3c7..b4b1e73 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
@@ -19,8 +19,8 @@
 import java.util.Map;
 
 import edu.uci.ics.genomix.hyracks.dataflow.ReadsKeyValueParserFactory;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.velvet.oldtype.PositionWritable;
+import edu.uci.ics.genomix.velvet.oldtype.KmerBytesWritable;
 import edu.uci.ics.hyracks.api.client.NodeControllerInfo;
 import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java
index 559060a..1e78b79 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java
@@ -19,8 +19,8 @@
 import java.util.Map;
 
 import edu.uci.ics.genomix.data.Marshal;
-import edu.uci.ics.genomix.oldtype.PositionListWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.velvet.oldtype.PositionListWritable;
+import edu.uci.ics.genomix.velvet.oldtype.KmerBytesWritable;
 import edu.uci.ics.hyracks.api.client.NodeControllerInfo;
 import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
index e9aede5..8e727959 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
@@ -20,8 +20,8 @@
 
 import edu.uci.ics.genomix.data.Marshal;
 import edu.uci.ics.genomix.hyracks.dataflow.MapKmerPositionToReadOperator;
-import edu.uci.ics.genomix.oldtype.PositionListWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.velvet.oldtype.PositionListWritable;
+import edu.uci.ics.genomix.velvet.oldtype.KmerBytesWritable;
 import edu.uci.ics.hyracks.api.client.NodeControllerInfo;
 import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ConnectorPolicyAssignmentPolicy.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ConnectorPolicyAssignmentPolicy.java
new file mode 100644
index 0000000..6919e76
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ConnectorPolicyAssignmentPolicy.java
@@ -0,0 +1,42 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.newgraph.dataflow;
+
+import edu.uci.ics.hyracks.api.dataflow.IConnectorDescriptor;
+import edu.uci.ics.hyracks.api.dataflow.connectors.IConnectorPolicy;
+import edu.uci.ics.hyracks.api.dataflow.connectors.IConnectorPolicyAssignmentPolicy;
+import edu.uci.ics.hyracks.api.dataflow.connectors.PipeliningConnectorPolicy;
+import edu.uci.ics.hyracks.api.dataflow.connectors.SendSideMaterializedPipeliningConnectorPolicy;
+import edu.uci.ics.hyracks.dataflow.std.connectors.MToNPartitioningMergingConnectorDescriptor;
+
+/**
+ * used by precluster groupby
+ */
+public class ConnectorPolicyAssignmentPolicy implements IConnectorPolicyAssignmentPolicy {
+    private static final long serialVersionUID = 1L;
+    private IConnectorPolicy senderSideMaterializePolicy = new SendSideMaterializedPipeliningConnectorPolicy();
+    private IConnectorPolicy pipeliningPolicy = new PipeliningConnectorPolicy();
+
+    @Override
+    public IConnectorPolicy getConnectorPolicyAssignment(IConnectorDescriptor c, int nProducers, int nConsumers,
+            int[] fanouts) {
+        if (c instanceof MToNPartitioningMergingConnectorDescriptor) {
+            return senderSideMaterializePolicy;
+        } else {
+            return pipeliningPolicy;
+        }
+    }
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
index 3650553..42d8db6 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
@@ -24,10 +24,12 @@
 import org.apache.hadoop.io.LongWritable;
 import org.apache.hadoop.io.Text;
 
-import edu.uci.ics.genomix.oldtype.IntermediateNodeWritable;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
+
 import edu.uci.ics.hyracks.api.comm.IFrameWriter;
 import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
 import edu.uci.ics.hyracks.api.dataflow.value.ISerializerDeserializer;
@@ -44,38 +46,53 @@
     private static final Log LOG = LogFactory.getLog(ReadsKeyValueParserFactory.class);
 
     public static final int OutputKmerField = 0;
-    public static final int OutputNodeIdField = 1;
-    public static final int OutputForwardForwardField = 2;
-    public static final int OutputForwardReverseField = 3;
-    public static final int OutputReverseForwardField = 4;
-    public static final int OutputReverseReverseField = 5;
+    public static final int OutputNodeField = 1;
+    
 
     private final int readLength;
     private final int kmerSize;
 
     public static final RecordDescriptor readKmerOutputRec = new RecordDescriptor(new ISerializerDeserializer[] { null,
-            null });
+            null});
 
-    public ReadsKeyValueParserFactory(int readlength, int k, boolean bGenerateReversed) {
+    public ReadsKeyValueParserFactory(int readlength, int k) {
         this.readLength = readlength;
         this.kmerSize = k;
     }
-
+    
+    public static enum KmerDir {
+        FORWARD,
+        REVERSE,
+    }
+    
     @Override
     public IKeyValueParser<LongWritable, Text> createKeyValueParser(final IHyracksTaskContext ctx) {
         final ArrayTupleBuilder tupleBuilder = new ArrayTupleBuilder(2);
         final ByteBuffer outputBuffer = ctx.allocateFrame();
         final FrameTupleAppender outputAppender = new FrameTupleAppender(ctx.getFrameSize());
         outputAppender.reset(outputBuffer, true);
-
+        KmerBytesWritable.setGlobalKmerLength(kmerSize);
         return new IKeyValueParser<LongWritable, Text>() {
-
-            private KmerBytesWritable kmer = new KmerBytesWritable(kmerSize);
-            private KmerBytesWritable nextKmer = new KmerBytesWritable(kmerSize);
+            
             private PositionWritable nodeId = new PositionWritable();
-            private KmerListWritable kmerList = new KmerListWritable(kmerSize);
-            private IntermediateNodeWritable interMediateNode = new IntermediateNodeWritable();
-            private byte mateId = 0;
+            private PositionListWritable nodeIdList = new PositionListWritable();
+            private VKmerListWritable edgeListForPreKmer = new VKmerListWritable();
+            private VKmerListWritable edgeListForNextKmer = new VKmerListWritable();
+            private NodeWritable outputNode = new NodeWritable();
+//            private NodeWritable outputNode2 = new NodeWritable();
+
+            private KmerBytesWritable preForwardKmer = new KmerBytesWritable();           
+            private KmerBytesWritable preReverseKmer = new KmerBytesWritable();
+            private KmerBytesWritable curForwardKmer = new KmerBytesWritable();
+            private KmerBytesWritable curReverseKmer = new KmerBytesWritable();
+            private KmerBytesWritable nextForwardKmer = new KmerBytesWritable();
+            private KmerBytesWritable nextReverseKmer = new KmerBytesWritable();
+            
+            private KmerDir preKmerDir = KmerDir.FORWARD;
+            private KmerDir curKmerDir = KmerDir.FORWARD;
+            private KmerDir nextKmerDir = KmerDir.FORWARD;
+
+            byte mateId = (byte) 0;
             
             @Override
             public void parse(LongWritable key, Text value, IFrameWriter writer) throws HyracksDataException {
@@ -104,54 +121,148 @@
             }
 
             private void SplitReads(int readID, byte[] array, IFrameWriter writer) {
-                /** first kmer */
+                /*first kmer*/
                 if (kmerSize >= array.length) {
                     return;
                 }
-                kmer.setByRead(array, 0);
-                nextKmer.set(kmer);
-                nextKmer.shiftKmerWithNextChar(array[kmerSize]);
-                kmerList.append(nextKmer);
-                nextKmer.toString();
-                kmerList.toString();
-//                nodeId.set(mateId, readID, 1);
-//                interMediateNode.setNodeId(nodeId);
-//                interMediateNode.setFFList(kmerList);
-                InsertToFrame(kmer, kmerList, writer);
+                outputNode.reset();
+                curForwardKmer.setByRead(array, 0);
+                curReverseKmer.setByReadReverse(array, 0);
+                curKmerDir = curForwardKmer.compareTo(curReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
+                setNextKmer(array[kmerSize]);
+                setnodeId(mateId, readID, 0);
+                setEdgeListForNextKmer();
+                writeToFrame(writer);
 
-                /** middle kmer */
+                /*middle kmer*/
                 int i = kmerSize;
                 for (; i < array.length - 1; i++) {
-                    kmer.shiftKmerWithNextChar(array[i]);
-                    nextKmer.set(kmer);
-                    nextKmer.shiftKmerWithNextChar(array[i+1]);
-                    kmerList.append(nextKmer);
-//                    nodeId.set(mateId, readID, i - kmerSize + 2);
-//                    interMediateNode.setNodeId(nodeId);
-//                    interMediateNode.setFFList(kmerList);
-                    InsertToFrame(kmer, kmerList, writer);
+                    outputNode.reset();
+                    setPreKmerByOldCurKmer();
+                    setCurKmerByOldNextKmer();
+                    setNextKmer(array[i]);
+                    setnodeId(mateId, readID, 0);//i - kmerSize + 1
+                    setEdgeListForPreKmer();
+                    setEdgeListForNextKmer();
+                    writeToFrame(writer);
                 }
-//                
-//                /** last kmer */
-//                kmer.shiftKmerWithNextChar(array[i]);
-//                nodeId.set(mateId, readID, i - kmerSize + 2);
-//                interMediateNode.setNodeId(nodeId);
-//                InsertToFrame(kmer, interMediateNode, writer);
+                
+                /*last kmer*/
+                outputNode.reset();
+                setPreKmerByOldCurKmer();
+                setCurKmerByOldNextKmer();
+                setnodeId(mateId, readID, 0);//array.length - kmerSize + 1
+                setEdgeListForPreKmer();
+                writeToFrame(writer);
             }
-            //IntermediateNodeWritable node
-            private void InsertToFrame(KmerBytesWritable kmer, KmerListWritable kmerList, IFrameWriter writer) {
+            
+            public void setnodeId(byte mateId, long readID, int posId){
+                nodeId.set(mateId, readID, posId);
+                nodeIdList.reset();
+                nodeIdList.append(nodeId);
+                outputNode.setNodeIdList(nodeIdList);
+            }
+            
+            public void setNextKmer(byte nextChar){
+                nextForwardKmer.setAsCopy(curForwardKmer);
+                nextForwardKmer.shiftKmerWithNextChar(nextChar);
+                nextReverseKmer.setByReadReverse(nextForwardKmer.toString().getBytes(), nextForwardKmer.getOffset());
+                nextKmerDir = nextForwardKmer.compareTo(nextReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
+            }
+            
+            public void setPreKmerByOldCurKmer(){
+                preKmerDir = curKmerDir;
+                preForwardKmer.setAsCopy(curForwardKmer);
+                preReverseKmer.setAsCopy(curReverseKmer);
+            }
+
+            public void setCurKmerByOldNextKmer(){
+                curKmerDir = nextKmerDir;
+                curForwardKmer.setAsCopy(nextForwardKmer);
+                curReverseKmer.setAsCopy(nextReverseKmer);
+            }
+            
+            public void writeToFrame(IFrameWriter writer) {
+                switch(curKmerDir){
+                    case FORWARD:
+                        InsertToFrame(curForwardKmer, outputNode, writer);
+                        break;
+                    case REVERSE:
+                        InsertToFrame(curReverseKmer, outputNode, writer);
+                        break;
+                }
+            }
+            public void setEdgeListForPreKmer(){
+                switch(curKmerDir){
+                    case FORWARD:
+                        switch(preKmerDir){
+                            case FORWARD:
+                                edgeListForPreKmer.reset();
+                                edgeListForPreKmer.append(preForwardKmer);
+                                outputNode.setRRList(edgeListForPreKmer);
+                                break;
+                            case REVERSE:
+                                edgeListForPreKmer.reset();
+                                edgeListForPreKmer.append(preReverseKmer);
+                                outputNode.setRFList(edgeListForPreKmer);
+                                break;
+                        }
+                        break;
+                    case REVERSE:
+                        switch(preKmerDir){
+                            case FORWARD:
+                                edgeListForPreKmer.reset();
+                                edgeListForPreKmer.append(preForwardKmer);
+                                outputNode.setFRList(edgeListForPreKmer);
+                                break;
+                            case REVERSE:
+                                edgeListForPreKmer.reset();
+                                edgeListForPreKmer.append(preReverseKmer);
+                                outputNode.setFFList(edgeListForPreKmer);
+                                break;
+                        }
+                        break;
+                }
+            }
+            
+            public void setEdgeListForNextKmer(){
+                switch(curKmerDir){
+                    case FORWARD:
+                        switch(nextKmerDir){
+                            case FORWARD:
+                                edgeListForNextKmer.reset();
+                                edgeListForNextKmer.append(nextForwardKmer);
+                                outputNode.setFFList(edgeListForNextKmer);
+                                break;
+                            case REVERSE:
+                                edgeListForNextKmer.reset();
+                                edgeListForNextKmer.append(nextReverseKmer);
+                                outputNode.setFRList(edgeListForNextKmer);
+                                break;
+                        }
+                        break;
+                    case REVERSE:
+                        switch(nextKmerDir){
+                            case FORWARD:
+                                edgeListForNextKmer.reset();
+                                edgeListForNextKmer.append(nextForwardKmer);
+                                outputNode.setRFList(edgeListForNextKmer);
+                                break;
+                            case REVERSE:
+                                edgeListForNextKmer.reset();
+                                edgeListForNextKmer.append(nextReverseKmer);
+                                outputNode.setRRList(edgeListForNextKmer);
+                                break;
+                        }
+                        break;
+                }
+            }
+            
+            private void InsertToFrame(KmerBytesWritable kmer, NodeWritable node, IFrameWriter writer) {
                 try {
-//                    if (Math.abs(node.getNodeId().getPosId()) > 32768) {
-//                        throw new IllegalArgumentException("Position id is beyond 32768 at " + node.getNodeId().getReadId());
-//                    }
                     tupleBuilder.reset();
                     tupleBuilder.addField(kmer.getBytes(), kmer.getOffset(), kmer.getLength());
-                    tupleBuilder.addField(kmerList.getByteArray(), kmer.getOffset(), kmer.getLength());
-                    //tupleBuilder.addField(node.getNodeId().getByteArray(), node.getNodeId().getStartOffset(), node.getNodeId().getLength());
-//                    tupleBuilder.addField(node.getFFList().getByteArray(), node.getFFList().getStartOffset(), node.getFFList().getLength());
-//                    tupleBuilder.addField(node.getFRList().getByteArray(), node.getFRList().getStartOffset(), node.getFRList().getLength());
-//                    tupleBuilder.addField(node.getRFList().getByteArray(), node.getRFList().getStartOffset(), node.getRFList().getLength());
-//                    tupleBuilder.addField(node.getRRList().getByteArray(), node.getRRList().getStartOffset(), node.getRRList().getLength());
+                    tupleBuilder.addField(node.marshalToByteArray(), 0, node.getSerializedLength());
                     
                     if (!outputAppender.append(tupleBuilder.getFieldEndOffsets(), tupleBuilder.getByteArray(), 0,
                             tupleBuilder.getSize())) {
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/AggregateKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/AggregateKmerAggregateFactory.java
new file mode 100644
index 0000000..46fdd0e
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/AggregateKmerAggregateFactory.java
@@ -0,0 +1,124 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.newgraph.dataflow.aggregators;
+
+import java.io.DataOutput;
+import java.io.IOException;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.hyracks.api.comm.IFrameTupleAccessor;
+import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
+import edu.uci.ics.hyracks.api.dataflow.value.RecordDescriptor;
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
+import edu.uci.ics.hyracks.dataflow.common.comm.io.ArrayTupleBuilder;
+import edu.uci.ics.hyracks.dataflow.std.group.AggregateState;
+import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptorFactory;
+
+public class AggregateKmerAggregateFactory implements IAggregatorDescriptorFactory {
+
+    /**
+     * local Aggregate
+     */
+    private static final long serialVersionUID = 1L;
+    private final int kmerSize;
+    
+    public AggregateKmerAggregateFactory(int k) {
+        this.kmerSize = k;
+    }
+    
+    @Override
+    public IAggregatorDescriptor createAggregator(IHyracksTaskContext ctx, RecordDescriptor inRecordDescriptor,
+            RecordDescriptor outRecordDescriptor, int[] keyFields, int[] keyFieldsInPartialResults)
+            throws HyracksDataException {
+        KmerBytesWritable.setGlobalKmerLength(kmerSize);
+        return new IAggregatorDescriptor() {
+            
+            private NodeWritable readNode = new NodeWritable();
+            
+            protected int getOffSet(IFrameTupleAccessor accessor, int tIndex, int fieldId) {
+                int tupleOffset = accessor.getTupleStartOffset(tIndex);
+                int fieldStart = accessor.getFieldStartOffset(tIndex, fieldId);
+                int offset = tupleOffset + fieldStart + accessor.getFieldSlotsLength();
+                return offset;
+            }
+
+            @Override
+            public void reset() {
+            }
+
+            @Override
+            public void close() {
+
+            }
+
+            @Override
+            public AggregateState createAggregateStates() {
+                return new AggregateState(new NodeWritable());
+            }
+
+            @Override
+            public void init(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+                    AggregateState state) throws HyracksDataException {
+                NodeWritable localUniNode = (NodeWritable) state.state;
+                localUniNode.reset();
+                readNode.setAsReference(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));
+                localUniNode.getNodeIdList().appendList(readNode.getNodeIdList());
+                localUniNode.getFFList().appendList(readNode.getFFList());
+                localUniNode.getFRList().appendList(readNode.getFRList());
+                localUniNode.getRFList().appendList(readNode.getRFList());
+                localUniNode.getRRList().appendList(readNode.getRRList());
+
+                // make an empty field
+                tupleBuilder.addFieldEndOffset();// mark question?
+            }
+
+            @Override
+            public void aggregate(IFrameTupleAccessor accessor, int tIndex, IFrameTupleAccessor stateAccessor,
+                    int stateTupleIndex, AggregateState state) throws HyracksDataException {
+                NodeWritable localUniNode = (NodeWritable) state.state;
+                readNode.setAsReference(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));
+                localUniNode.getNodeIdList().appendList(readNode.getNodeIdList());
+                localUniNode.getFFList().appendList(readNode.getFFList());
+                localUniNode.getFRList().appendList(readNode.getFRList());
+                localUniNode.getRFList().appendList(readNode.getRFList());
+                localUniNode.getRRList().appendList(readNode.getRRList());
+            }
+
+            @Override
+            public void outputPartialResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+                    AggregateState state) throws HyracksDataException {
+                throw new IllegalStateException("partial result method should not be called");
+            }
+
+            @Override
+            public void outputFinalResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+                    AggregateState state) throws HyracksDataException {
+                DataOutput fieldOutput = tupleBuilder.getDataOutput();
+                NodeWritable localUniNode = (NodeWritable) state.state;
+                try {
+                    fieldOutput.write(localUniNode.marshalToByteArray(), 0, localUniNode.getSerializedLength());
+
+                    tupleBuilder.addFieldEndOffset();
+                } catch (IOException e) {
+                    throw new HyracksDataException("I/O exception when writing aggregation to the output buffer.");
+                }
+            }
+
+        };
+    }
+
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/MergeKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/MergeKmerAggregateFactory.java
new file mode 100644
index 0000000..1ee6cae
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/MergeKmerAggregateFactory.java
@@ -0,0 +1,130 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.newgraph.dataflow.aggregators;
+
+import java.io.DataOutput;
+import java.io.IOException;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.hyracks.api.comm.IFrameTupleAccessor;
+import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
+import edu.uci.ics.hyracks.api.dataflow.value.RecordDescriptor;
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
+import edu.uci.ics.hyracks.dataflow.common.comm.io.ArrayTupleBuilder;
+import edu.uci.ics.hyracks.dataflow.std.group.AggregateState;
+import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptorFactory;
+
+public class MergeKmerAggregateFactory implements IAggregatorDescriptorFactory {
+    private static final long serialVersionUID = 1L;
+    private static final Log LOG = LogFactory.getLog(MergeKmerAggregateFactory.class);
+    
+    private final int kmerSize;
+    
+    public MergeKmerAggregateFactory(int k) {
+        this.kmerSize = k;
+    }
+    
+    @Override
+    public IAggregatorDescriptor createAggregator(IHyracksTaskContext ctx, RecordDescriptor inRecordDescriptor,
+            RecordDescriptor outRecordDescriptor, int[] keyFields, int[] keyFieldsInPartialResults)
+            throws HyracksDataException {
+        final int frameSize = ctx.getFrameSize();
+        KmerBytesWritable.setGlobalKmerLength(kmerSize);
+        return new IAggregatorDescriptor() {
+
+            private NodeWritable readNode = new NodeWritable();
+            
+            protected int getOffSet(IFrameTupleAccessor accessor, int tIndex, int fieldId) {
+                int tupleOffset = accessor.getTupleStartOffset(tIndex);
+                int fieldStart = accessor.getFieldStartOffset(tIndex, fieldId);
+                int offset = tupleOffset + fieldStart + accessor.getFieldSlotsLength();
+                return offset;
+            }
+            
+            @Override
+            public AggregateState createAggregateStates() {
+                return new AggregateState(new NodeWritable());
+            }
+
+            @Override
+            public void init(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+                    AggregateState state) throws HyracksDataException {
+                NodeWritable localUniNode = (NodeWritable) state.state;
+                localUniNode.reset();
+                readNode.setAsReference(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));
+                localUniNode.getNodeIdList().unionUpdate(readNode.getNodeIdList());
+                localUniNode.getFFList().unionUpdate(readNode.getFFList());
+                localUniNode.getFRList().unionUpdate(readNode.getFRList());
+                localUniNode.getRFList().unionUpdate(readNode.getRFList());
+                localUniNode.getRRList().unionUpdate(readNode.getRRList());
+                
+                //make a fake feild to cheat caller
+                tupleBuilder.addFieldEndOffset();
+            }
+
+            @Override
+            public void reset() {
+
+            }
+
+            @Override
+            public void aggregate(IFrameTupleAccessor accessor, int tIndex, IFrameTupleAccessor stateAccessor,
+                    int stateTupleIndex, AggregateState state) throws HyracksDataException {
+                NodeWritable localUniNode = (NodeWritable) state.state;
+                readNode.setAsReference(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));
+                localUniNode.getNodeIdList().unionUpdate(readNode.getNodeIdList());
+                localUniNode.getFFList().unionUpdate(readNode.getFFList());
+                localUniNode.getFRList().unionUpdate(readNode.getFRList());
+                localUniNode.getRFList().unionUpdate(readNode.getRFList());
+                localUniNode.getRRList().unionUpdate(readNode.getRRList());
+            }
+
+            @Override
+            public void outputPartialResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+                    AggregateState state) throws HyracksDataException {
+                throw new IllegalStateException("partial result method should not be called");
+            }
+
+            @Override
+            public void outputFinalResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+                    AggregateState state) throws HyracksDataException {
+                DataOutput fieldOutput = tupleBuilder.getDataOutput();
+                NodeWritable localUniNode = (NodeWritable) state.state;
+                try {
+                    if (localUniNode.getSerializedLength() > frameSize / 2) {
+                        LOG.warn("MergeKmer: output data kmerByteSize is too big: " + localUniNode.getSerializedLength());
+                    }
+                    fieldOutput.write(localUniNode.marshalToByteArray(), 0, localUniNode.getSerializedLength());
+                    tupleBuilder.addFieldEndOffset();
+
+                } catch (IOException e) {
+                    throw new HyracksDataException("I/O exception when writing aggregation to the output buffer.");
+                }
+            }
+
+            @Override
+            public void close() {
+
+            }
+
+        };
+
+    }
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java
index 6d6e1e6..4602ed2 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.hyracks.newgraph.driver;
 
 import java.net.URL;
@@ -6,10 +21,12 @@
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.util.GenericOptionsParser;
 
-import edu.uci.ics.genomix.hyracks.driver.Driver.Plan;
-import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.hyracks.job.JobGen;
+import edu.uci.ics.genomix.hyracks.newgraph.job.GenomixJobConf;
+import edu.uci.ics.genomix.hyracks.newgraph.job.JobGen;
+import edu.uci.ics.genomix.hyracks.newgraph.job.JobGenBrujinGraph;
 import edu.uci.ics.genomix.hyracks.newgraph.job.JobGenCheckReader;
 
 import edu.uci.ics.hyracks.api.client.HyracksConnection;
@@ -23,19 +40,21 @@
 
 public class Driver {
     public static enum Plan {
+        BUILD_DEBRUJIN_GRAPH,
         CHECK_KMERREADER,
     }
-    
+
     private static final String IS_PROFILING = "genomix.driver.profiling";
     private static final String CPARTITION_PER_MACHINE = "genomix.driver.duplicate.num";
     private static final Log LOG = LogFactory.getLog(Driver.class);
     private JobGen jobGen;
     private boolean profiling;
+
     private int numPartitionPerMachine;
 
     private IHyracksClientConnection hcc;
     private Scheduler scheduler;
-    
+
     public Driver(String ipAddress, int port, int numPartitionPerMachine) throws HyracksException {
         try {
             hcc = new HyracksConnection(ipAddress, port);
@@ -45,9 +64,9 @@
         }
         this.numPartitionPerMachine = numPartitionPerMachine;
     }
-    
+
     public void runJob(GenomixJobConf job) throws HyracksException {
-        runJob(job, Plan.CHECK_KMERREADER, false);
+        runJob(job, Plan.BUILD_DEBRUJIN_GRAPH, false);
     }
 
     public void runJob(GenomixJobConf job, Plan planChoice, boolean profiling) throws HyracksException {
@@ -69,8 +88,11 @@
             Map<String, NodeControllerInfo> ncMap = hcc.getNodeControllerInfos();
             LOG.info("ncmap:" + ncMap.size() + " " + ncMap.keySet().toString());
             switch (planChoice) {
-                case CHECK_KMERREADER:
+                case BUILD_DEBRUJIN_GRAPH:
                 default:
+                    jobGen = new JobGenBrujinGraph(job, scheduler, ncMap, numPartitionPerMachine);
+                    break;
+                case CHECK_KMERREADER:
                     jobGen = new JobGenCheckReader(job, scheduler, ncMap, numPartitionPerMachine);
                     break;
             }
@@ -85,7 +107,7 @@
             throw new HyracksException(e);
         }
     }
-    
+
     private void run(JobGen jobGen) throws Exception {
         try {
             JobSpecification createJob = jobGen.generateJob();
@@ -95,11 +117,37 @@
             throw e;
         }
     }
-    
+
     private void execute(JobSpecification job) throws Exception {
         job.setUseConnectorPolicyForScheduling(false);
-        JobId jobId = hcc
-                .startJob(job, profiling ? EnumSet.of(JobFlag.PROFILE_RUNTIME) : EnumSet.noneOf(JobFlag.class));
+        JobId jobId = hcc.startJob(job, profiling ? EnumSet.of(JobFlag.PROFILE_RUNTIME) : EnumSet.noneOf(JobFlag.class));
         hcc.waitForCompletion(jobId);
     }
+
+    public static void main(String[] args) throws Exception {
+        GenomixJobConf jobConf = new GenomixJobConf();
+        String[] otherArgs = new GenericOptionsParser(jobConf, args).getRemainingArgs();
+        if (otherArgs.length < 4) {
+            System.err.println("Need <serverIP> <port> <input> <output>");
+            System.exit(-1);
+        }
+        String ipAddress = otherArgs[0];
+        int port = Integer.parseInt(otherArgs[1]);
+        int numOfDuplicate = jobConf.getInt(CPARTITION_PER_MACHINE, 2);
+        boolean bProfiling = jobConf.getBoolean(IS_PROFILING, true);
+        // FileInputFormat.setInputPaths(job, otherArgs[2]);
+        {
+            @SuppressWarnings("deprecation")
+            Path path = new Path(jobConf.getWorkingDirectory(), otherArgs[2]);
+            jobConf.set("mapred.input.dir", path.toString());
+
+            @SuppressWarnings("deprecation")
+            Path outputDir = new Path(jobConf.getWorkingDirectory(), otherArgs[3]);
+            jobConf.set("mapred.output.dir", outputDir.toString());
+        }
+        // FileInputFormat.addInputPath(jobConf, new Path(otherArgs[2]));
+        // FileOutputFormat.setOutputPath(job, new Path(otherArgs[3]));
+        Driver driver = new Driver(ipAddress, port, numOfDuplicate);
+        driver.runJob(jobConf, Plan.BUILD_DEBRUJIN_GRAPH, bProfiling);
+    }
 }
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/io/NodeTextWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/io/NodeTextWriterFactory.java
new file mode 100644
index 0000000..b7b7054
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/io/NodeTextWriterFactory.java
@@ -0,0 +1,75 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.genomix.hyracks.newgraph.io;
+
+import java.io.DataOutput;
+import java.io.IOException;
+
+import edu.uci.ics.genomix.hyracks.newgraph.dataflow.ReadsKeyValueParserFactory;
+import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
+import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
+import edu.uci.ics.hyracks.hdfs.api.ITupleWriter;
+import edu.uci.ics.hyracks.hdfs.api.ITupleWriterFactory;
+
+public class NodeTextWriterFactory implements ITupleWriterFactory {
+
+    /**
+     * Write the node to Text
+     */
+    private static final long serialVersionUID = 1L;
+    private final int kmerSize;
+    public static final int OutputKmerField = ReadsKeyValueParserFactory.OutputKmerField;
+    public static final int outputNodeField = ReadsKeyValueParserFactory.OutputNodeField;
+    
+    public NodeTextWriterFactory(int k) {
+        this.kmerSize = k;
+    }
+
+    @Override
+    public ITupleWriter getTupleWriter(IHyracksTaskContext ctx) throws HyracksDataException {
+        KmerBytesWritable.setGlobalKmerLength(kmerSize);
+        return new ITupleWriter() {
+            NodeWritable node = new NodeWritable();
+            
+            @Override
+            public void open(DataOutput output) throws HyracksDataException {
+
+            }
+
+            @Override
+            public void write(DataOutput output, ITupleReference tuple) throws HyracksDataException {
+                node.setAsReference(tuple.getFieldData(outputNodeField), tuple.getFieldStart(outputNodeField));
+                node.getKmer().reset(kmerSize);
+                node.getKmer().setAsReference(tuple.getFieldData(OutputKmerField), tuple.getFieldStart(OutputKmerField));
+                try {
+                    output.write(node.toString().getBytes());
+                    output.writeByte('\n');
+                } catch (IOException e) {
+                    throw new HyracksDataException(e);
+                }
+            }
+
+            @Override
+            public void close(DataOutput output) throws HyracksDataException {
+
+            }
+
+        };
+    }
+
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/GenomixJobConf.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/GenomixJobConf.java
new file mode 100644
index 0000000..b0edf77
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/GenomixJobConf.java
@@ -0,0 +1,104 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.newgraph.job;
+
+import java.io.IOException;
+
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.mapred.JobConf;
+
+@SuppressWarnings("deprecation")
+public class GenomixJobConf extends JobConf {
+
+    public static final String JOB_NAME = "genomix";
+
+    /** Kmers length */
+    public static final String KMER_LENGTH = "genomix.kmerlen";
+    /** Read length */
+    public static final String READ_LENGTH = "genomix.readlen";
+    /** Frame Size */
+    public static final String FRAME_SIZE = "genomix.framesize";
+    /** Frame Limit, hyracks need */
+    public static final String FRAME_LIMIT = "genomix.framelimit";
+    /** Table Size, hyracks need */
+    public static final String TABLE_SIZE = "genomix.tablesize";
+    /** Groupby types */
+    public static final String GROUPBY_TYPE = "genomix.graph.groupby.type";
+    /** Graph outputformat */
+    public static final String OUTPUT_FORMAT = "genomix.graph.output";
+    /** Get reversed Kmer Sequence */
+    public static final String REVERSED_KMER = "genomix.kmer.reversed";
+
+    /** Configurations used by hybrid groupby function in graph build phrase */
+    public static final String GROUPBY_HYBRID_INPUTSIZE = "genomix.graph.groupby.hybrid.inputsize";
+    public static final String GROUPBY_HYBRID_INPUTKEYS = "genomix.graph.groupby.hybrid.inputkeys";
+    public static final String GROUPBY_HYBRID_RECORDSIZE_SINGLE = "genomix.graph.groupby.hybrid.recordsize.single";
+    public static final String GROUPBY_HYBRID_RECORDSIZE_CROSS = "genomix.graph.groupby.hybrid.recordsize.cross";
+    public static final String GROUPBY_HYBRID_HASHLEVEL = "genomix.graph.groupby.hybrid.hashlevel";
+
+    public static final int DEFAULT_KMERLEN = 21;
+    public static final int DEFAULT_READLEN = 124;
+    public static final int DEFAULT_FRAME_SIZE = 128 * 1024;
+    public static final int DEFAULT_FRAME_LIMIT = 4096;
+    public static final int DEFAULT_TABLE_SIZE = 10485767;
+    public static final long DEFAULT_GROUPBY_HYBRID_INPUTSIZE = 154000000L;
+    public static final long DEFAULT_GROUPBY_HYBRID_INPUTKEYS = 38500000L;
+    public static final int DEFAULT_GROUPBY_HYBRID_RECORDSIZE_SINGLE = 9;
+    public static final int DEFAULT_GROUPBY_HYBRID_HASHLEVEL = 1;
+    public static final int DEFAULT_GROUPBY_HYBRID_RECORDSIZE_CROSS = 13;
+
+    public static final boolean DEFAULT_REVERSED = true;
+
+    public static final String JOB_PLAN_GRAPHBUILD = "graphbuild";
+    public static final String JOB_PLAN_GRAPHSTAT = "graphstat";
+
+    public static final String GROUPBY_TYPE_HYBRID = "hybrid";
+    public static final String GROUPBY_TYPE_EXTERNAL = "external";
+    public static final String GROUPBY_TYPE_PRECLUSTER = "precluster";
+    public static final String OUTPUT_FORMAT_BINARY = "binary";
+    public static final String OUTPUT_FORMAT_TEXT = "text";
+
+    public GenomixJobConf() throws IOException {
+        super(new Configuration());
+    }
+
+    public GenomixJobConf(Configuration conf) throws IOException {
+        super(conf);
+    }
+
+    /**
+     * Set the kmer length
+     * 
+     * @param the
+     *            desired frame kmerByteSize
+     */
+    final public void setKmerLength(int kmerlength) {
+        setInt(KMER_LENGTH, kmerlength);
+    }
+
+    final public void setFrameSize(int frameSize) {
+        setInt(FRAME_SIZE, frameSize);
+    }
+
+    final public void setFrameLimit(int frameLimit) {
+        setInt(FRAME_LIMIT, frameLimit);
+    }
+
+    final public void setTableSize(int tableSize) {
+        setInt(TABLE_SIZE, tableSize);
+    }
+
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGen.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGen.java
new file mode 100644
index 0000000..9649566
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGen.java
@@ -0,0 +1,40 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.newgraph.job;
+
+import java.io.Serializable;
+import java.util.UUID;
+
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
+import edu.uci.ics.hyracks.api.exceptions.HyracksException;
+import edu.uci.ics.hyracks.api.job.JobSpecification;
+import edu.uci.ics.hyracks.hdfs.dataflow.ConfFactory;
+
+public abstract class JobGen implements Serializable {
+
+    /**
+     * generate the jobId
+     */
+    private static final long serialVersionUID = 1L;
+    protected final ConfFactory confFactory;
+    protected String jobId = new UUID(System.currentTimeMillis(), System.nanoTime()).toString();
+
+    public JobGen(GenomixJobConf job) throws HyracksDataException {
+        this.confFactory = new ConfFactory(job);
+    }
+
+    public abstract JobSpecification generateJob() throws HyracksException;
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
index abfff00..afc1cf7 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
@@ -24,18 +24,39 @@
 import org.apache.hadoop.mapred.InputSplit;
 import org.apache.hadoop.mapred.JobConf;
 
-import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.hyracks.job.JobGen;
+import edu.uci.ics.genomix.hyracks.data.accessors.KmerHashPartitioncomputerFactory;
+import edu.uci.ics.genomix.hyracks.data.accessors.KmerNormarlizedComputerFactory;
+import edu.uci.ics.genomix.hyracks.data.primitive.KmerPointable;
+import edu.uci.ics.genomix.hyracks.newgraph.dataflow.ConnectorPolicyAssignmentPolicy;
 import edu.uci.ics.genomix.hyracks.newgraph.dataflow.ReadsKeyValueParserFactory;
+import edu.uci.ics.genomix.hyracks.newgraph.dataflow.aggregators.AggregateKmerAggregateFactory;
+import edu.uci.ics.genomix.hyracks.newgraph.dataflow.aggregators.MergeKmerAggregateFactory;
+import edu.uci.ics.genomix.hyracks.newgraph.io.NodeTextWriterFactory;
+
 import edu.uci.ics.hyracks.api.client.NodeControllerInfo;
 import edu.uci.ics.hyracks.api.constraints.PartitionConstraintHelper;
 import edu.uci.ics.hyracks.api.dataflow.IConnectorDescriptor;
 import edu.uci.ics.hyracks.api.dataflow.IOperatorDescriptor;
+import edu.uci.ics.hyracks.api.dataflow.value.IBinaryComparatorFactory;
+import edu.uci.ics.hyracks.api.dataflow.value.INormalizedKeyComputerFactory;
+import edu.uci.ics.hyracks.api.dataflow.value.ISerializerDeserializer;
+import edu.uci.ics.hyracks.api.dataflow.value.ITuplePartitionComputerFactory;
+import edu.uci.ics.hyracks.api.dataflow.value.RecordDescriptor;
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
 import edu.uci.ics.hyracks.api.exceptions.HyracksException;
 import edu.uci.ics.hyracks.api.job.JobSpecification;
+import edu.uci.ics.hyracks.data.std.accessors.PointableBinaryComparatorFactory;
+import edu.uci.ics.hyracks.data.std.api.IPointableFactory;
+import edu.uci.ics.hyracks.dataflow.std.base.AbstractOperatorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.connectors.MToNPartitioningMergingConnectorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.connectors.OneToOneConnectorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptorFactory;
+import edu.uci.ics.hyracks.dataflow.std.group.preclustered.PreclusteredGroupOperatorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.sort.ExternalSortOperatorDescriptor;
+import edu.uci.ics.hyracks.hdfs.api.ITupleWriterFactory;
 import edu.uci.ics.hyracks.hdfs.dataflow.ConfFactory;
 import edu.uci.ics.hyracks.hdfs.dataflow.HDFSReadOperatorDescriptor;
+import edu.uci.ics.hyracks.hdfs.dataflow.HDFSWriteOperatorDescriptor;
 import edu.uci.ics.hyracks.hdfs.scheduler.Scheduler;
 
 @SuppressWarnings("deprecation")
@@ -68,7 +89,7 @@
     protected int tableSize;
     protected GroupbyType groupbyType;
     protected OutputFormat outputFormat;
-    protected boolean bGenerateReversedKmer;
+
 
     protected void logDebug(String status) {
         LOG.debug(status + " nc nodes:" + ncNodeNames.length);
@@ -85,7 +106,116 @@
         }
         initJobConfiguration(scheduler);
     }
-    
+
+    private Object[] generateAggeragateDescriptorbyType(JobSpecification jobSpec, int[] keyFields,
+            IAggregatorDescriptorFactory aggregator, IAggregatorDescriptorFactory merger,
+            ITuplePartitionComputerFactory partition, INormalizedKeyComputerFactory normalizer,
+            IPointableFactory pointable, RecordDescriptor combineRed, RecordDescriptor finalRec)
+            throws HyracksDataException {
+
+        Object[] obj = new Object[3];
+
+        switch (groupbyType) {
+            case PRECLUSTER:
+            default:
+                obj[0] = new PreclusteredGroupOperatorDescriptor(jobSpec, keyFields,
+                        new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory.of(pointable) }, aggregator,
+                        combineRed);
+                obj[1] = new MToNPartitioningMergingConnectorDescriptor(jobSpec, partition, keyFields,
+                        new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory.of(pointable) });
+                obj[2] = new PreclusteredGroupOperatorDescriptor(jobSpec, keyFields,
+                        new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory.of(pointable) }, merger,
+                        finalRec);
+                jobSpec.setConnectorPolicyAssignmentPolicy(new ConnectorPolicyAssignmentPolicy());
+                break;
+        }
+        return obj;
+    }
+
+    public HDFSReadOperatorDescriptor createHDFSReader(JobSpecification jobSpec) throws HyracksDataException {
+        try {
+            InputSplit[] splits = hadoopJobConfFactory.getConf().getInputFormat()
+                    .getSplits(hadoopJobConfFactory.getConf(), ncNodeNames.length);
+
+            return new HDFSReadOperatorDescriptor(jobSpec, ReadsKeyValueParserFactory.readKmerOutputRec,
+                    hadoopJobConfFactory.getConf(), splits, readSchedule, new ReadsKeyValueParserFactory(readLength,
+                            kmerSize));
+        } catch (Exception e) {
+            throw new HyracksDataException(e);
+        }
+    }
+
+    public static void connectOperators(JobSpecification jobSpec, IOperatorDescriptor preOp, String[] preNodes,
+            IOperatorDescriptor nextOp, String[] nextNodes, IConnectorDescriptor conn) {
+        PartitionConstraintHelper.addAbsoluteLocationConstraint(jobSpec, preOp, preNodes);
+        PartitionConstraintHelper.addAbsoluteLocationConstraint(jobSpec, nextOp, nextNodes);
+        jobSpec.connect(conn, preOp, 0, nextOp, 0);
+    }
+
+    public AbstractOperatorDescriptor generateGroupbyKmerJob(JobSpecification jobSpec,
+            AbstractOperatorDescriptor readOperator) throws HyracksDataException {
+        int[] keyFields = new int[] { 0 }; // the id of grouped key
+
+        ExternalSortOperatorDescriptor sorter = new ExternalSortOperatorDescriptor(jobSpec, frameLimits, keyFields,
+                new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory.of(KmerPointable.FACTORY) },
+                ReadsKeyValueParserFactory.readKmerOutputRec);
+        
+        connectOperators(jobSpec, readOperator, ncNodeNames, sorter, ncNodeNames, new OneToOneConnectorDescriptor(
+                jobSpec));
+
+        RecordDescriptor combineKmerOutputRec = new RecordDescriptor(new ISerializerDeserializer[] { null, null });
+        jobSpec.setFrameSize(frameSize);
+
+        Object[] objs = generateAggeragateDescriptorbyType(jobSpec, keyFields, new AggregateKmerAggregateFactory(kmerSize),
+                new MergeKmerAggregateFactory(kmerSize), new KmerHashPartitioncomputerFactory(),
+                new KmerNormarlizedComputerFactory(), KmerPointable.FACTORY, combineKmerOutputRec, combineKmerOutputRec);
+        AbstractOperatorDescriptor kmerLocalAggregator = (AbstractOperatorDescriptor) objs[0];
+        logDebug("LocalKmerGroupby Operator");
+        connectOperators(jobSpec, sorter, ncNodeNames, kmerLocalAggregator, ncNodeNames,
+                new OneToOneConnectorDescriptor(jobSpec));
+
+        logDebug("CrossKmerGroupby Operator");
+        IConnectorDescriptor kmerConnPartition = (IConnectorDescriptor) objs[1];
+        AbstractOperatorDescriptor kmerCrossAggregator = (AbstractOperatorDescriptor) objs[2];
+        connectOperators(jobSpec, kmerLocalAggregator, ncNodeNames, kmerCrossAggregator, ncNodeNames, kmerConnPartition);
+        return kmerCrossAggregator;
+    }
+
+    public AbstractOperatorDescriptor generateNodeWriterOpertator(JobSpecification jobSpec,
+            AbstractOperatorDescriptor mapEachReadToNode) throws HyracksException {
+        ITupleWriterFactory nodeWriter = null;
+        switch (outputFormat) {
+            case TEXT:
+                nodeWriter = new NodeTextWriterFactory(kmerSize);
+                break;
+        }
+        logDebug("WriteOperator");
+        // Output Node
+        HDFSWriteOperatorDescriptor writeNodeOperator = new HDFSWriteOperatorDescriptor(jobSpec,
+                hadoopJobConfFactory.getConf(), nodeWriter);
+        connectOperators(jobSpec, mapEachReadToNode, ncNodeNames, writeNodeOperator, ncNodeNames,
+                new OneToOneConnectorDescriptor(jobSpec));
+        return writeNodeOperator;
+    }
+
+    @Override
+    public JobSpecification generateJob() throws HyracksException {
+
+        JobSpecification jobSpec = new JobSpecification();
+        logDebug("ReadKmer Operator");
+
+        HDFSReadOperatorDescriptor readOperator = createHDFSReader(jobSpec);
+
+        logDebug("Group by Kmer");
+        AbstractOperatorDescriptor lastOperator = generateGroupbyKmerJob(jobSpec, readOperator);
+
+        logDebug("Write node to result");
+        lastOperator = generateNodeWriterOpertator(jobSpec, lastOperator);
+
+        jobSpec.addRoot(readOperator);//what's this? why we need this? why I can't seet it in the JobGenCheckReader
+        return jobSpec;
+    }
+
     protected void initJobConfiguration(Scheduler scheduler) throws HyracksDataException {
         Configuration conf = confFactory.getConf();
         readLength = conf.getInt(GenomixJobConf.READ_LENGTH, GenomixJobConf.DEFAULT_READLEN);
@@ -98,18 +228,11 @@
         tableSize = conf.getInt(GenomixJobConf.TABLE_SIZE, GenomixJobConf.DEFAULT_TABLE_SIZE);
         frameSize = conf.getInt(GenomixJobConf.FRAME_SIZE, GenomixJobConf.DEFAULT_FRAME_SIZE);
 
-        bGenerateReversedKmer = conf.getBoolean(GenomixJobConf.REVERSED_KMER, GenomixJobConf.DEFAULT_REVERSED);
-
         String type = conf.get(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
-        if (type.equalsIgnoreCase(GenomixJobConf.GROUPBY_TYPE_EXTERNAL)) {
-            groupbyType = GroupbyType.EXTERNAL;
-        } else if (type.equalsIgnoreCase(GenomixJobConf.GROUPBY_TYPE_PRECLUSTER)) {
-            groupbyType = GroupbyType.PRECLUSTER;
-        } else {
-            groupbyType = GroupbyType.HYBRIDHASH;
-        }
+        groupbyType = GroupbyType.PRECLUSTER;
 
-        String output = conf.get(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_BINARY);
+        String output = conf.get(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_TEXT);
+        
         if (output.equalsIgnoreCase("text")) {
             outputFormat = OutputFormat.TEXT;
         } else {
@@ -131,30 +254,5 @@
         LOG.info("Frame limit" + frameLimits);
         LOG.info("Frame kmerByteSize" + frameSize);
     }
-    
-    public HDFSReadOperatorDescriptor createHDFSReader(JobSpecification jobSpec) throws HyracksDataException {
-        try {
-            InputSplit[] splits = hadoopJobConfFactory.getConf().getInputFormat()
-                    .getSplits(hadoopJobConfFactory.getConf(), ncNodeNames.length);
 
-            return new HDFSReadOperatorDescriptor(jobSpec, ReadsKeyValueParserFactory.readKmerOutputRec,
-                    hadoopJobConfFactory.getConf(), splits, readSchedule, new ReadsKeyValueParserFactory(readLength,
-                            kmerSize, bGenerateReversedKmer));
-        } catch (Exception e) {
-            throw new HyracksDataException(e);
-        }
-    }
-
-    public static void connectOperators(JobSpecification jobSpec, IOperatorDescriptor preOp, String[] preNodes,
-            IOperatorDescriptor nextOp, String[] nextNodes, IConnectorDescriptor conn) {
-        PartitionConstraintHelper.addAbsoluteLocationConstraint(jobSpec, preOp, preNodes);
-        PartitionConstraintHelper.addAbsoluteLocationConstraint(jobSpec, nextOp, nextNodes);
-        jobSpec.connect(conn, preOp, 0, nextOp, 0);
-    }
-
-    @Override
-    public JobSpecification generateJob() throws HyracksException {
-        // TODO Auto-generated method stub
-        return null;
-    }
 }
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java
index 6026ac1..f512f43 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java
@@ -18,12 +18,11 @@
 import java.io.IOException;
 import java.util.Map;
 
+import org.apache.hadoop.conf.Configuration;
 import edu.uci.ics.genomix.hyracks.newgraph.dataflow.ReadsKeyValueParserFactory;
-import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.oldtype.IntermediateNodeWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+
 import edu.uci.ics.hyracks.api.client.NodeControllerInfo;
 import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
@@ -34,12 +33,16 @@
 import edu.uci.ics.hyracks.dataflow.std.connectors.OneToOneConnectorDescriptor;
 import edu.uci.ics.hyracks.hdfs.api.ITupleWriter;
 import edu.uci.ics.hyracks.hdfs.api.ITupleWriterFactory;
+import edu.uci.ics.hyracks.hdfs.dataflow.ConfFactory;
 import edu.uci.ics.hyracks.hdfs.dataflow.HDFSReadOperatorDescriptor;
 import edu.uci.ics.hyracks.hdfs.dataflow.HDFSWriteOperatorDescriptor;
 import edu.uci.ics.hyracks.hdfs.scheduler.Scheduler;
 
 public class JobGenCheckReader extends JobGenBrujinGraph {
 
+    /**
+     * 
+     */
     private static final long serialVersionUID = 1L;
 
     public JobGenCheckReader(GenomixJobConf job, Scheduler scheduler, Map<String, NodeControllerInfo> ncMap,
@@ -62,7 +65,7 @@
 
     public AbstractSingleActivityOperatorDescriptor generateRootByWriteKmerReader(JobSpecification jobSpec,
             HDFSReadOperatorDescriptor readOperator) throws HyracksException {
-        // Output Kmer
+        
         HDFSWriteOperatorDescriptor writeKmerOperator = new HDFSWriteOperatorDescriptor(jobSpec,
                 hadoopJobConfFactory.getConf(), new ITupleWriterFactory() {
 
@@ -70,11 +73,11 @@
 
                     @Override
                     public ITupleWriter getTupleWriter(IHyracksTaskContext ctx) throws HyracksDataException {
+                        KmerBytesWritable.setGlobalKmerLength(kmerSize);
                         return new ITupleWriter() {
 
-                            private KmerBytesWritable kmer = new KmerBytesWritable(kmerSize);
-                            private KmerListWritable kmerList = new KmerListWritable();
-                            //private IntermediateNodeWritable intermediateNode = new IntermediateNodeWritable();
+                            private NodeWritable outputNode = new NodeWritable();
+                            private KmerBytesWritable outputKmer = new KmerBytesWritable();
 
                             @Override
                             public void open(DataOutput output) throws HyracksDataException {
@@ -83,36 +86,20 @@
                             @Override
                             public void write(DataOutput output, ITupleReference tuple) throws HyracksDataException {
                                 try {
-                                    if (kmer.getLength() > tuple
+                                    if (outputKmer.getLength() > tuple
                                             .getFieldLength(ReadsKeyValueParserFactory.OutputKmerField)) {
                                         throw new IllegalArgumentException("Not enough kmer bytes");
                                     }
-                                    //kemr
-                                    kmer.setNewReference(
+                                    outputKmer.setAsReference(
                                             tuple.getFieldData(ReadsKeyValueParserFactory.OutputKmerField),
                                             tuple.getFieldStart(ReadsKeyValueParserFactory.OutputKmerField));
-                                    kmerList.setNewReference(tuple.getFieldLength(ReadsKeyValueParserFactory.OutputNodeIdField), 
-                                            tuple.getFieldData(ReadsKeyValueParserFactory.OutputNodeIdField), 
-                                            tuple.getFieldStart(ReadsKeyValueParserFactory.OutputNodeIdField));
-//                                    //nodeId
-//                                    intermediateNode.getNodeId().setNewReference(tuple.getFieldData(ReadsKeyValueParserFactory.OutputNodeIdField), 
-//                                            tuple.getFieldStart(ReadsKeyValueParserFactory.OutputNodeIdField));
-                                    //FF list
-//                                    intermediateNode.getFFList().setNewReference(tuple.getFieldLength(ReadsKeyValueParserFactory.OutputForwardForwardField) / 2 ,
-//                                            tuple.getFieldData(ReadsKeyValueParserFactory.OutputForwardForwardField), tuple.getFieldStart(ReadsKeyValueParserFactory.OutputForwardForwardField));
-//                                    //FR list
-//                                    intermediateNode.getFRList().setNewReference(tuple.getFieldLength(ReadsKeyValueParserFactory.OutputForwardReverseField / kmer.getLength()),
-//                                            tuple.getFieldData(ReadsKeyValueParserFactory.OutputForwardReverseField), tuple.getFieldStart(ReadsKeyValueParserFactory.OutputForwardReverseField));
-//                                    //RF list
-//                                    intermediateNode.getRFList().setNewReference(tuple.getFieldLength(ReadsKeyValueParserFactory.OutputReverseForwardField / kmer.getLength()),
-//                                            tuple.getFieldData(ReadsKeyValueParserFactory.OutputReverseForwardField), tuple.getFieldStart(ReadsKeyValueParserFactory.OutputReverseForwardField));
-//                                    //RR list
-//                                    intermediateNode.getRRList().setNewReference(tuple.getFieldLength(ReadsKeyValueParserFactory.OutputReverseReverseField / kmer.getLength()),
-//                                            tuple.getFieldData(ReadsKeyValueParserFactory.OutputReverseReverseField), tuple.getFieldStart(ReadsKeyValueParserFactory.OutputReverseReverseField));
-//                                    
-                                    output.write(kmer.toString().getBytes());
+                                    outputNode.setAsReference(
+                                            tuple.getFieldData(ReadsKeyValueParserFactory.OutputNodeField),
+                                            tuple.getFieldStart(ReadsKeyValueParserFactory.OutputNodeField));
+
+                                    output.write(outputKmer.toString().getBytes());
                                     output.writeByte('\t');
-                                    output.write(kmerList.toString().getBytes());
+                                    output.write(outputNode.toString().getBytes());
                                     output.writeByte('\n');
                                 } catch (IOException e) {
                                     throw new HyracksDataException(e);
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
index dfae011..25915aa 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
@@ -8,7 +8,6 @@
 import java.io.IOException;
 
 import junit.framework.Assert;
-
 import org.apache.commons.io.FileUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
@@ -24,16 +23,16 @@
 import org.junit.Before;
 import org.junit.Test;
 
-import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
+import edu.uci.ics.genomix.hyracks.newgraph.job.GenomixJobConf;
 import edu.uci.ics.genomix.hyracks.newgraph.driver.Driver;
 import edu.uci.ics.genomix.hyracks.newgraph.driver.Driver.Plan;
 import edu.uci.ics.genomix.hyracks.test.TestUtils;
-import edu.uci.ics.genomix.oldtype.NodeWritable;
+//import edu.uci.ics.genomix.oldtype.NodeWritable;
 
 @SuppressWarnings("deprecation")
 public class JobRun {
     private static final int KmerSize = 5;
-    private static final int ReadLength = 8;
+    private static final int ReadLength = 6;
     private static final String ACTUAL_RESULT_DIR = "actual";
     private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
 
@@ -41,16 +40,7 @@
     private static final String HDFS_INPUT_PATH = "/webmap";
     private static final String HDFS_OUTPUT_PATH = "/webmap_result";
 
-    private static final String EXPECTED_DIR = "src/test/resources/expected/";
-    private static final String EXPECTED_READER_RESULT = EXPECTED_DIR + "result_after_initial_read";
-//    private static final String EXPECTED_OUPUT_KMER = EXPECTED_DIR + "result_after_kmerAggregate";
-//    private static final String EXPECTED_KMER_TO_READID = EXPECTED_DIR + "result_after_kmer2readId";
-//    private static final String EXPECTED_GROUPBYREADID = EXPECTED_DIR + "result_after_readIDAggreage";
-//    private static final String EXPECTED_OUPUT_NODE = EXPECTED_DIR + "result_after_generateNode";
-//    private static final String EXPECTED_UNMERGED = EXPECTED_DIR + "result_unmerged";
-
     private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + "/merged.txt";
-    private static final String CONVERT_RESULT = DUMPED_RESULT + ".txt";
     private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";;
     private MiniDFSCluster dfsCluster;
     
@@ -63,13 +53,22 @@
     @Test
     public void TestAll() throws Exception {
         TestReader();
+//        TestGroupby();
     }
     
     public void TestReader() throws Exception {
         cleanUpReEntry();
         conf.set(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_TEXT);
         driver.runJob(new GenomixJobConf(conf), Plan.CHECK_KMERREADER, true);
-        Assert.assertEquals(true, checkResults(EXPECTED_READER_RESULT, null));
+        dumpResult();
+    }
+    
+    public void TestGroupby() throws Exception {
+        conf.set(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_TEXT);
+        cleanUpReEntry();
+        conf.set(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
+        driver.runJob(new GenomixJobConf(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+//        dumpResult();
     }
     
     @Before
@@ -129,54 +128,12 @@
         }
     }
     
-    private boolean checkResults(String expectedPath, int[] poslistField) throws Exception {
-        File dumped = null;
+    private void dumpResult() throws Exception {
         String format = conf.get(GenomixJobConf.OUTPUT_FORMAT);
         if (GenomixJobConf.OUTPUT_FORMAT_TEXT.equalsIgnoreCase(format)) {
             FileUtil.copyMerge(FileSystem.get(conf), new Path(HDFS_OUTPUT_PATH),
                     FileSystem.getLocal(new Configuration()), new Path(DUMPED_RESULT), false, conf, null);
-            dumped = new File(DUMPED_RESULT);
-        } else {
-
-            FileSystem.getLocal(new Configuration()).mkdirs(new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH));
-            File filePathTo = new File(CONVERT_RESULT);
-            BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
-            for (int i = 0; i < numPartitionPerMachine * numberOfNC; i++) {
-                String partname = "/part-" + i;
-                // FileUtil.copy(FileSystem.get(conf), new Path(HDFS_OUTPUT_PATH
-                // + partname), FileSystem.getLocal(new Configuration()),
-                // new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + partname),
-                // false, conf);
-
-                Path path = new Path(HDFS_OUTPUT_PATH + partname);
-                FileSystem dfs = FileSystem.get(conf);
-                if (dfs.getFileStatus(path).getLen() == 0) {
-                    continue;
-                }
-                SequenceFile.Reader reader = new SequenceFile.Reader(dfs, path, conf);
-
-                NodeWritable node = new NodeWritable(conf.getInt(GenomixJobConf.KMER_LENGTH, KmerSize));
-                NullWritable value = NullWritable.get();
-                while (reader.next(node, value)) {
-                    if (node == null) {
-                        break;
-                    }
-                    bw.write(node.toString());
-                    System.out.println(node.toString());
-                    bw.newLine();
-                }
-                reader.close();
-            }
-            bw.close();
-            dumped = new File(CONVERT_RESULT);
-        }
-
-        if (poslistField != null) {
-            TestUtils.compareWithUnSortedPosition(new File(expectedPath), dumped, poslistField);
-        } else {
-            TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
-        }
-        return true;
+        } 
     }
     
     @After
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/JobRunStepByStepTest.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/JobRunStepByStepTest.java
index bd761a5..51a0d15 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/JobRunStepByStepTest.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/JobRunStepByStepTest.java
@@ -41,7 +41,7 @@
 import edu.uci.ics.genomix.hyracks.driver.Driver;
 import edu.uci.ics.genomix.hyracks.driver.Driver.Plan;
 import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.oldtype.NodeWritable;
+import edu.uci.ics.genomix.velvet.oldtype.NodeWritable;
 
 @SuppressWarnings("deprecation")
 public class JobRunStepByStepTest {
@@ -75,11 +75,11 @@
 
     @Test
     public void TestAll() throws Exception {
-        TestReader();
+//        TestReader();
 //        TestGroupbyKmer();
 //        TestMapKmerToRead();
 //        TestGroupByReadID();
-//        TestEndToEnd();
+        TestEndToEnd();
 //        TestUnMergedNode();
     }
 
diff --git a/genomix/genomix-hyracks/src/test/resources/data/webmap/test1.txt b/genomix/genomix-hyracks/src/test/resources/data/webmap/test1.txt
index 17770fa..3f1cd5c 100644
--- a/genomix/genomix-hyracks/src/test/resources/data/webmap/test1.txt
+++ b/genomix/genomix-hyracks/src/test/resources/data/webmap/test1.txt
@@ -1 +1 @@
-1	AATAGAAG
+1	AATAGA
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
index 5c28134..859ddba 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
@@ -60,7 +60,7 @@
             /**
              * set the src vertex id
              */
-            vertexId.set(getRecordReader().getCurrentKey());
+            vertexId.setAsCopy(getRecordReader().getCurrentKey());
             vertex.setVertexId(vertexId);
             /**
              * set the vertex value
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
index 0d685de..4dfff11 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
@@ -11,6 +11,7 @@
 import edu.uci.ics.pregelix.api.io.VertexReader;
 import edu.uci.ics.pregelix.api.util.BspUtils;
 import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
@@ -64,19 +65,20 @@
             /**
              * set the src vertex id
              */
-            vertexId.set(getRecordReader().getCurrentKey());
+            vertexId.setAsCopy(getRecordReader().getCurrentKey());
             vertex.setVertexId(vertexId);
             /**
              * set the vertex value
              */
             node.set(getRecordReader().getCurrentValue());
-            vertexValue.setKmerlength(node.getKmerlength());
+            vertexValue.setKmerlength(node.getKmerLength());
             vertexValue.setNodeIdList(node.getNodeIdList());
             vertexValue.setFFList(node.getFFList());
             vertexValue.setFRList(node.getFRList());
             vertexValue.setRFList(node.getRFList());
             vertexValue.setRRList(node.getRRList());
-            vertexValue.setKmer(getRecordReader().getCurrentKey());
+            // TODO make this more efficient (don't use toString)
+            vertexValue.setKmer(new VKmerBytesWritable(getRecordReader().getCurrentKey().toString()));
             vertexValue.setState(State.IS_NON);
             vertex.setVertexValue(vertexValue);
         }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
index a15ceeb..44fa444 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
@@ -6,25 +6,25 @@
 
 import org.apache.hadoop.io.WritableComparable;
 
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
 
 public class AdjacencyListWritable implements WritableComparable<AdjacencyListWritable>{
-    private KmerListWritable forwardList;
-    private KmerListWritable reverseList;
+    private VKmerListWritable forwardList;
+    private VKmerListWritable reverseList;
     
     public AdjacencyListWritable(){
-        forwardList = new KmerListWritable();
-        reverseList = new KmerListWritable();
+        forwardList = new VKmerListWritable();
+        reverseList = new VKmerListWritable();
     }
     
     public AdjacencyListWritable(int kmerSize){
-        forwardList = new KmerListWritable(kmerSize);
-        reverseList = new KmerListWritable(kmerSize);
+        forwardList = new VKmerListWritable();
+        reverseList = new VKmerListWritable();
     }
 
     public void set(AdjacencyListWritable adjacencyList){
-        forwardList.set(adjacencyList.getForwardList());
-        reverseList.set(adjacencyList.getReverseList());
+        forwardList.setCopy(adjacencyList.getForwardList());
+        reverseList.setCopy(adjacencyList.getReverseList());
     }
     
     public void reset(){
@@ -33,27 +33,27 @@
     }
     
     public void reset(int kmerSize){
-        forwardList.reset(kmerSize);
-        reverseList.reset(kmerSize);
+        forwardList.reset();
+        reverseList.reset();
     }
     
     public int getCountOfPosition(){
     	return forwardList.getCountOfPosition() + reverseList.getCountOfPosition();
     }
 
-    public KmerListWritable getForwardList() {
+    public VKmerListWritable getForwardList() {
         return forwardList;
     }
 
-    public void setForwardList(KmerListWritable forwardList) {
+    public void setForwardList(VKmerListWritable forwardList) {
         this.forwardList = forwardList;
     }
 
-    public KmerListWritable getReverseList() {
+    public VKmerListWritable getReverseList() {
         return reverseList;
     }
 
-    public void setReverseList(KmerListWritable reverseList) {
+    public void setReverseList(VKmerListWritable reverseList) {
         this.reverseList = reverseList;
     }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
index 3200e14..5702146 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
@@ -27,7 +27,7 @@
 
     public MergeBubbleMessageWritable() {
         sourceVertexId = new PositionWritable();
-        chainVertexId = new KmerBytesWritable(0);
+        chainVertexId = new KmerBytesWritable();
         neighberNode = new AdjacencyListWritable();
         startVertexId = new PositionWritable();
         message = Message.NON;
@@ -42,7 +42,7 @@
         }
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.ACUTUALKMER;
-            this.chainVertexId.set(msg.getChainVertexId());
+            this.chainVertexId.setAsCopy(msg.getChainVertexId());
         }
         if (neighberNode != null) {
             checkMessage |= CheckMessage.NEIGHBER;
@@ -63,7 +63,7 @@
         }
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.ACUTUALKMER;
-            this.chainVertexId.set(chainVertexId);
+            this.chainVertexId.setAsCopy(chainVertexId);
         }
         if (neighberNode != null) {
             checkMessage |= CheckMessage.NEIGHBER;
@@ -78,7 +78,7 @@
 
     public void reset() {
         checkMessage = 0;
-        chainVertexId.reset(1);
+//        chainVertexId.reset();
         neighberNode.reset();
         message = Message.NON;
     }
@@ -101,7 +101,7 @@
     public void setChainVertexId(KmerBytesWritable chainVertexId) {
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.ACUTUALKMER;
-            this.chainVertexId.set(chainVertexId);
+            this.chainVertexId.setAsCopy(chainVertexId);
         }
     }
     
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
index 1eba346..80ce45a 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
@@ -8,8 +8,9 @@
 
 import edu.uci.ics.genomix.pregelix.type.CheckMessage;
 import edu.uci.ics.genomix.pregelix.type.Message;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.PositionListWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
 
 public class MessageWritable implements WritableComparable<MessageWritable> {
     /**
@@ -17,23 +18,23 @@
      * stores neighber vertexValue when pathVertex sends the message
      * file stores the point to the file that stores the chains of connected DNA
      */
-    private KmerBytesWritable sourceVertexId;
-    private KmerBytesWritable kmer;
+    private VKmerBytesWritable sourceVertexId;
+    private VKmerBytesWritable kmer;
     private AdjacencyListWritable neighberNode; //incoming or outgoing
     private PositionListWritable nodeIdList = new PositionListWritable();
     private byte flag;
     private boolean isFlip;
     private int kmerlength = 0;
     private boolean updateMsg = false;
-    private KmerBytesWritable startVertexId;
+    private VKmerBytesWritable startVertexId;
     
     private byte checkMessage;
 
     public MessageWritable() {
-        sourceVertexId = new KmerBytesWritable();
-        kmer = new KmerBytesWritable(0);
+        sourceVertexId = new VKmerBytesWritable();
+        kmer = new VKmerBytesWritable();
         neighberNode = new AdjacencyListWritable();
-        startVertexId = new KmerBytesWritable();
+        startVertexId = new VKmerBytesWritable();
         flag = Message.NON;
         isFlip = false;
         checkMessage = (byte) 0;
@@ -41,10 +42,10 @@
     
     public MessageWritable(int kmerSize) {
         kmerlength = kmerSize;
-        sourceVertexId = new KmerBytesWritable(kmerSize);
-        kmer = new KmerBytesWritable(0);
+        sourceVertexId = new VKmerBytesWritable(kmerSize);
+        kmer = new VKmerBytesWritable(0);
         neighberNode = new AdjacencyListWritable(kmerSize);
-        startVertexId = new KmerBytesWritable(kmerSize);
+        startVertexId = new VKmerBytesWritable(kmerSize);
         flag = Message.NON;
         isFlip = false;
         checkMessage = (byte) 0;
@@ -55,11 +56,11 @@
         checkMessage = 0;
         if (sourceVertexId != null) {
             checkMessage |= CheckMessage.SOURCE;
-            this.sourceVertexId.set(msg.getSourceVertexId());
+            this.sourceVertexId.setAsCopy(msg.getSourceVertexId());
         }
         if (kmer != null) {
             checkMessage |= CheckMessage.ACUTUALKMER;
-            this.kmer.set(msg.getActualKmer());
+            this.kmer.setAsCopy(msg.getActualKmer());
         }
         if (neighberNode != null) {
             checkMessage |= CheckMessage.NEIGHBER;
@@ -67,23 +68,23 @@
         }
         if (startVertexId != null) {
             checkMessage |= CheckMessage.START;
-            this.startVertexId.set(msg.getStartVertexId());
+            this.startVertexId.setAsCopy(msg.getStartVertexId());
         }
         checkMessage |= CheckMessage.ADJMSG;
         this.flag = msg.getFlag();
         updateMsg = msg.isUpdateMsg();
     }
 
-    public void set(int kmerlength, KmerBytesWritable sourceVertexId, KmerBytesWritable chainVertexId, AdjacencyListWritable neighberNode, byte message) {
+    public void set(int kmerlength, VKmerBytesWritable sourceVertexId, VKmerBytesWritable chainVertexId, AdjacencyListWritable neighberNode, byte message) {
         this.kmerlength = kmerlength;
         checkMessage = 0;
         if (sourceVertexId != null) {
             checkMessage |= CheckMessage.SOURCE;
-            this.sourceVertexId.set(sourceVertexId);
+            this.sourceVertexId.setAsCopy(sourceVertexId);
         }
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.ACUTUALKMER;
-            this.kmer.set(chainVertexId);
+            this.kmer.setAsCopy(chainVertexId);
         }
         if (neighberNode != null) {
             checkMessage |= CheckMessage.NEIGHBER;
@@ -99,43 +100,43 @@
     public void reset(int kmerSize) {
         checkMessage = (byte) 0;
         kmerlength = kmerSize;
-        kmer.reset(1);
+//        kmer.reset();
         neighberNode.reset(kmerSize);
         startVertexId.reset(kmerSize);
         flag = Message.NON;
         isFlip = false;
     }
 
-    public KmerBytesWritable getSourceVertexId() {
+    public VKmerBytesWritable getSourceVertexId() {
         return sourceVertexId;
     }
 
-    public void setSourceVertexId(KmerBytesWritable sourceVertexId) {
+    public void setSourceVertexId(VKmerBytesWritable sourceVertexId) {
         if (sourceVertexId != null) {
             checkMessage |= CheckMessage.SOURCE;
-            this.sourceVertexId.set(sourceVertexId);
+            this.sourceVertexId.setAsCopy(sourceVertexId);
         }
     }
     
-    public KmerBytesWritable getActualKmer() {
+    public VKmerBytesWritable getActualKmer() {
         return kmer;
     }
 
-    public void setAcutalKmer(KmerBytesWritable actualKmer) {
+    public void setActualKmer(VKmerBytesWritable actualKmer) {
         if (actualKmer != null) {
             checkMessage |= CheckMessage.ACUTUALKMER;
-            this.kmer.set(actualKmer);
+            this.kmer.setAsCopy(actualKmer);
         }
     }
     
-    public KmerBytesWritable getCreatedVertexId() {
+    public VKmerBytesWritable getCreatedVertexId() {
         return kmer;
     }
 
-    public void setCreatedVertexId(KmerBytesWritable actualKmer) {
+    public void setCreatedVertexId(VKmerBytesWritable actualKmer) {
         if (actualKmer != null) {
             checkMessage |= CheckMessage.ACUTUALKMER;
-            this.kmer.set(actualKmer);
+            this.kmer.setAsCopy(actualKmer);
         }
     }
     
@@ -150,19 +151,19 @@
         }
     }
     
-    public KmerBytesWritable getStartVertexId() {
+    public VKmerBytesWritable getStartVertexId() {
         return startVertexId;
     }
 
-    public void setStartVertexId(KmerBytesWritable startVertexId) {
+    public void setStartVertexId(VKmerBytesWritable startVertexId) {
         if(startVertexId != null){
             checkMessage |= CheckMessage.START;
-            this.startVertexId.set(startVertexId);
+            this.startVertexId.setAsCopy(startVertexId);
         }
     }
 
     public int getLengthOfChain() {
-        return kmer.getKmerLength();
+        return kmer.getKmerLetterLength();
     }
 
     public byte getFlag() {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index 5847aae..e78f090 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -6,8 +6,8 @@
 
 import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
 
 public class VertexValueWritable implements WritableComparable<VertexValueWritable> {
 
@@ -47,7 +47,7 @@
     private AdjacencyListWritable incomingList;
     private AdjacencyListWritable outgoingList;
     private byte state;
-    private KmerBytesWritable kmer;
+    private VKmerBytesWritable kmer;
     private int kmerlength = 0;
     private boolean isFakeVertex = false;
 
@@ -61,27 +61,27 @@
         incomingList = new AdjacencyListWritable();
         outgoingList = new AdjacencyListWritable();
         state = State.IS_NON;
-        kmer = new KmerBytesWritable(kmerSize);
+        kmer = new VKmerBytesWritable();
     }
 
-    public VertexValueWritable(PositionListWritable nodeIdList, KmerListWritable forwardForwardList, KmerListWritable forwardReverseList,
-            KmerListWritable reverseForwardList, KmerListWritable reverseReverseList,
-            byte state, KmerBytesWritable kmer) {
+    public VertexValueWritable(PositionListWritable nodeIdList, VKmerListWritable forwardForwardList, VKmerListWritable forwardReverseList,
+            VKmerListWritable reverseForwardList, VKmerListWritable reverseReverseList,
+            byte state, VKmerBytesWritable kmer) {
         set(nodeIdList, forwardForwardList, forwardReverseList, 
                 reverseForwardList, reverseReverseList,
                 state, kmer);
     }
     
-    public void set(PositionListWritable nodeIdList, KmerListWritable forwardForwardList, KmerListWritable forwardReverseList,
-            KmerListWritable reverseForwardList, KmerListWritable reverseReverseList, 
-            byte state, KmerBytesWritable kmer) {
-        this.kmerlength = kmer.kmerByteSize;
+    public void set(PositionListWritable nodeIdList, VKmerListWritable forwardForwardList, VKmerListWritable forwardReverseList,
+            VKmerListWritable reverseForwardList, VKmerListWritable reverseReverseList, 
+            byte state, VKmerBytesWritable kmer) {
+        this.kmerlength = kmer.getKmerLetterLength();
         this.incomingList.setForwardList(reverseForwardList);
         this.incomingList.setReverseList(reverseReverseList);
         this.outgoingList.setForwardList(forwardForwardList);
         this.outgoingList.setReverseList(forwardReverseList);
         this.state = state;
-        this.kmer.set(kmer);
+        this.kmer.setAsCopy(kmer);
     }
     
     public void set(VertexValueWritable value) {
@@ -99,35 +99,35 @@
         this.nodeIdList.set(nodeIdList);
     }
 
-    public KmerListWritable getFFList() {
+    public VKmerListWritable getFFList() {
         return outgoingList.getForwardList();
     }
 
-    public KmerListWritable getFRList() {
+    public VKmerListWritable getFRList() {
         return outgoingList.getReverseList();
     }
 
-    public KmerListWritable getRFList() {
+    public VKmerListWritable getRFList() {
         return incomingList.getForwardList();
     }
 
-    public KmerListWritable getRRList() {
+    public VKmerListWritable getRRList() {
         return incomingList.getReverseList();
     }
     
-    public void setFFList(KmerListWritable forwardForwardList){
+    public void setFFList(VKmerListWritable forwardForwardList){
         outgoingList.setForwardList(forwardForwardList);
     }
     
-    public void setFRList(KmerListWritable forwardReverseList){
+    public void setFRList(VKmerListWritable forwardReverseList){
         outgoingList.setReverseList(forwardReverseList);
     }
     
-    public void setRFList(KmerListWritable reverseForwardList){
+    public void setRFList(VKmerListWritable reverseForwardList){
         incomingList.setForwardList(reverseForwardList);
     }
 
-    public void setRRList(KmerListWritable reverseReverseList){
+    public void setRRList(VKmerListWritable reverseReverseList){
         incomingList.setReverseList(reverseReverseList);
     }
     
@@ -165,17 +165,17 @@
     }
 
     public int getLengthOfKmer() {
-        return kmer.getKmerLength();
+        return kmer.getKmerLetterLength();
     }
 
-    public KmerBytesWritable getKmer() {
+    public VKmerBytesWritable getKmer() {
         return kmer;
     }
 
-    public void setKmer(KmerBytesWritable kmer) {
-        this.kmer.set(kmer);
+    public void setKmer(VKmerBytesWritable kmer) {
+        this.kmer.setAsCopy(kmer);
     }
-        
+
     public int getKmerlength() {
         return kmerlength;
     }
@@ -187,11 +187,11 @@
     public void reset(int kmerSize) {
         this.kmerlength = kmerSize;
         this.nodeIdList.reset();
-        this.incomingList.getForwardList().reset(kmerSize);
-        this.incomingList.getReverseList().reset(kmerSize);
-        this.outgoingList.getForwardList().reset(kmerSize);
-        this.outgoingList.getReverseList().reset(kmerSize);
-        this.kmer.reset(0);
+        this.incomingList.getForwardList().reset();
+        this.incomingList.getReverseList().reset();
+        this.outgoingList.getForwardList().reset();
+        this.outgoingList.getReverseList().reset();
+//        this.kmer.reset(0);
     }
     
     @Override
@@ -250,7 +250,7 @@
     /*
      * Delete the corresponding edge
      */
-    public void processDelete(byte neighborToDeleteDir, KmerBytesWritable nodeToDelete){
+    public void processDelete(byte neighborToDeleteDir, VKmerBytesWritable nodeToDelete){
         switch (neighborToDeleteDir & MessageFlag.DIR_MASK) {
             case MessageFlag.DIR_FF:
                 this.getFFList().remove(nodeToDelete);
@@ -270,8 +270,8 @@
     /*
      * Process any changes to value.  This is for edge updates
      */
-    public void processUpdates(byte neighborToDeleteDir, KmerBytesWritable nodeToDelete,
-            byte neighborToMergeDir, KmerBytesWritable nodeToAdd){
+    public void processUpdates(byte neighborToDeleteDir, VKmerBytesWritable nodeToDelete,
+            byte neighborToMergeDir, VKmerBytesWritable nodeToAdd){
 //        TODO
 //        this.getListFromDir(neighborToDeleteDir).remove(nodeToDelete);
 //        this.getListFromDir(neighborToMergeDir).append(nodeToDelete);
@@ -309,9 +309,9 @@
     /*
      * Process any changes to value.  This is for merging
      */
-    public void processMerges(byte neighborToDeleteDir, KmerBytesWritable nodeToDelete,
-            byte neighborToMergeDir, KmerBytesWritable nodeToAdd, 
-            int kmerSize, KmerBytesWritable kmer){
+    public void processMerges(byte neighborToDeleteDir, VKmerBytesWritable nodeToDelete,
+            byte neighborToMergeDir, VKmerBytesWritable nodeToAdd, 
+            int kmerSize, VKmerBytesWritable kmer){
         switch (neighborToDeleteDir & MessageFlag.DIR_MASK) {
             case MessageFlag.DIR_FF:
                 this.getFFList().remove(nodeToDelete); //set(null);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java
index bb60a25..95e070f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java
@@ -4,7 +4,7 @@
 import java.util.logging.Handler;
 import java.util.logging.LogRecord;
 
-import edu.uci.ics.genomix.oldtype.NodeWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
 
 public class DataLoadLogFormatter extends Formatter {
     private NodeWritable key;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
index 82ca03f..dd78cde 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
@@ -12,11 +12,11 @@
     // Create a DateFormat to format the logger timestamp.
     //
     private long step;
-    private KmerBytesWritable sourceVertexId = new KmerBytesWritable(1);
-    private KmerBytesWritable destVertexId = new KmerBytesWritable(1);
+    private KmerBytesWritable sourceVertexId = new KmerBytesWritable();
+    private KmerBytesWritable destVertexId = new KmerBytesWritable();
     private MessageWritable msg = new MessageWritable();
     private byte state;
-    private KmerBytesWritable mergeChain = new KmerBytesWritable(1);;
+    private KmerBytesWritable mergeChain = new KmerBytesWritable();
     //private boolean testDelete = false;
     /**
      * 0: general operation
@@ -32,8 +32,8 @@
     public void set(long step, KmerBytesWritable sourceVertexId, KmerBytesWritable destVertexId,
             MessageWritable msg, byte state) {
         this.step = step;
-        this.sourceVertexId.set(sourceVertexId);
-        this.destVertexId.set(destVertexId);
+        this.sourceVertexId.setAsCopy(sourceVertexId);
+        this.destVertexId.setAsCopy(destVertexId);
         this.msg = msg;
         this.state = state;
         this.operation = 0;
@@ -42,24 +42,24 @@
     public void setMergeChain(long step, KmerBytesWritable sourceVertexId, KmerBytesWritable mergeChain) {
         this.reset();
         this.step = step;
-        this.sourceVertexId.set(sourceVertexId);
-        this.mergeChain.set(mergeChain);
+        this.sourceVertexId.setAsCopy(sourceVertexId);
+        this.mergeChain.setAsCopy(mergeChain);
         this.operation = 2;
     }
 
     public void setVotoToHalt(long step, KmerBytesWritable sourceVertexId) {
         this.reset();
         this.step = step;
-        this.sourceVertexId.set(sourceVertexId);
+        this.sourceVertexId.setAsCopy(sourceVertexId);
         this.operation = 3;
     }
 
     public void reset() {
-        this.sourceVertexId = new KmerBytesWritable(1);
-        this.destVertexId = new KmerBytesWritable(1);
+        this.sourceVertexId = new KmerBytesWritable();
+        this.destVertexId = new KmerBytesWritable();
         this.msg = new MessageWritable();
         this.state = 0;
-        this.mergeChain = new KmerBytesWritable(1);
+        this.mergeChain = new KmerBytesWritable();
     }
 
     public String format(LogRecord record) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
index 4a5850a..6b23074 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
@@ -15,8 +15,8 @@
 
     public void set(long step, KmerBytesWritable sourceVertexId, KmerBytesWritable destVertexId) {
         this.step = step;
-        this.sourceVertexId.set(sourceVertexId);
-        this.destVertexId.set(destVertexId);
+        this.sourceVertexId.setAsCopy(sourceVertexId);
+        this.destVertexId.setAsCopy(destVertexId);
     }
 
     public String format(LogRecord record) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
index 11f6af1..5cb6aac 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
@@ -4,7 +4,8 @@
 import org.apache.hadoop.io.NullWritable;
 
 import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 import edu.uci.ics.pregelix.api.util.BspUtils;
@@ -46,8 +47,8 @@
  * Naive Algorithm for path merge graph
  */
 public class BridgeAddVertex extends
-        Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
-    public static final String KMER_SIZE = "BridgeRemoveVertex.kmerSize";
+        Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
+    public static final String KMER_SIZE = "BridgeRemoveVertex.kmerSize"; // TODO consolidate config options
     public static final String LENGTH = "BridgeRemoveVertex.length";
     public static int kmerSize = -1;
     private int length = -1;
@@ -56,10 +57,12 @@
      * initiate kmerSize, maxIteration
      */
     public void initVertex() {
-        if (kmerSize == -1)
+        if (kmerSize == -1) {
             kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
+            KmerBytesWritable.setGlobalKmerLength(kmerSize);
+        }
         if (length == -1)
-            length = getContext().getConfiguration().getInt(LENGTH, kmerSize + 5);
+            length = getContext().getConfiguration().getInt(LENGTH, kmerSize + 5); // TODO fail on parse
     }
 
     @SuppressWarnings("unchecked")
@@ -68,7 +71,7 @@
         initVertex();
         if(getSuperstep() == 1){
             if(getVertexId().toString().equals("ATA")){
-            	KmerBytesWritable vertexId = new KmerBytesWritable(kmerSize);
+            	VKmerBytesWritable vertexId = new VKmerBytesWritable(kmerSize);
                 vertexId.setByRead("GTA".getBytes(), 0);
                 getVertexValue().getFRList().append(vertexId);
                 
@@ -85,12 +88,12 @@
                 /**
                  * set the vertex value
                  */
-                KmerListWritable kmerFRList = new KmerListWritable(kmerSize);
+                VKmerListWritable kmerFRList = new VKmerListWritable();
                 kmerFRList.append(getVertexId());
                 vertexValue.setFRList(kmerFRList);
-                KmerBytesWritable otherVertexId = new KmerBytesWritable(kmerSize);
+                VKmerBytesWritable otherVertexId = new VKmerBytesWritable(kmerSize);
                 otherVertexId.setByRead("ACG".getBytes(), 0);
-                KmerListWritable kmerRFList = new KmerListWritable(kmerSize);
+                VKmerListWritable kmerRFList = new VKmerListWritable();
                 kmerRFList.append(otherVertexId);
                 vertexValue.setRFList(kmerRFList);
                 vertexValue.setKmer(vertexId);
@@ -99,7 +102,7 @@
                 addVertex(vertexId, vertex);
             } 
             else if(getVertexId().toString().equals("ACG")){
-                KmerBytesWritable brdgeVertexId = new KmerBytesWritable(kmerSize);
+                VKmerBytesWritable brdgeVertexId = new VKmerBytesWritable(kmerSize);
                 brdgeVertexId.setByRead("GTA".getBytes(), 0);
                 getVertexValue().getRFList().append(brdgeVertexId);
             }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
index caf7a36..039f5b4 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
@@ -12,7 +12,7 @@
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 /*
  * vertexId: BytesWritable
@@ -67,7 +67,7 @@
         else
             outgoingMsg.reset(kmerSize);
         if(destVertexId == null)
-            destVertexId = new KmerBytesWritable(kmerSize);
+            destVertexId = new VKmerBytesWritable(kmerSize);
         receivedMsgList.clear();
     }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
index f5aa3a1..3df090c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
@@ -3,8 +3,8 @@
 import java.util.Iterator;
 import org.apache.hadoop.io.NullWritable;
 
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 import edu.uci.ics.pregelix.api.util.BspUtils;
@@ -46,7 +46,7 @@
  *  Remove tip or single node when l > constant
  */
 public class BubbleAddVertex extends
-        Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
+        Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "BubbleAddVertex.kmerSize";
     public static int kmerSize = -1;
    
@@ -64,7 +64,7 @@
         initVertex(); 
         if(getSuperstep() == 1){
             if(getVertexId().toString().equals("ATA")){
-                KmerBytesWritable vertexId = new KmerBytesWritable(kmerSize);
+                VKmerBytesWritable vertexId = new VKmerBytesWritable(kmerSize);
                 vertexId.setByRead("GTA".getBytes(), 0);
                 getVertexValue().getFRList().append(vertexId);
                 
@@ -81,12 +81,12 @@
                 /**
                  * set the vertex value
                  */
-                KmerListWritable kmerFRList = new KmerListWritable(kmerSize);
+                VKmerListWritable kmerFRList = new VKmerListWritable();
                 kmerFRList.append(getVertexId());
                 vertexValue.setFRList(kmerFRList);
-                KmerBytesWritable otherVertexId = new KmerBytesWritable(kmerSize);
+                VKmerBytesWritable otherVertexId = new VKmerBytesWritable(kmerSize);
                 otherVertexId.setByRead("AGA".getBytes(), 0);
-                KmerListWritable kmerRFList = new KmerListWritable(kmerSize);
+                VKmerListWritable kmerRFList = new VKmerListWritable();
                 kmerRFList.append(otherVertexId);
                 vertexValue.setRFList(kmerRFList);
                 vertexValue.setKmer(vertexId);
@@ -95,7 +95,7 @@
                 addVertex(vertexId, vertex);
             } 
             else if(getVertexId().toString().equals("AGA")){
-                KmerBytesWritable brdgeVertexId = new KmerBytesWritable(kmerSize);
+                VKmerBytesWritable brdgeVertexId = new VKmerBytesWritable(kmerSize);
                 brdgeVertexId.setByRead("GTA".getBytes(), 0);
                 getVertexValue().getRFList().append(brdgeVertexId);
             }
@@ -112,7 +112,7 @@
         job.setVertexInputFormatClass(GraphCleanInputFormat.class);
         job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
index e92eaed..4cdeb89 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
@@ -7,7 +7,7 @@
 
 import org.apache.hadoop.io.NullWritable;
 
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.genomix.type.KmerBytesWritableFactory;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
@@ -30,7 +30,7 @@
 
     private KmerBytesWritableFactory kmerFactory = new KmerBytesWritableFactory(1);
     
-    private Map<KmerBytesWritable, ArrayList<MessageWritable>> receivedMsgMap = new HashMap<KmerBytesWritable, ArrayList<MessageWritable>>();
+    private Map<VKmerBytesWritable, ArrayList<MessageWritable>> receivedMsgMap = new HashMap<VKmerBytesWritable, ArrayList<MessageWritable>>();
     private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
     
     /**
@@ -65,8 +65,8 @@
                             if(hasNextDest(getVertexValue())){
                                 outgoingMsg.setStartVertexId(incomingMsg.getSourceVertexId());
                                 outgoingMsg.setSourceVertexId(getVertexId());
-                                outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
-                                destVertexId.set(getNextDestVertexId(getVertexValue()));
+                                outgoingMsg.setActualKmer(getVertexValue().getKmer());
+                                destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
                                 sendMsg(destVertexId, outgoingMsg);
                             }
                             break;
@@ -75,8 +75,8 @@
                             if(hasPrevDest(getVertexValue())){
                                 outgoingMsg.setStartVertexId(incomingMsg.getSourceVertexId());
                                 outgoingMsg.setSourceVertexId(getVertexId());
-                                outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
-                                destVertexId.set(getPrevDestVertexId(getVertexValue()));
+                                outgoingMsg.setActualKmer(getVertexValue().getKmer());
+                                destVertexId.setAsCopy(getPrevDestVertexId(getVertexValue()));
                                 sendMsg(destVertexId, outgoingMsg);
                             }
                             break;
@@ -98,7 +98,7 @@
                     receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MessageWritable>)receivedMsgList.clone());
                 }
             }
-            for(KmerBytesWritable prevId : receivedMsgMap.keySet()){
+            for(VKmerBytesWritable prevId : receivedMsgMap.keySet()){
                 receivedMsgList = receivedMsgMap.get(prevId);
                 if(receivedMsgList.size() > 1){
                     /** for each startVertex, sort the node by decreasing order of coverage **/
@@ -173,7 +173,7 @@
         job.setVertexInputFormatClass(GraphCleanInputFormat.class);
         job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
index f201fb1..ca4b088 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
@@ -12,13 +12,13 @@
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
 import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 /**
  * Naive Algorithm for path merge graph
  */
 public class BasicGraphCleanVertex extends
-        Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
+        Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "BasicGraphCleanVertex.kmerSize";
     public static final String ITERATIONS = "BasicGraphCleanVertex.iteration";
     public static int kmerSize = -1;
@@ -26,9 +26,9 @@
     
     protected MessageWritable incomingMsg = null; 
     protected MessageWritable outgoingMsg = null; 
-    protected KmerBytesWritable destVertexId = null;
-    protected Iterator<KmerBytesWritable> kmerIterator;
-    protected KmerBytesWritable tmpKmer = new KmerBytesWritable(kmerSize);
+    protected VKmerBytesWritable destVertexId = null;
+    protected Iterator<VKmerBytesWritable> kmerIterator;
+    protected VKmerBytesWritable tmpKmer = new VKmerBytesWritable(kmerSize);
     byte headFlag;
     protected byte outFlag;
     protected byte inFlag;
@@ -65,7 +65,7 @@
     /**
      * get destination vertex
      */
-    public KmerBytesWritable getNextDestVertexId(VertexValueWritable value) {
+    public VKmerBytesWritable getNextDestVertexId(VertexValueWritable value) {
         if (value.getFFList().getCountOfPosition() > 0){ //#FFList() > 0
             kmerIterator = value.getFFList().iterator();
             return kmerIterator.next();
@@ -77,7 +77,7 @@
         }
     }
 
-    public KmerBytesWritable getPrevDestVertexId(VertexValueWritable value) {
+    public VKmerBytesWritable getPrevDestVertexId(VertexValueWritable value) {
         if (value.getRFList().getCountOfPosition() > 0){ //#RFList() > 0
             kmerIterator = value.getRFList().iterator();
             return kmerIterator.next();
@@ -92,7 +92,7 @@
     /**
      * get destination vertex
      */
-    public KmerBytesWritable getNextDestVertexIdAndSetFlag(VertexValueWritable value) {
+    public VKmerBytesWritable getNextDestVertexIdAndSetFlag(VertexValueWritable value) {
         if (value.getFFList().getCountOfPosition() > 0){ // #FFList() > 0
             kmerIterator = value.getFFList().iterator();
             outFlag &= MessageFlag.DIR_CLEAR;
@@ -109,7 +109,7 @@
         
     }
 
-    public KmerBytesWritable getPrevDestVertexIdAndSetFlag(VertexValueWritable value) {
+    public VKmerBytesWritable getPrevDestVertexIdAndSetFlag(VertexValueWritable value) {
         if (value.getRFList().getCountOfPosition() > 0){ // #RFList() > 0
             kmerIterator = value.getRFList().iterator();
             outFlag &= MessageFlag.DIR_CLEAR;
@@ -131,12 +131,12 @@
     public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
         kmerIterator = value.getRFList().iterator(); // RFList
         while(kmerIterator.hasNext()){
-            destVertexId.set(kmerIterator.next());
+            destVertexId.setAsCopy(kmerIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         kmerIterator = value.getRRList().iterator(); // RRList
         while(kmerIterator.hasNext()){
-            destVertexId.set(kmerIterator.next());
+            destVertexId.setAsCopy(kmerIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -147,12 +147,12 @@
     public void sendMsgToAllNextNodes(VertexValueWritable value) {
         kmerIterator = value.getFFList().iterator(); // FFList
         while(kmerIterator.hasNext()){
-            destVertexId.set(kmerIterator.next());
+            destVertexId.setAsCopy(kmerIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         kmerIterator = value.getFRList().iterator(); // FRList
         while(kmerIterator.hasNext()){
-            destVertexId.set(kmerIterator.next());
+            destVertexId.setAsCopy(kmerIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -175,7 +175,7 @@
 		else if(getVertexValue().getFRList().getCountOfPosition() > 0)
 			outgoingMsg.setFlag(MessageFlag.DIR_FR);
 		outgoingMsg.setSourceVertexId(getVertexId());
-		destVertexId.set(getNextDestVertexId(getVertexValue()));
+		destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
 		sendMsg(destVertexId, outgoingMsg);
     }
     
@@ -189,7 +189,7 @@
         else if(getVertexValue().getRRList().getCountOfPosition() > 0)
             outgoingMsg.setFlag(MessageFlag.DIR_RR);
         outgoingMsg.setSourceVertexId(getVertexId());
-        destVertexId.set(getPrevDestVertexId(getVertexValue()));
+        destVertexId.setAsCopy(getPrevDestVertexId(getVertexValue()));
         sendMsg(destVertexId, outgoingMsg);
     }
     
@@ -201,14 +201,14 @@
         while(kmerIterator.hasNext()){
             outgoingMsg.setFlag(MessageFlag.DIR_RF);
             outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.set(kmerIterator.next());
+            destVertexId.setAsCopy(kmerIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         kmerIterator = value.getRRList().iterator(); // RRList
         while(kmerIterator.hasNext()){
             outgoingMsg.setFlag(MessageFlag.DIR_RR);
             outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.set(kmerIterator.next());
+            destVertexId.setAsCopy(kmerIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -221,14 +221,14 @@
         while(kmerIterator.hasNext()){
             outgoingMsg.setFlag(MessageFlag.DIR_FF);
             outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.set(kmerIterator.next());
+            destVertexId.setAsCopy(kmerIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         kmerIterator = value.getFRList().iterator(); // FRList
         while(kmerIterator.hasNext()){
             outgoingMsg.setFlag(MessageFlag.DIR_FR);
             outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.set(kmerIterator.next());
+            destVertexId.setAsCopy(kmerIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -406,7 +406,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
+                outgoingMsg.setActualKmer(getVertexValue().getKmer());
                 sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getNextDestVertexId(getVertexValue())
                 break;
             case MessageFlag.DIR_RF:
@@ -419,7 +419,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
+                outgoingMsg.setActualKmer(getVertexValue().getKmer());
                 sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getPreDestVertexId(getVertexValue())
                 break; 
         }
@@ -444,7 +444,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
+                outgoingMsg.setActualKmer(getVertexValue().getKmer());
                 sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getNextDestVertexId(getVertexValue())
                 break;
             case MessageFlag.DIR_RF:
@@ -457,7 +457,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
+                outgoingMsg.setActualKmer(getVertexValue().getKmer());
                 sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getPreDestVertexId(getVertexValue())
                 break; 
         }
@@ -480,7 +480,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
+                outgoingMsg.setActualKmer(getVertexValue().getKmer());
                 sendMsg(getNextDestVertexId(getVertexValue()), outgoingMsg);
                 deleteVertex(getVertexId());
                 break;
@@ -493,7 +493,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
+                outgoingMsg.setActualKmer(getVertexValue().getKmer());
                 sendMsg(getPrevDestVertexId(getVertexValue()), outgoingMsg);
                 deleteVertex(getVertexId());
                 break; 
@@ -653,7 +653,7 @@
                 match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
                 msgString = msg.getActualKmer().toString();
                 index = msgString.indexOf(match);
-                tmpKmer.reset(msgString.length() - index);
+//                tmpKmer.reset(msgString.length() - index);
                 tmpKmer.setByRead(msgString.substring(index).getBytes(), 0);
                 break;
             case MessageFlag.DIR_FR:
@@ -661,7 +661,7 @@
                 match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
                 msgString = GeneCode.reverseComplement(msg.getActualKmer().toString());
                 index = msgString.indexOf(match);
-                tmpKmer.reset(msgString.length() - index);
+//                tmpKmer.reset(msgString.length() - index);
                 tmpKmer.setByReadReverse(msgString.substring(index).getBytes(), 0);
                 break;
             case MessageFlag.DIR_RF:
@@ -669,7 +669,7 @@
                 match = selfString.substring(0,kmerSize - 1); 
                 msgString = GeneCode.reverseComplement(msg.getActualKmer().toString());
                 index = msgString.lastIndexOf(match) + kmerSize - 2;
-                tmpKmer.reset(index + 1);
+//                tmpKmer.reset(index + 1);
                 tmpKmer.setByReadReverse(msgString.substring(0, index + 1).getBytes(), 0);
                 break;
             case MessageFlag.DIR_RR:
@@ -677,7 +677,7 @@
                 match = selfString.substring(0,kmerSize - 1); 
                 msgString = msg.getActualKmer().toString();
                 index = msgString.lastIndexOf(match) + kmerSize - 2;
-                tmpKmer.reset(index + 1);
+//                tmpKmer.reset(index + 1); // TODO: fix ALL of these resets (only if you need to)
                 tmpKmer.setByRead(msgString.substring(0, index + 1).getBytes(), 0);
                 break;
         }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
index c7fc7bc..027d295 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
@@ -12,8 +12,8 @@
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 import edu.uci.ics.pregelix.api.util.BspUtils;
@@ -22,11 +22,11 @@
     BasicGraphCleanVertex {
     
     public static boolean fakeVertexExist = false;
-    protected static KmerBytesWritable fakeVertex = null;
+    protected static VKmerBytesWritable fakeVertex = null;
     
-    protected KmerBytesWritable reverseKmer;
-    protected KmerListWritable kmerList = null;
-    protected Map<KmerBytesWritable, KmerListWritable> kmerMapper = new HashMap<KmerBytesWritable, KmerListWritable>();
+    protected VKmerBytesWritable reverseKmer;
+    protected VKmerListWritable kmerList = null;
+    protected Map<VKmerBytesWritable, VKmerListWritable> kmerMapper = new HashMap<VKmerBytesWritable, VKmerListWritable>();
 
     /**
      * initiate kmerSize, maxIteration
@@ -43,18 +43,19 @@
         else
             outgoingMsg.reset(kmerSize);
         if(reverseKmer == null)
-            reverseKmer = new KmerBytesWritable(kmerSize);
+            reverseKmer = new VKmerBytesWritable();
         if(kmerList == null)
-            kmerList = new KmerListWritable(kmerSize);
+            kmerList = new VKmerListWritable();
         else
-            kmerList.reset(kmerSize);
+            kmerList.reset();
         if(fakeVertex == null){
-            fakeVertex = new KmerBytesWritable(kmerSize + 1);
+//            fakeVertex = new KmerBytesWritable(kmerSize + 1); // TODO check if merge is correct
+            fakeVertex = new VKmerBytesWritable();
             String random = generaterRandomString(kmerSize + 1);
             fakeVertex.setByRead(random.getBytes(), 0); 
         }
         if(destVertexId == null)
-            destVertexId = new KmerBytesWritable(kmerSize);
+            destVertexId = new VKmerBytesWritable(kmerSize);
     }
     
     /**
@@ -96,7 +97,7 @@
     public void sendMsgToFakeVertex(){
         if(!getVertexValue().isFakeVertex()){
             outgoingMsg.setSourceVertexId(getVertexId());
-            outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
+            outgoingMsg.setActualKmer(getVertexValue().getKmer());
             sendMsg(fakeVertex, outgoingMsg);
             voteToHalt();
         }
@@ -107,18 +108,18 @@
             incomingMsg = msgIterator.next();
             String kmerString = incomingMsg.getActualKmer().toString();
             tmpKmer.reset(kmerString.length());
-            reverseKmer.reset(kmerString.length());
+//            reverseKmer.reset(kmerString.length());//kmerbyteswritable 
             tmpKmer.setByRead(kmerString.getBytes(), 0);
             reverseKmer.setByReadReverse(kmerString.getBytes(), 0);
 
             if(reverseKmer.compareTo(tmpKmer) < 0)
-                tmpKmer.set(reverseKmer);
+                tmpKmer.setAsCopy(reverseKmer);
             if(!kmerMapper.containsKey(tmpKmer)){
                 kmerList.reset();
                 kmerList.append(incomingMsg.getSourceVertexId());
                 kmerMapper.put(tmpKmer, kmerList);
             } else{
-                kmerList.set(kmerMapper.get(tmpKmer));
+                kmerList.setCopy(kmerMapper.get(tmpKmer));
                 kmerList.append(incomingMsg.getSourceVertexId());
                 kmerMapper.put(tmpKmer, kmerList);
             }
@@ -126,12 +127,12 @@
     }
     
     public void reduceKeyByActualKmer(){
-        for(KmerBytesWritable key : kmerMapper.keySet()){
+        for(VKmerBytesWritable key : kmerMapper.keySet()){
             kmerList = kmerMapper.get(key);
             for(int i = 1; i < kmerList.getCountOfPosition(); i++){
                 //send kill message
                 outgoingMsg.setFlag(MessageFlag.KILL);
-                destVertexId.set(kmerList.getPosition(i));
+                destVertexId.setAsCopy(kmerList.getPosition(i));
                 sendMsg(destVertexId, outgoingMsg);
             }
         }
@@ -187,7 +188,7 @@
         job.setVertexInputFormatClass(GraphCleanInputFormat.class);
         job.setVertexOutputFormatClass(P2PathMergeOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java
index 31fb897..f6a005c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java
@@ -3,12 +3,11 @@
 import java.util.Iterator;
 import org.apache.hadoop.io.NullWritable;
 
-import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.KmerBytesWritableFactory;
 
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.genomix.pregelix.client.Client;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
@@ -50,7 +49,7 @@
  * Naive Algorithm for path merge graph
  */
 public class P1ForPathMergeVertex extends
-        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
+        Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "P1ForPathMergeVertex.kmerSize";
     public static final String ITERATIONS = "P1ForPathMergeVertex.iteration";
     public static int kmerSize = -1;
@@ -60,10 +59,10 @@
     private MessageWritable outgoingMsg = new MessageWritable();
   
     private KmerBytesWritableFactory kmerFactory = new KmerBytesWritableFactory(1);
-    private KmerBytesWritable lastKmer = new KmerBytesWritable(1);
+    private VKmerBytesWritable lastKmer = new VKmerBytesWritable();
     
-    private PositionWritable destVertexId = new PositionWritable();
-    private Iterator<PositionWritable> posIterator;
+    private VKmerBytesWritable destVertexId = new VKmerBytesWritable();
+    private Iterator<VKmerBytesWritable> posIterator;
     
     /**
      * initiate kmerSize, maxIteration
@@ -79,7 +78,7 @@
     /**
      * get destination vertex
      */
-    public PositionWritable getNextDestVertexId(VertexValueWritable value) {
+    public VKmerBytesWritable getNextDestVertexId(VertexValueWritable value) {
         if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
             posIterator = value.getFFList().iterator();
         else // #FRList() > 0
@@ -87,7 +86,7 @@
         return posIterator.next();
     }
 
-    public PositionWritable getPreDestVertexId(VertexValueWritable value) {
+    public VKmerBytesWritable getPreDestVertexId(VertexValueWritable value) {
         if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
             posIterator = value.getRFList().iterator();
         else // #RRList() > 0
@@ -101,12 +100,12 @@
     public void sendMsgToAllNextNodes(VertexValueWritable value) {
         posIterator = value.getFFList().iterator(); // FFList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         posIterator = value.getFRList().iterator(); // FRList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -117,12 +116,12 @@
     public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
         posIterator = value.getRFList().iterator(); // RFList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         posIterator = value.getRRList().iterator(); // RRList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -184,7 +183,7 @@
      */
     public void mergeChainVertex() {
         //merge chain
-        lastKmer.set(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
+        lastKmer.setAsCopy(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
                 incomingMsg.getActualKmer()));
         getVertexValue().setKmer(kmerFactory.mergeTwoKmer(getVertexValue().getKmer(), lastKmer));
         getVertexValue().setOutgoingList(incomingMsg.getNeighberNode());
@@ -196,7 +195,7 @@
     public void sendMsgToPathVertex(Iterator<MessageWritable> msgIterator) {
         if (getSuperstep() == 3) {
             outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.set(getNextDestVertexId(getVertexValue()));
+            destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
             sendMsg(destVertexId, outgoingMsg);
         } else {
             while (msgIterator.hasNext()) {
@@ -204,7 +203,7 @@
                 if (incomingMsg.getFlag() != Message.STOP) {
                     mergeChainVertex();
                     outgoingMsg.setSourceVertexId(getVertexId());
-                    destVertexId.set(getNextDestVertexId(getVertexValue()));
+                    destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
                     sendMsg(destVertexId, outgoingMsg);
                 } else {
                     mergeChainVertex();
@@ -222,10 +221,10 @@
     public void responseMsgToHeadVertex() {
         deleteVertex(getVertexId());
         outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
-        outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
+        outgoingMsg.setActualKmer(getVertexValue().getKmer());
         if (getVertexValue().getState() == State.IS_HEAD)//is_tail
             outgoingMsg.setFlag(Message.STOP);
-        destVertexId.set(incomingMsg.getSourceVertexId());
+        destVertexId.setAsCopy(incomingMsg.getSourceVertexId());
         sendMsg(destVertexId, outgoingMsg);
     }
 
@@ -259,7 +258,7 @@
         job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
         job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
index fc78c34..da83dcf 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
@@ -12,8 +12,8 @@
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.pregelix.type.MessageFromHead;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 /*
  * vertexId: BytesWritable
  * vertexValue: VertexValueWritable
@@ -46,7 +46,7 @@
     MapReduceVertex {
 
     private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
-    KmerBytesWritable tmpKmer = new KmerBytesWritable();
+    VKmerBytesWritable tmpKmer = new VKmerBytesWritable();
     
     private boolean isFakeVertex = false;
     /**
@@ -67,19 +67,20 @@
             outgoingMsg.reset(kmerSize);
         receivedMsgList.clear();
         if(reverseKmer == null)
-            reverseKmer = new KmerBytesWritable(kmerSize);
+            reverseKmer = new VKmerBytesWritable();
         if(kmerList == null)
-            kmerList = new KmerListWritable(kmerSize);
+            kmerList = new VKmerListWritable();
         else
-            kmerList.reset(kmerSize);
+            kmerList.reset();
         if(fakeVertex == null){
-            fakeVertex = new KmerBytesWritable(kmerSize + 1);
+//            fakeVertex = new KmerBytesWritable(kmerSize + 1);
+            fakeVertex = new VKmerBytesWritable();
             String random = generaterRandomString(kmerSize + 1);
             fakeVertex.setByRead(random.getBytes(), 0); 
         }
         isFakeVertex = ((byte)getVertexValue().getState() & State.FAKEFLAG_MASK) > 0 ? true : false;
         if(destVertexId == null)
-            destVertexId = new KmerBytesWritable(kmerSize);
+            destVertexId = new VKmerBytesWritable(kmerSize);
     }
 
     /**
@@ -89,7 +90,7 @@
         //send wantToMerge to next
         tmpKmer = getNextDestVertexIdAndSetFlag(getVertexValue());
         if(tmpKmer != null){
-            destVertexId.set(tmpKmer);
+            destVertexId.setAsCopy(tmpKmer);
             outgoingMsg.setFlag(outFlag);
             outgoingMsg.setSourceVertexId(getVertexId());
             sendMsg(destVertexId, outgoingMsg);
@@ -98,7 +99,7 @@
         //send wantToMerge to prev
         tmpKmer = getPrevDestVertexIdAndSetFlag(getVertexValue());
         if(tmpKmer != null){
-            destVertexId.set(tmpKmer);
+            destVertexId.setAsCopy(tmpKmer);
             outgoingMsg.setFlag(outFlag);
             outgoingMsg.setSourceVertexId(getVertexId());
             sendMsg(destVertexId, outgoingMsg);
@@ -298,7 +299,7 @@
          */
         job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
         job.setVertexOutputFormatClass(P2PathMergeOutputFormat.class);
-        job.setOutputKeyClass(KmerBytesWritable.class);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         job.setDynamicVertexValueSize(true);
         Client.run(args, job);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
index d806094..184a7b2 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
@@ -3,12 +3,11 @@
 import java.util.Iterator;
 import org.apache.hadoop.io.NullWritable;
 
-import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.KmerBytesWritableFactory;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.client.Client;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
@@ -50,7 +49,7 @@
  * Naive Algorithm for path merge graph
  */
 public class P3ForPathMergeVertex extends
-        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
+        Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "P3ForPathMergeVertex.kmerSize";
     public static final String ITERATIONS = "P3ForPathMergeVertex.iteration";
     public static final String PSEUDORATE = "P3ForPathMergeVertex.pseudoRate";
@@ -64,10 +63,10 @@
     private MessageWritable outgoingMsg = new MessageWritable();
 
     private KmerBytesWritableFactory kmerFactory = new KmerBytesWritableFactory(1);
-    private KmerBytesWritable lastKmer = new KmerBytesWritable(1);
+    private VKmerBytesWritable lastKmer = new VKmerBytesWritable(1);
 
-    private PositionWritable destVertexId = new PositionWritable();
-    private Iterator<PositionWritable> posIterator;
+    private VKmerBytesWritable destVertexId = new VKmerBytesWritable();
+    private Iterator<VKmerBytesWritable> posIterator;
     /**
      * initiate kmerSize, maxIteration
      */
@@ -86,7 +85,7 @@
     /**
      * get destination vertex
      */
-    public PositionWritable getNextDestVertexId(VertexValueWritable value) {
+    public VKmerBytesWritable getNextDestVertexId(VertexValueWritable value) {
         if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
             posIterator = value.getFFList().iterator();
         else // #FRList() > 0
@@ -94,7 +93,7 @@
         return posIterator.next();
     }
 
-    public PositionWritable getPreDestVertexId(VertexValueWritable value) {
+    public VKmerBytesWritable getPreDestVertexId(VertexValueWritable value) {
         if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
             posIterator = value.getRFList().iterator();
         else // #RRList() > 0
@@ -108,12 +107,12 @@
     public void sendMsgToAllNextNodes(VertexValueWritable value) {
         posIterator = value.getFFList().iterator(); // FFList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         posIterator = value.getFRList().iterator(); // FRList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -124,12 +123,12 @@
     public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
         posIterator = value.getRFList().iterator(); // RFList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         posIterator = value.getRRList().iterator(); // RRList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -206,8 +205,7 @@
     public void markPseudoHead() {
         getVertexValue().setState(State2.PSEUDOHEAD);
         outgoingMsg.setFlag(Message.FROMPSEUDOHEAD);
-        destVertexId
-                .set(getPreDestVertexId(getVertexValue()));
+        destVertexId.setAsCopy(getPreDestVertexId(getVertexValue()));
         sendMsg(destVertexId, outgoingMsg);
     }
 
@@ -230,7 +228,7 @@
      * merge chain vertex
      */
     public void mergeChainVertex(){
-        lastKmer.set(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
+        lastKmer.setAsCopy(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
                 incomingMsg.getActualKmer()));
         getVertexValue().setKmer(
                 kmerFactory.mergeTwoKmer(getVertexValue().getKmer(), 
@@ -244,7 +242,7 @@
     public void sendMsgToPathVertexMergePhase(Iterator<MessageWritable> msgIterator) {
         if (getSuperstep() == 3 + 2 * maxRound + 2) {
             outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.set(getNextDestVertexId(getVertexValue()));
+            destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
             sendMsg(destVertexId, outgoingMsg);
         } else {
             while (msgIterator.hasNext()) {
@@ -252,8 +250,7 @@
                 if (incomingMsg.getFlag() != Message.STOP) {
                     mergeChainVertex();
                     outgoingMsg.setSourceVertexId(getVertexId());
-                    destVertexId
-                            .set(getNextDestVertexId(getVertexValue()));
+                    destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
                     sendMsg(destVertexId, outgoingMsg);
                 } else {
                     mergeChainVertex();
@@ -271,7 +268,7 @@
     public void responseMsgToHeadVertexMergePhase() {
         deleteVertex(getVertexId());
         outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
-        outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
+        outgoingMsg.setActualKmer(getVertexValue().getKmer());
         if (getVertexValue().getState() == State2.END_VERTEX)
             outgoingMsg.setFlag(Message.STOP);
         sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg);
@@ -284,7 +281,7 @@
         if (getSuperstep() == 4) {
             if(getVertexValue().getState() != State2.START_HALT){
                 outgoingMsg.setSourceVertexId(getVertexId());
-                destVertexId.set(getNextDestVertexId(getVertexValue()));
+                destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
                 sendMsg(destVertexId, outgoingMsg);
                 voteToHalt();
             }
@@ -297,7 +294,7 @@
                     if (incomingMsg.getFlag() != Message.STOP 
                             && incomingMsg.getFlag() != Message.FROMPSEUDOREAR) {
                         outgoingMsg.setSourceVertexId(getVertexId());
-                        destVertexId.set(getNextDestVertexId(getVertexValue()));
+                        destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
                         sendMsg(destVertexId, outgoingMsg);
                         voteToHalt();
                     } else {
@@ -325,7 +322,7 @@
         else {
             deleteVertex(getVertexId());
             outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList()); //incomingMsg.getNeighberNode()
-            outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
+            outgoingMsg.setActualKmer(getVertexValue().getKmer());
             if (getVertexValue().getState() == State2.PSEUDOREAR)
                 outgoingMsg.setFlag(Message.FROMPSEUDOREAR);
             else if (getVertexValue().getState() == State2.END_VERTEX)
@@ -410,7 +407,7 @@
         job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
         job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
index 59270fa..28d0563 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
@@ -5,7 +5,6 @@
 
 
 import edu.uci.ics.pregelix.api.job.PregelixJob;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.client.Client;
 import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat;
@@ -14,7 +13,7 @@
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 /*
  * vertexId: BytesWritable
@@ -56,9 +55,9 @@
     private float probBeingRandomHead = -1;
     private Random randGenerator;
     
-    private KmerBytesWritable curKmer = new KmerBytesWritable();
-    private KmerBytesWritable nextKmer = new KmerBytesWritable();
-    private KmerBytesWritable prevKmer = new KmerBytesWritable();
+    private VKmerBytesWritable curKmer = new VKmerBytesWritable();
+    private VKmerBytesWritable nextKmer = new VKmerBytesWritable();
+    private VKmerBytesWritable prevKmer = new VKmerBytesWritable();
     private boolean hasNext;
     private boolean hasPrev;
     private boolean curHead;
@@ -81,7 +80,7 @@
         else
             outgoingMsg.reset(kmerSize);
         if(destVertexId == null)
-            destVertexId = new KmerBytesWritable(kmerSize);
+            destVertexId = new VKmerBytesWritable(kmerSize);
         randSeed = getSuperstep();
         randGenerator = new Random(randSeed);
         if (probBeingRandomHead < 0)
@@ -97,7 +96,7 @@
         headFlag = (byte) (State.IS_HEAD & getVertexValue().getState());
     }
 
-    protected boolean isNodeRandomHead(KmerBytesWritable nodeKmer) {
+    protected boolean isNodeRandomHead(VKmerBytesWritable nodeKmer) {
         // "deterministically random", based on node id
         //randGenerator.setSeed(randSeed);
         //randSeed = randGenerator.nextInt();
@@ -112,12 +111,12 @@
      */
     protected boolean setNextInfo(VertexValueWritable value) {
         if (value.getFFList().getCountOfPosition() > 0) {
-            nextKmer.set(value.getFFList().getPosition(0));
+            nextKmer.setAsCopy(value.getFFList().getPosition(0));
             nextHead = isNodeRandomHead(nextKmer);
             return true;
         }
         if (value.getFRList().getCountOfPosition() > 0) {
-            nextKmer.set(value.getFRList().getPosition(0));
+            nextKmer.setAsCopy(value.getFRList().getPosition(0));
             nextHead = isNodeRandomHead(nextKmer);
             return true;
         }
@@ -129,12 +128,12 @@
      */
     protected boolean setPrevInfo(VertexValueWritable value) {
         if (value.getRRList().getCountOfPosition() > 0) {
-            prevKmer.set(value.getRRList().getPosition(0));
+            prevKmer.setAsCopy(value.getRRList().getPosition(0));
             prevHead = isNodeRandomHead(prevKmer);
             return true;
         }
         if (value.getRFList().getCountOfPosition() > 0) {
-            prevKmer.set(value.getRFList().getPosition(0));
+            prevKmer.setAsCopy(value.getRFList().getPosition(0));
             prevHead = isNodeRandomHead(prevKmer);
             return true;
         }
@@ -157,7 +156,7 @@
             setStateAsNoMerge();
             
             // only PATH vertices are present. Find the ID's for my neighbors
-            curKmer.set(getVertexId());
+            curKmer.setAsCopy(getVertexId());
             
             curHead = isNodeRandomHead(curKmer);
             
@@ -234,7 +233,7 @@
         job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
         job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
new file mode 100644
index 0000000..154fbda
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
@@ -0,0 +1,501 @@
+package edu.uci.ics.genomix.pregelix.operator.pathmerge;
+
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.Random;
+
+import org.apache.hadoop.io.NullWritable;
+
+
+import edu.uci.ics.pregelix.api.graph.Vertex;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.pregelix.client.Client;
+import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat;
+import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
+import edu.uci.ics.genomix.pregelix.type.Message;
+import edu.uci.ics.genomix.pregelix.type.MessageFlag;
+import edu.uci.ics.genomix.pregelix.util.VertexUtil;
+
+/*
+ * vertexId: BytesWritable
+ * vertexValue: ByteWritable
+ * edgeValue: NullWritable
+ * message: MessageWritable
+ * 
+ * DNA:
+ * A: 00
+ * C: 01
+ * G: 10
+ * T: 11
+ * 
+ * succeed node
+ *  A 00000001 1
+ *  G 00000010 2
+ *  C 00000100 4
+ *  T 00001000 8
+ * precursor node
+ *  A 00010000 16
+ *  G 00100000 32
+ *  C 01000000 64
+ *  T 10000000 128
+ *  
+ * For example, ONE LINE in input file: 00,01,10    0001,0010,
+ * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
+ * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
+ * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
+ */
+/**
+ * Naive Algorithm for path merge graph
+ */
+public class P5ForPathMergeVertex extends
+        Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
+    public static final String KMER_SIZE = "P5ForPathMergeVertex.kmerSize";
+    public static final String ITERATIONS = "P5ForPathMergeVertex.iteration";
+    public static final String RANDSEED = "P5ForPathMergeVertex.randSeed";
+    public static final String PROBBEINGRANDOMHEAD = "P4ForPathMergeVertex.probBeingRandomHead";
+    public static int kmerSize = -1;
+    private int maxIteration = -1;
+
+    private static long randSeed = -1;
+    private float probBeingRandomHead = -1;
+    private Random randGenerator;
+    
+    private VKmerBytesWritable curID = new VKmerBytesWritable();
+    private VKmerBytesWritable nextID = new VKmerBytesWritable();
+    private VKmerBytesWritable prevID = new VKmerBytesWritable();
+    private boolean hasNext;
+    private boolean hasPrev;
+    private boolean curHead;
+    private boolean nextHead;
+    private boolean prevHead;
+    private byte headFlag;
+    private byte tailFlag;
+    private byte outFlag;
+    
+    private MessageWritable incomingMsg = new MessageWritable();
+    private MessageWritable outgoingMsg = new MessageWritable();
+    private VKmerBytesWritable destVertexId = new VKmerBytesWritable();
+    private Iterator<VKmerBytesWritable> posIterator;
+    
+    /**
+     * initiate kmerSize, maxIteration
+     */
+    public void initVertex() {
+        if (kmerSize == -1)
+            kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
+        if (maxIteration < 0)
+            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
+        if (randSeed < 0)
+            randSeed = getContext().getConfiguration().getLong("randomSeed", 0);
+        randGenerator = new Random(randSeed);
+        if (probBeingRandomHead < 0)
+            probBeingRandomHead = getContext().getConfiguration().getFloat("probBeingRandomHead", 0.5f);
+        hasNext = false;
+        hasPrev = false;
+        curHead = false;
+        nextHead = false;
+        prevHead = false;
+        outgoingMsg.reset();
+    }
+
+    protected boolean isNodeRandomHead(VKmerBytesWritable nodeID) {
+        // "deterministically random", based on node id
+        randGenerator.setSeed(randSeed ^ nodeID.hashCode());
+        return randGenerator.nextFloat() < probBeingRandomHead;
+    }
+
+    /**
+     * set nextID to the element that's next (in the node's FF or FR list), returning true when there is a next neighbor
+     */
+    protected boolean setNextInfo(VertexValueWritable value) {
+        if (value.getFFList().getCountOfPosition() > 0) {
+            nextID.setAsCopy(value.getFFList().getPosition(0));
+            nextHead = isNodeRandomHead(nextID);
+            return true;
+        }
+        if (value.getFRList().getCountOfPosition() > 0) {
+            nextID.setAsCopy(value.getFRList().getPosition(0));
+            nextHead = isNodeRandomHead(nextID);
+            return true;
+        }
+        return false;
+    }
+
+    /**
+     * set prevID to the element that's previous (in the node's RR or RF list), returning true when there is a previous neighbor
+     */
+    protected boolean setPrevInfo(VertexValueWritable value) {
+        if (value.getRRList().getCountOfPosition() > 0) {
+            prevID.setAsCopy(value.getRRList().getPosition(0));
+            prevHead = isNodeRandomHead(prevID);
+            return true;
+        }
+        if (value.getRFList().getCountOfPosition() > 0) {
+            prevID.setAsCopy(value.getRFList().getPosition(0));
+            prevHead = isNodeRandomHead(prevID);
+            return true;
+        }
+        return false;
+    }
+    
+    /**
+     * get destination vertex
+     */
+    public VKmerBytesWritable getNextDestVertexId(VertexValueWritable value) {
+        if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
+            posIterator = value.getFFList().iterator();
+        else // #FRList() > 0
+            posIterator = value.getFRList().iterator();
+        return posIterator.next();
+    }
+
+    public VKmerBytesWritable getPreDestVertexId(VertexValueWritable value) {
+        if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
+            posIterator = value.getRFList().iterator();
+        else // #RRList() > 0
+            posIterator = value.getRRList().iterator();
+        return posIterator.next();
+    }
+
+    /**
+     * head send message to all next nodes
+     */
+    public void sendMsgToAllNextNodes(VertexValueWritable value) {
+        posIterator = value.getFFList().iterator(); // FFList
+        while(posIterator.hasNext()){
+            destVertexId.setAsCopy(posIterator.next());
+            sendMsg(destVertexId, outgoingMsg);
+        }
+        posIterator = value.getFRList().iterator(); // FRList
+        while(posIterator.hasNext()){
+            destVertexId.setAsCopy(posIterator.next());
+            sendMsg(destVertexId, outgoingMsg);
+        }
+    }
+
+    /**
+     * head send message to all previous nodes
+     */
+    public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
+        posIterator = value.getRFList().iterator(); // RFList
+        while(posIterator.hasNext()){
+            destVertexId.setAsCopy(posIterator.next());
+            sendMsg(destVertexId, outgoingMsg);
+        }
+        posIterator = value.getRRList().iterator(); // RRList
+        while(posIterator.hasNext()){
+            destVertexId.setAsCopy(posIterator.next());
+            sendMsg(destVertexId, outgoingMsg);
+        }
+    }
+
+    /**
+     * start sending message
+     */
+    public void startSendMsg() {
+        if (VertexUtil.isHeadVertexWithIndegree(getVertexValue())) {
+            outgoingMsg.setFlag(Message.START);
+            sendMsgToAllNextNodes(getVertexValue());
+            voteToHalt();
+        }
+        if (VertexUtil.isRearVertexWithOutdegree(getVertexValue())) {
+            outgoingMsg.setFlag(Message.END);
+            sendMsgToAllPreviousNodes(getVertexValue());
+            voteToHalt();
+        }
+        if (VertexUtil.isHeadWithoutIndegree(getVertexValue())){
+            outgoingMsg.setFlag(Message.START);
+            sendMsg(getVertexId(), outgoingMsg); //send to itself
+            voteToHalt();
+        }
+        if (VertexUtil.isRearWithoutOutdegree(getVertexValue())){
+            outgoingMsg.setFlag(Message.END);
+            sendMsg(getVertexId(), outgoingMsg); //send to itself
+            voteToHalt();
+        }
+    }
+
+    /**
+     * initiate head, rear and path node
+     */
+    public void initState(Iterator<MessageWritable> msgIterator) {
+        while (msgIterator.hasNext()) {
+            if (!VertexUtil.isPathVertex(getVertexValue())
+                    && !VertexUtil.isHeadWithoutIndegree(getVertexValue())
+                    && !VertexUtil.isRearWithoutOutdegree(getVertexValue())) {
+                msgIterator.next();
+                voteToHalt();
+            } else {
+                incomingMsg = msgIterator.next();
+                setState();
+            }
+        }
+    }
+
+    /**
+     * set vertex state
+     */
+    public void setState() {
+        if (incomingMsg.getFlag() == Message.START) {
+            getVertexValue().setState(MessageFlag.IS_HEAD); //State.START_VERTEX
+        } else if (incomingMsg.getFlag() == Message.END && getVertexValue().getState() != State.IS_HEAD) {
+            getVertexValue().setState(MessageFlag.IS_HEAD);
+            getVertexValue().setKmer(getVertexValue().getKmer());
+            //voteToHalt();
+        } //else
+            //voteToHalt();
+    }
+    
+    /**
+     * check if A need to be flipped with successor
+     */
+    public boolean ifFilpWithSuccessor(){
+        if(getVertexValue().getFRList().getLength() > 0)
+            return true;
+        else
+            return false;
+    }
+    
+    /**
+     * check if A need to be filpped with predecessor
+     */
+    public boolean ifFlipWithPredecessor(){
+        if(getVertexValue().getRFList().getLength() > 0)
+            return true;
+        else
+            return false;
+    }
+    
+    /**
+     * set adjMessage to successor(from predecessor)
+     */
+    public void setSuccessorAdjMsg(){
+        if(getVertexValue().getFFList().getLength() > 0)
+            outFlag |= MessageFlag.DIR_FF;
+        else
+            outFlag |= MessageFlag.DIR_FR;
+    }
+    
+    /**
+     * set adjMessage to predecessor(from successor)
+     */
+    public void setPredecessorAdjMsg(){
+        if(getVertexValue().getRFList().getLength() > 0)
+            outFlag |= MessageFlag.DIR_RF;
+        else
+            outFlag |= MessageFlag.DIR_RF;
+    }
+    
+    /**
+     * send update message to neighber
+     * @throws IOException 
+     */
+    public void broadcastUpdateMsg(){
+       /* switch(getVertexValue().getState() & 0b0001){
+            case MessageFlag.SHOULD_MERGEWITHPREV:
+                setSuccessorAdjMsg();
+                if(ifFlipWithPredecessor())
+                    outFlag |= MessageFlag.FLIP;
+                outgoingMsg.setFlag(outFlag);
+                outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
+                outgoingMsg.setSourceVertexId(getVertexId());
+                sendMsg(getNextDestVertexId(getVertexValue()), outgoingMsg);
+                break;
+            case MessageFlag.SHOULD_MERGEWITHNEXT:
+                setPredecessorAdjMsg();
+                if(ifFilpWithSuccessor())
+                    outFlag |= MessageFlag.FLIP;
+                outgoingMsg.setFlag(outFlag);
+                outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
+                outgoingMsg.setSourceVertexId(getVertexId());
+                sendMsg(getPreDestVertexId(getVertexValue()), outgoingMsg);
+                break; 
+        }*/
+    }
+    
+    /**
+     * This vertex tries to merge with next vertex and send update msg to neighber
+     * @throws IOException 
+     */
+    public void sendUpMsgFromPredecessor(){
+        byte state = getVertexValue().getState();
+        state |= MessageFlag.SHOULD_MERGEWITHNEXT;
+        getVertexValue().setState(state);
+        if(getVertexValue().getFFList().getLength() > 0)
+            getVertexValue().setMergeDest(getVertexValue().getFFList().getPosition(0));
+        else
+            getVertexValue().setMergeDest(getVertexValue().getFRList().getPosition(0));
+        broadcastUpdateMsg();
+    }
+    
+    /**
+     * This vertex tries to merge with next vertex and send update msg to neighber
+     * @throws IOException 
+     */
+    public void sendUpMsgFromSuccessor(){
+        byte state = getVertexValue().getState();
+        state |= MessageFlag.SHOULD_MERGEWITHPREV;
+        getVertexValue().setState(state);
+        if(getVertexValue().getRFList().getLength() > 0)
+            getVertexValue().setMergeDest(getVertexValue().getRFList().getPosition(0));
+        else
+            getVertexValue().setMergeDest(getVertexValue().getRRList().getPosition(0));
+        broadcastUpdateMsg();
+    }
+    
+    /**
+     * Returns the edge dir for B->A when the A->B edge is type @dir
+     */
+    public byte mirrorDirection(byte dir) {
+        switch (dir) {
+            case MessageFlag.DIR_FF:
+                return MessageFlag.DIR_RR;
+            case MessageFlag.DIR_FR:
+                return MessageFlag.DIR_FR;
+            case MessageFlag.DIR_RF:
+                return MessageFlag.DIR_RF;
+            case MessageFlag.DIR_RR:
+                return MessageFlag.DIR_FF;
+            default:
+                throw new RuntimeException("Unrecognized direction in flipDirection: " + dir);
+        }
+    }
+    
+    /**
+     * check if need filp
+     */
+    public byte flipDirection(byte neighborDir, boolean flip){
+        if(flip){
+            switch (neighborDir) {
+                case MessageFlag.DIR_FF:
+                    return MessageFlag.DIR_FR;
+                case MessageFlag.DIR_FR:
+                    return MessageFlag.DIR_FF;
+                case MessageFlag.DIR_RF:
+                    return MessageFlag.DIR_RR;
+                case MessageFlag.DIR_RR:
+                    return MessageFlag.DIR_RF;
+                default:
+                    throw new RuntimeException("Unrecognized direction for neighborDir: " + neighborDir);
+            }
+        } else 
+            return neighborDir;
+    }
+    
+    /**
+     * updateAdjList
+     */
+    public void processUpdate(){
+        /*byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+        byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+        
+        boolean flip;
+        if((outFlag & MessageFlag.FLIP) > 0)
+            flip = true;
+        else
+            flip = false;
+        byte neighborToMergeDir = flipDirection(neighborToMeDir, flip);
+        
+        getVertexValue().processUpdates(neighborToMeDir, incomingMsg.getSourceVertexId(), 
+                neighborToMergeDir, VertexUtil.getNodeIdFromAdjacencyList(incomingMsg.getNeighberNode()));*/
+    }
+    
+    /**
+     * merge and updateAdjList
+     */
+    public void processMerge(){
+        /*byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+        byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+        
+        boolean flip;
+        if((outFlag & MessageFlag.FLIP) > 0)
+            flip = true;
+        else
+            flip = false;
+        byte neighborToMergeDir = flipDirection(neighborToMeDir, flip);
+        
+        getVertexValue().processMerges(neighborToMeDir, incomingMsg.getSourceVertexId(), 
+                neighborToMergeDir, VertexUtil.getNodeIdFromAdjacencyList(incomingMsg.getNeighberNode()),
+                kmerSize, incomingMsg.getKmer());*/
+    }
+    
+    @Override
+    public void compute(Iterator<MessageWritable> msgIterator) {
+        initVertex();
+        if (getSuperstep() == 1)
+            startSendMsg();
+        else if (getSuperstep() == 2)
+            initState(msgIterator);
+        else if (getSuperstep() % 4 == 3){
+            // Node may be marked as head b/c it's a real head or a real tail
+            headFlag = (byte) (State.IS_HEAD & getVertexValue().getState());
+            tailFlag = (byte) (State.IS_HEAD & getVertexValue().getState()); //is_tail
+            outFlag = (byte) (headFlag | tailFlag);
+            
+            // only PATH vertices are present. Find the ID's for my neighbors
+            curID.setAsCopy(getVertexId());
+            
+            curHead = isNodeRandomHead(curID);
+            
+            // the headFlag and tailFlag's indicate if the node is at the beginning or end of a simple path. 
+            // We prevent merging towards non-path nodes
+            hasNext = setNextInfo(getVertexValue()) && tailFlag == 0;
+            hasPrev = setPrevInfo(getVertexValue()) && headFlag == 0;
+            if ((outFlag & MessageFlag.IS_HEAD) > 0 && (outFlag & MessageFlag.IS_HEAD) > 0) {
+                getVertexValue().setState(outFlag);
+                voteToHalt();
+            }
+            if (hasNext || hasPrev) {
+                if (curHead) {
+                    if (hasNext && !nextHead) {
+                        // compress this head to the forward tail
+                        sendUpMsgFromPredecessor();
+                    } else if (hasPrev && !prevHead) {
+                        // compress this head to the reverse tail
+                        sendUpMsgFromSuccessor();
+                    }
+                } else {
+                    // I'm a tail
+                    if (hasNext && hasPrev) {
+                        if ((!nextHead && !prevHead) && (curID.compareTo(nextID) < 0 && curID.compareTo(prevID) < 0)) {
+                            // tails on both sides, and I'm the "local minimum"
+                            // compress me towards the tail in forward dir
+                            sendUpMsgFromPredecessor();
+                        }
+                    } else if (!hasPrev) {
+                        // no previous node
+                        if (!nextHead && curID.compareTo(nextID) < 0) {
+                            // merge towards tail in forward dir
+                            sendUpMsgFromPredecessor();
+                        }
+                    } else if (!hasNext) {
+                        // no next node
+                        if (!prevHead && curID.compareTo(prevID) < 0) {
+                            // merge towards tail in reverse dir
+                            sendUpMsgFromSuccessor();
+                        }
+                    }
+                }
+            }
+        }
+      
+    }
+
+    public static void main(String[] args) throws Exception {
+        PregelixJob job = new PregelixJob(P5ForPathMergeVertex.class.getSimpleName());
+        job.setVertexClass(P5ForPathMergeVertex.class);
+        /**
+         * BinaryInput and BinaryOutput
+         */
+        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
+        Client.run(args, job);
+    }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
index 4533f55..e4e797f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
@@ -14,9 +14,9 @@
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 import edu.uci.ics.pregelix.api.util.BspUtils;
@@ -33,11 +33,11 @@
     
     public class DeletedEdge{
         private byte dir;
-        private KmerBytesWritable edge;
+        private VKmerBytesWritable edge;
         
         public DeletedEdge(){
             dir = 0;
-            edge = new KmerBytesWritable(kmerSize);
+            edge = new VKmerBytesWritable(kmerSize);
         }
 
         public byte getDir() {
@@ -48,12 +48,12 @@
             this.dir = dir;
         }
 
-        public KmerBytesWritable getEdge() {
+        public VKmerBytesWritable getEdge() {
             return edge;
         }
 
-        public void setEdge(KmerBytesWritable edge) {
-            this.edge.set(edge);
+        public void setEdge(VKmerBytesWritable edge) {
+            this.edge.setAsCopy(edge);
         }
     }
     
@@ -69,13 +69,13 @@
     private Set<Long> outgoingReadIdSet = new HashSet<Long>();
     private Set<Long> selfReadIdSet = new HashSet<Long>();
     private Set<Long> neighborEdgeIntersection = new HashSet<Long>();
-    private Map<KmerBytesWritable, Set<Long>> kmerMap = new HashMap<KmerBytesWritable, Set<Long>>();
-    private KmerListWritable incomingEdgeList = null; 
-    private KmerListWritable outgoingEdgeList = null; 
+    private Map<VKmerBytesWritable, Set<Long>> kmerMap = new HashMap<VKmerBytesWritable, Set<Long>>();
+    private VKmerListWritable incomingEdgeList = null; 
+    private VKmerListWritable outgoingEdgeList = null; 
     private byte incomingEdgeDir = 0;
     private byte outgoingEdgeDir = 0;
     
-    protected KmerBytesWritable createdVertexId = null;  
+    protected VKmerBytesWritable createdVertexId = null;  
     
     /**
      * initiate kmerSize, maxIteration
@@ -92,13 +92,13 @@
         else
             outgoingMsg.reset(kmerSize);
         if(incomingEdgeList == null)
-            incomingEdgeList = new KmerListWritable(kmerSize);
+            incomingEdgeList = new VKmerListWritable();
         if(outgoingEdgeList == null)
-            outgoingEdgeList = new KmerListWritable(kmerSize);
+            outgoingEdgeList = new VKmerListWritable();
         if(createdVertexId == null)
-            createdVertexId = new KmerBytesWritable(kmerSize);//kmerSize + 1
+            createdVertexId = new VKmerBytesWritable(kmerSize);//kmerSize + 1
         if(destVertexId == null)
-            destVertexId = new KmerBytesWritable(kmerSize);
+            destVertexId = new VKmerBytesWritable(kmerSize);
     }
     
     /**
@@ -152,11 +152,11 @@
     }
     
     @SuppressWarnings({ "rawtypes", "unchecked" })
-    public void createNewVertex(int i, KmerBytesWritable incomingEdge, KmerBytesWritable outgoingEdge){
+    public void createNewVertex(int i, VKmerBytesWritable incomingEdge, VKmerBytesWritable outgoingEdge){
         Vertex vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
         vertex.getMsgList().clear();
         vertex.getEdges().clear();
-        KmerBytesWritable vertexId = new KmerBytesWritable(kmerSize);
+        VKmerBytesWritable vertexId = new VKmerBytesWritable(kmerSize);
         VertexValueWritable vertexValue = new VertexValueWritable(kmerSize);
         //add the corresponding edge to new vertex
         switch(connectedTable[i][0]){
@@ -175,27 +175,27 @@
                 vertexValue.getFRList().append(outgoingEdge);
                 break;
         }
-        vertexId.set(createdVertexId);
+        vertexId.setAsCopy(createdVertexId);
         vertex.setVertexId(vertexId);
         vertex.setVertexValue(vertexValue);
         
         addVertex(vertexId, vertex);
     }
     
-    public void sendMsgToUpdateEdge(KmerBytesWritable incomingEdge, KmerBytesWritable outgoingEdge){
+    public void sendMsgToUpdateEdge(VKmerBytesWritable incomingEdge, VKmerBytesWritable outgoingEdge){
         outgoingMsg.setCreatedVertexId(createdVertexId);
         outgoingMsg.setSourceVertexId(getVertexId());
         
         outgoingMsg.setFlag(incomingEdgeDir);
-        destVertexId.set(incomingEdge);
+        destVertexId.setAsCopy(incomingEdge);
         sendMsg(destVertexId, outgoingMsg);
         
         outgoingMsg.setFlag(outgoingEdgeDir);
-        destVertexId.set(outgoingEdge);
+        destVertexId.setAsCopy(outgoingEdge);
         sendMsg(destVertexId, outgoingMsg);
     }
     
-    public void storeDeletedEdge(Set<DeletedEdge> deletedEdges, int i, KmerBytesWritable incomingEdge, KmerBytesWritable outgoingEdge){
+    public void storeDeletedEdge(Set<DeletedEdge> deletedEdges, int i, VKmerBytesWritable incomingEdge, VKmerBytesWritable outgoingEdge){
         DeletedEdge deletedIncomingEdge = new DeletedEdge();
         DeletedEdge deletedOutgoingEdge = new DeletedEdge();
         switch(connectedTable[i][0]){
@@ -241,32 +241,32 @@
     public void setEdgeListAndEdgeDir(int i){
         switch(connectedTable[i][0]){
             case EdgeDir.DIR_RF:
-                incomingEdgeList.set(getVertexValue().getRFList());
+                incomingEdgeList.setCopy(getVertexValue().getRFList());
                 incomingEdgeDir = MessageFlag.DIR_RF;
                 break;
             case EdgeDir.DIR_RR:
-                incomingEdgeList.set(getVertexValue().getRRList());
+                incomingEdgeList.setCopy(getVertexValue().getRRList());
                 incomingEdgeDir = MessageFlag.DIR_RR;
                 break;
         }
         switch(connectedTable[i][1]){
             case EdgeDir.DIR_FF:
-                outgoingEdgeList.set(getVertexValue().getFFList());
+                outgoingEdgeList.setCopy(getVertexValue().getFFList());
                 outgoingEdgeDir = MessageFlag.DIR_FF;
                 break;
             case EdgeDir.DIR_FR:
-                outgoingEdgeList.set(getVertexValue().getFRList());
+                outgoingEdgeList.setCopy(getVertexValue().getFRList());
                 outgoingEdgeDir = MessageFlag.DIR_FR;
                 break;
         }
     }
     
-    public void setNeighborEdgeIntersection(KmerBytesWritable incomingEdge, KmerBytesWritable outgoingEdge){
+    public void setNeighborEdgeIntersection(VKmerBytesWritable incomingEdge, VKmerBytesWritable outgoingEdge){
         outgoingReadIdSet.clear(); 
         incomingReadIdSet.clear();
-        tmpKmer.set(incomingEdge);
+        tmpKmer.setAsCopy(incomingEdge);
         incomingReadIdSet.addAll(kmerMap.get(tmpKmer));
-        tmpKmer.set(outgoingEdge);
+        tmpKmer.setAsCopy(outgoingEdge);
         outgoingReadIdSet.addAll(kmerMap.get(tmpKmer));
         
         //set all neighberEdge readId intersection
@@ -330,12 +330,12 @@
                 /** set edgeList and edgeDir based on connectedTable **/
                 setEdgeListAndEdgeDir(i);
                 
-                KmerBytesWritable incomingEdge = new KmerBytesWritable(kmerSize);
-                KmerBytesWritable outgoingEdge = new KmerBytesWritable(kmerSize);
+                VKmerBytesWritable incomingEdge = new VKmerBytesWritable(kmerSize);
+                VKmerBytesWritable outgoingEdge = new VKmerBytesWritable(kmerSize);
                 for(int x = 0; x < incomingEdgeList.getCountOfPosition(); x++){
                     for(int y = 0; y < outgoingEdgeList.getCountOfPosition(); y++){
-                        incomingEdge.set(incomingEdgeList.getPosition(x));
-                        outgoingEdge.set(outgoingEdgeList.getPosition(y));
+                        incomingEdge.setAsCopy(incomingEdgeList.getPosition(x));
+                        outgoingEdge.setAsCopy(outgoingEdgeList.getPosition(y));
                         /** set neighborEdge readId intersection **/
                         setNeighborEdgeIntersection(incomingEdge, outgoingEdge);
                         
@@ -411,7 +411,7 @@
         job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
         job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
index 7b695dc..4a540b8 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
@@ -3,8 +3,8 @@
 import java.util.Iterator;
 import org.apache.hadoop.io.NullWritable;
 
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 import edu.uci.ics.pregelix.api.util.BspUtils;
@@ -46,7 +46,7 @@
  *  Remove tip or single node when l > constant
  */
 public class TipAddVertex extends
-        Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
+        Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "TipAddVertex.kmerSize";
     public static int kmerSize = -1;
    
@@ -68,7 +68,7 @@
         initVertex(); 
         if(getSuperstep() == 1){
             if(getVertexId().toString().equals("CTA")){
-                KmerBytesWritable vertexId = new KmerBytesWritable(kmerSize);
+                VKmerBytesWritable vertexId = new VKmerBytesWritable(kmerSize);
                 vertexId.setByRead("AGC".getBytes(), 0);
                 getVertexValue().getRFList().append(vertexId);
                 
@@ -86,7 +86,7 @@
                 /**
                  * set the vertex value
                  */
-                KmerListWritable kmerList = new KmerListWritable(kmerSize);
+                VKmerListWritable kmerList = new VKmerListWritable();
                 kmerList.append(getVertexId());
                 vertexValue.setRFList(kmerList);
                 vertexValue.setKmer(vertexId);
@@ -107,7 +107,7 @@
         job.setVertexInputFormatClass(GraphCleanInputFormat.class);
         job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
index ddf2964..527fb66 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
@@ -3,7 +3,6 @@
 import java.util.Iterator;
 
 import edu.uci.ics.pregelix.api.job.PregelixJob;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.client.Client;
 import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
@@ -11,7 +10,7 @@
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 /*
  * vertexId: BytesWritable
@@ -64,7 +63,7 @@
         else
             outgoingMsg.reset(kmerSize);
         if(destVertexId == null)
-            destVertexId = new KmerBytesWritable(kmerSize);
+            destVertexId = new VKmerBytesWritable(kmerSize);
     }
 
     @Override
@@ -106,7 +105,7 @@
         job.setVertexInputFormatClass(GraphCleanInputFormat.class);
         job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputKeyClass(VKmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
new file mode 100644
index 0000000..13d9d98
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
@@ -0,0 +1,58 @@
+package edu.uci.ics.genomix.pregelix.sequencefile;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.NullWritable;
+import org.apache.hadoop.io.SequenceFile;
+import org.apache.hadoop.io.SequenceFile.CompressionType;
+
+import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
+
+
+public class ConvertNodeToIdValue {
+
+    public static void convert(Path inFile, Path outFile)
+            throws IOException {
+        Configuration conf = new Configuration();
+        FileSystem fileSys = FileSystem.get(conf);
+
+        SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
+        SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf, outFile, PositionWritable.class,
+                VertexValueWritable.class, CompressionType.NONE);
+        NodeWritable node = new NodeWritable();
+        NullWritable value = NullWritable.get();
+        PositionWritable outputKey = new PositionWritable();
+        VertexValueWritable outputValue = new VertexValueWritable();
+
+        while(reader.next(node, value)) {
+//            System.out.println(node.getNodeID().toString());
+//            outputKey.set(node.getNodeID());
+            outputValue.setFFList(node.getFFList());
+            outputValue.setFRList(node.getFRList());
+            outputValue.setRFList(node.getRFList());
+            outputValue.setRRList(node.getRRList());
+            outputValue.setKmer(node.getKmer());
+            outputValue.setState(State.IS_HEAD);
+            writer.append(outputKey, outputValue);
+        }
+        writer.close();
+        reader.close();
+    }
+    
+    public static void main(String[] args) throws IOException {
+        Path dir = new Path("data/test");
+        Path outDir = new Path("data/input");
+        FileUtils.cleanDirectory(new File("data/input"));
+        Path inFile = new Path(dir, "result.graphbuild.txt.bin");
+        Path outFile = new Path(outDir, "out");
+        convert(inFile,outFile);
+    }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
index 6b9eb4e..d3180c8 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
@@ -28,7 +28,8 @@
         SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
         SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf, outFile, KmerBytesWritable.class,
                 NullWritable.class, CompressionType.NONE);
-        KmerBytesWritable outKey = new KmerBytesWritable(55);
+        KmerBytesWritable.setGlobalKmerLength(55);
+        KmerBytesWritable outKey = new KmerBytesWritable();
         int i = 0;
 
         for (i = 0; i < numOfLines; i++) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
index bc08600..8618237 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
@@ -19,6 +19,7 @@
 public class GenerateTextFile {
 
     public static void generateFromPathmergeResult(int kmerSize, String strSrcDir, String outPutDir) throws IOException {
+        KmerBytesWritable.setGlobalKmerLength(kmerSize);
         Configuration conf = new Configuration();
         FileSystem fileSys = FileSystem.getLocal(conf);
 
@@ -44,13 +45,14 @@
     }
 
     public static void generateSpecificLengthChainFromNaivePathmergeResult(int maxLength) throws IOException {
+        KmerBytesWritable.setGlobalKmerLength(55);
         BufferedWriter bw = new BufferedWriter(new FileWriter("naive_text_" + maxLength));
         Configuration conf = new Configuration();
         FileSystem fileSys = FileSystem.get(conf);
         for (int i = 0; i < 2; i++) {
             Path path = new Path("/home/anbangx/genomix_result/final_naive/part-" + i);
             SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
-            KmerBytesWritable key = new KmerBytesWritable(55);
+            KmerBytesWritable key = new KmerBytesWritable();
             VertexValueWritable value = new VertexValueWritable();
 
             while (reader.next(key, value)) {
@@ -68,13 +70,14 @@
     }
 
     public static void generateSpecificLengthChainFromLogPathmergeResult(int maxLength) throws IOException {
+        KmerBytesWritable.setGlobalKmerLength(55);
         BufferedWriter bw = new BufferedWriter(new FileWriter("log_text_" + maxLength));
         Configuration conf = new Configuration();
         FileSystem fileSys = FileSystem.get(conf);
         for (int i = 0; i < 2; i++) {
             Path path = new Path("/home/anbangx/genomix_result/improvelog2/part-" + i);
             SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
-            KmerBytesWritable key = new KmerBytesWritable(55);
+            KmerBytesWritable key = new KmerBytesWritable();
             VertexValueWritable value = new VertexValueWritable();
 
             while (reader.next(key, value)) {
@@ -93,12 +96,13 @@
     }
 
     public static void generateFromGraphbuildResult() throws IOException {
+        KmerBytesWritable.setGlobalKmerLength(55);
         BufferedWriter bw = new BufferedWriter(new FileWriter("textfile"));
         Configuration conf = new Configuration();
         FileSystem fileSys = FileSystem.get(conf);
         Path path = new Path("data/input/part-0-out-3000000");
         SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
-        KmerBytesWritable key = new KmerBytesWritable(55);
+        KmerBytesWritable key = new KmerBytesWritable();
 
         while (reader.next(key, null)) {
             if (key == null) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
index 5a0591d..4582557 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
@@ -2,7 +2,7 @@
 
 import edu.uci.ics.genomix.pregelix.io.AdjacencyListWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 public class VertexUtil {
     /**
@@ -67,7 +67,7 @@
     /**
      * check if mergeChain is cycle
      */
-    public static boolean isCycle(KmerBytesWritable kmer, KmerBytesWritable mergeChain, int kmerSize) {
+    public static boolean isCycle(VKmerBytesWritable kmer, VKmerBytesWritable mergeChain, int kmerSize) {
         String chain = mergeChain.toString().substring(1);
         return chain.contains(kmer.toString());
 
@@ -116,7 +116,7 @@
     /**
      * get nodeId from Ad
      */
-    public static KmerBytesWritable getNodeIdFromAdjacencyList(AdjacencyListWritable adj){
+    public static VKmerBytesWritable getNodeIdFromAdjacencyList(AdjacencyListWritable adj){
         if(adj.getForwardList().getCountOfPosition() > 0)
             return adj.getForwardList().getPosition(0);
         else if(adj.getReverseList().getCountOfPosition() > 0)
diff --git a/patch.diff b/patch.diff
new file mode 100644
index 0000000..a333970
--- /dev/null
+++ b/patch.diff
@@ -0,0 +1,245 @@
+From 9e006501f9e33467a8428199bd94b71dbff063ef Mon Sep 17 00:00:00 2001
+From: Anbang Xu <anbangx@gmail.com>
+Date: Fri, 26 Jul 2013 14:10:33 -0700
+Subject: [PATCH] p2 pass all the tests except 9
+
+---
+ .../genomix/data/test/KmerBytesWritableTest.java   | 76 +++++++++++++++++++++-
+ .../genomix/pregelix/io/VertexValueWritable.java   |  2 +-
+ .../operator/pathmerge/BasicPathMergeVertex.java   | 35 +++++-----
+ .../pathmerge/LogAlgorithmForPathMergeVertex.java  |  8 +--
+ .../pregelix/JobRun/PathMergeSmallTestSuite.java   |  2 +-
+ 5 files changed, 98 insertions(+), 25 deletions(-)
+
+diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
+index bda73e5..fbfbeeb 100644
+--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
++++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
+@@ -229,14 +229,34 @@ public class KmerBytesWritableTest {
+         merge.mergeWithRFKmer(i, kmer2);
+         Assert.assertEquals("GGCACAACAACCC", merge.toString());
+         
+-        String test1 = "CTA";
+-        String test2 = "AGA";
++        String test1;
++        String test2;
++        test1 = "CTA";
++        test2 = "AGA";
+         KmerBytesWritable k1 = new KmerBytesWritable(3);
+         KmerBytesWritable k2 = new KmerBytesWritable(3);
+         k1.setByRead(test1.getBytes(), 0);
+         k2.setByRead(test2.getBytes(), 0);
+         k1.mergeWithRFKmer(3, k2);
+         Assert.assertEquals("TCTA", k1.toString());
++        
++        test1 = "CTA";
++        test2 = "ATA"; //TAT
++        k1 = new KmerBytesWritable(3);
++        k2 = new KmerBytesWritable(3);
++        k1.setByRead(test1.getBytes(), 0);
++        k2.setByRead(test2.getBytes(), 0);
++        k1.mergeWithFRKmer(3, k2);
++        Assert.assertEquals("CTAT", k1.toString());
++        
++        test1 = "ATA";
++        test2 = "CTA"; //TAT
++        k1 = new KmerBytesWritable(3);
++        k2 = new KmerBytesWritable(3);
++        k1.setByRead(test1.getBytes(), 0);
++        k2.setByRead(test2.getBytes(), 0);
++        k1.mergeWithFRKmer(3, k2);
++        Assert.assertEquals("ATAG", k1.toString());
+     }
+     
+     
+@@ -281,5 +301,55 @@ public class KmerBytesWritableTest {
+             }
+         }
+     }
+-
++    
++    @Test
++    public void TestFinalMerge() {
++        String selfString;
++        String match;
++        String msgString;
++        int index;
++        KmerBytesWritable kmer = new KmerBytesWritable();
++        int kmerSize = 3;
++        
++        String F1 = "AATAG";
++        String F2 = "TAGAA";
++        String R1 = "CTATT";
++        String R2 = "TTCTA";
++        
++        //FF test
++        selfString = F1;
++        match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
++        msgString = F2;
++        index = msgString.indexOf(match);
++        kmer.reset(msgString.length() - index);
++        kmer.setByRead(msgString.substring(index).getBytes(), 0);
++        System.out.println(kmer.toString());
++        
++        //FR test
++        selfString = F1;
++        match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
++        msgString = GeneCode.reverseComplement(R2);
++        index = msgString.indexOf(match);
++        kmer.reset(msgString.length() - index);
++        kmer.setByRead(msgString.substring(index).getBytes(), 0);
++        System.out.println(kmer.toString());
++        
++        //RF test
++        selfString = R1;
++        match = selfString.substring(0,kmerSize - 1); 
++        msgString = GeneCode.reverseComplement(F2);
++        index = msgString.lastIndexOf(match) + kmerSize - 2;
++        kmer.reset(index + 1);
++        kmer.setByReadReverse(msgString.substring(0, index + 1).getBytes(), 0);
++        System.out.println(kmer.toString());
++        
++        //RR test
++        selfString = R1;
++        match = selfString.substring(0,kmerSize - 1); 
++        msgString = R2;
++        index = msgString.lastIndexOf(match) + kmerSize - 2;
++        kmer.reset(index + 1);
++        kmer.setByRead(msgString.substring(0, index + 1).getBytes(), 0);
++        System.out.println(kmer.toString());
++    }
+ }
+diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+index 6d4f683..065bfd5 100644
+--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
++++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+@@ -32,7 +32,7 @@ public class VertexValueWritable implements WritableComparable<VertexValueWritab
+         public static final byte SHOULD_MERGEWITHNEXT = 0b01 << 3;
+         public static final byte SHOULD_MERGEWITHPREV = 0b10 << 3;
+         public static final byte SHOULD_MERGE_MASK = 0b11 << 3;
+-        public static final byte SHOULD_MERGE_CLEAR = 0b1110011;
++        public static final byte SHOULD_MERGE_CLEAR = 0b1100111;
+     }
+     
+     private PositionListWritable nodeIdList;
+diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
+index b7b0814..ec608c5 100644
+--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
++++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
+@@ -495,6 +495,7 @@ public class BasicPathMergeVertex extends
+     
+     public void setStateAsMergeWithNext(){
+     	byte state = getVertexValue().getState();
++    	state &= State.SHOULD_MERGE_CLEAR;
+         state |= State.SHOULD_MERGEWITHNEXT;
+         getVertexValue().setState(state);
+     }
+@@ -512,6 +513,7 @@ public class BasicPathMergeVertex extends
+     
+     public void setStateAsMergeWithPrev(){
+         byte state = getVertexValue().getState();
++        state &= State.SHOULD_MERGE_CLEAR;
+         state |= State.SHOULD_MERGEWITHPREV;
+         getVertexValue().setState(state);
+     }
+@@ -638,7 +640,7 @@ public class BasicPathMergeVertex extends
+         String match;
+         String msgString;
+         int index;
+-        switch(neighborToMergeDir){
++        switch(neighborToMeDir){
+             case MessageFlag.DIR_FF:
+                 selfString = getVertexValue().getKmer().toString();
+                 match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
+@@ -648,28 +650,29 @@ public class BasicPathMergeVertex extends
+                 kmer.setByRead(msgString.substring(index).getBytes(), 0);
+                 break;
+             case MessageFlag.DIR_FR:
+-                selfString = getVertexId().toString();
+-                match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length());
++                selfString = getVertexValue().getKmer().toString();
++                match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
+                 msgString = GeneCode.reverseComplement(msg.getKmer().toString());
+                 index = msgString.indexOf(match);
+                 kmer.reset(msgString.length() - index);
+-                kmer.setByRead(msgString.substring(index).getBytes(), 0);
++                kmer.setByReadReverse(msgString.substring(index).getBytes(), 0);
+                 break;
+             case MessageFlag.DIR_RF:
+-                selfString = GeneCode.reverseComplement(getVertexValue().getKmer().toString());
+-                match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length());
+-                msgString = msg.getKmer().toString();
+-                index = msgString.indexOf(match);
+-                kmer.reset(msgString.length() - index);
+-                kmer.setByRead(msgString.substring(index).getBytes(), 0);
++                selfString = getVertexValue().getKmer().toString();
++                match = selfString.substring(0,kmerSize - 1); 
++                msgString = GeneCode.reverseComplement(msg.getKmer().toString());
++                index = msgString.lastIndexOf(match) + kmerSize - 2;
++                kmer.reset(index + 1);
++                kmer.setByReadReverse(msgString.substring(0, index + 1).getBytes(), 0);
+                 break;
+             case MessageFlag.DIR_RR:
+-                selfString = GeneCode.reverseComplement(getVertexValue().getKmer().toString());
+-                match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length());
+-                msgString = GeneCode.reverseComplement(msg.getKmer().toString());
+-                index = msgString.indexOf(match);
+-                kmer.reset(msgString.length() - index);
+-                kmer.setByRead(msgString.substring(index).getBytes(), 0);
++                selfString = getVertexValue().getKmer().toString();
++                match = selfString.substring(0,kmerSize - 1); 
++                msgString = msg.getKmer().toString();
++                index = msgString.lastIndexOf(match) + kmerSize - 2;
++                kmer.reset(index + 1);
++                kmer.setByRead(msgString.substring(0, index + 1).getBytes(), 0);
++                System.out.println(kmer.toString());
+                 break;
+         }
+        
+diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
+index a68b646..3b5a782 100644
+--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
++++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
+@@ -170,22 +170,22 @@ public class LogAlgorithmForPathMergeVertex extends
+                 case MessageFromHead.BothMsgsFromHead:
+                 case MessageFromHead.OneMsgFromOldHeadAndOneFromHead:
+                     for(int i = 0; i < 2; i++)
+-                        processMerge(receivedMsgList.get(i));
++                        processFinalMerge(receivedMsgList.get(i)); //processMerge()
+                     getVertexValue().setState(State.IS_FINAL);
+                     voteToHalt();
+                     break;
+                 case MessageFromHead.OneMsgFromHeadAndOneFromNonHead:
+                     for(int i = 0; i < 2; i++)
+-                        processMerge(receivedMsgList.get(i));
++                        processFinalMerge(receivedMsgList.get(i));
+                     getVertexValue().setState(State .IS_HEAD);
+                     break;
+                 case MessageFromHead.BothMsgsFromNonHead:
+                     for(int i = 0; i < 2; i++)
+-                        processMerge(receivedMsgList.get(i));
++                        processFinalMerge(receivedMsgList.get(i));
+                     break;
+                 case MessageFromHead.NO_MSG:
+                     //halt
+-                    deleteVertex(getVertexId());
++                    voteToHalt(); //deleteVertex(getVertexId());
+                     break;
+             }
+         }
+diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
+index 9f96b5a..1578dfc 100644
+--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
++++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
+@@ -52,7 +52,7 @@ public class PathMergeSmallTestSuite extends TestSuite {
+ //    + "6", PreFix + File.separator
+ //    + "7", PreFix + File.separator
+ //    + "8", PreFix + File.separator
+-    + "5"};
++    + "9"};
+     private static final String ACTUAL_RESULT_DIR = "data/actual/pathmerge";
+     private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
+     private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";
+-- 
+1.7.11.1
+