diff --git a/genomix/genomix-data/src/main/assembly/binary-assembly.xml b/genomix/genomix-data/src/main/assembly/binary-assembly.xml
index 0500499..68d424a 100644
--- a/genomix/genomix-data/src/main/assembly/binary-assembly.xml
+++ b/genomix/genomix-data/src/main/assembly/binary-assembly.xml
@@ -1,19 +1,19 @@
 <assembly>
-  <id>binary-assembly</id>
-  <formats>
-    <format>zip</format>
-    <format>dir</format>
-  </formats>
-  <includeBaseDirectory>false</includeBaseDirectory>
-  <fileSets>
-    <fileSet>
-      <directory>target/appassembler/bin</directory>
-      <outputDirectory>bin</outputDirectory>
-      <fileMode>0755</fileMode>
-    </fileSet>
-    <fileSet>
-      <directory>target/appassembler/lib</directory>
-      <outputDirectory>lib</outputDirectory>
-    </fileSet>
-  </fileSets>
+	<id>binary-assembly</id>
+	<formats>
+		<format>zip</format>
+		<format>dir</format>
+	</formats>
+	<includeBaseDirectory>false</includeBaseDirectory>
+	<fileSets>
+		<fileSet>
+			<directory>target/appassembler/bin</directory>
+			<outputDirectory>bin</outputDirectory>
+			<fileMode>0755</fileMode>
+		</fileSet>
+		<fileSet>
+			<directory>target/appassembler/lib</directory>
+			<outputDirectory>lib</outputDirectory>
+		</fileSet>
+	</fileSets>
 </assembly>
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java
index ef5a62b..1ed6f80 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java
@@ -1,126 +1,126 @@
 package edu.uci.ics.genomix.type;
 
 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 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 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 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 getSymbolFromCode(byte code) {
-		if (code > 3) {
-			return '!';
-		}
-		return GENE_SYMBOL[code];
-	}
+    public static byte getSymbolFromCode(byte code) {
+        if (code > 3) {
+            return '!';
+        }
+        return GENE_SYMBOL[code];
+    }
 
-	public static byte getAdjBit(byte t) {
-		byte r = 0;
-		switch (t) {
-		case 'A':
-		case 'a':
-			r = 1 << A;
-			break;
-		case 'C':
-		case 'c':
-			r = 1 << C;
-			break;
-		case 'G':
-		case 'g':
-			r = 1 << G;
-			break;
-		case 'T':
-		case 't':
-			r = 1 << T;
-			break;
-		}
-		return r;
-	}
+    public static byte getAdjBit(byte t) {
+        byte r = 0;
+        switch (t) {
+            case 'A':
+            case 'a':
+                r = 1 << A;
+                break;
+            case 'C':
+            case 'c':
+                r = 1 << C;
+                break;
+            case 'G':
+            case 'g':
+                r = 1 << G;
+                break;
+            case 'T':
+            case 't':
+                r = 1 << T;
+                break;
+        }
+        return r;
+    }
 
-	/**
-	 * It works for path merge. Merge the kmer by his next, we need to make sure
-	 * the @{t} is a single neighbor.
-	 * 
-	 * @param t
-	 *            the neighbor code in BitMap
-	 * @return the genecode
-	 */
-	public static byte getGeneCodeFromBitMap(byte t) {
-		switch (t) {
-		case 1 << A:
-			return A;
-		case 1 << C:
-			return C;
-		case 1 << G:
-			return G;
-		case 1 << T:
-			return T;
-		}
-		return -1;
-	}
-	
-	public static int countNumberOfBitSet(int i) {
-		int c = 0;
-		for (; i != 0; c++) {
-			i &= i - 1;
-		}
-		return c;
-	}
-	
-	public static int inDegree(byte bitmap) {
-		return countNumberOfBitSet((bitmap >> 4) & 0x0f);
-	}
+    /**
+     * It works for path merge. Merge the kmer by his next, we need to make sure
+     * the @{t} is a single neighbor.
+     * 
+     * @param t
+     *            the neighbor code in BitMap
+     * @return the genecode
+     */
+    public static byte getGeneCodeFromBitMap(byte t) {
+        switch (t) {
+            case 1 << A:
+                return A;
+            case 1 << C:
+                return C;
+            case 1 << G:
+                return G;
+            case 1 << T:
+                return T;
+        }
+        return -1;
+    }
 
-	public static int outDegree(byte bitmap) {
-		return countNumberOfBitSet(bitmap & 0x0f);
-	}
+    public static int countNumberOfBitSet(int i) {
+        int c = 0;
+        for (; i != 0; c++) {
+            i &= i - 1;
+        }
+        return c;
+    }
 
-	public static byte mergePreNextAdj(byte pre, byte next) {
-		return (byte) (pre << 4 | (next & 0x0f));
-	}
+    public static int inDegree(byte bitmap) {
+        return countNumberOfBitSet((bitmap >> 4) & 0x0f);
+    }
 
-	public static String getSymbolFromBitMap(byte code) {
-		int left = (code >> 4) & 0x0F;
-		int right = code & 0x0F;
-		StringBuilder str = new StringBuilder();
-		for (int i = A; i <= T; i++) {
-			if ((left & (1 << i)) != 0) {
-				str.append((char) GENE_SYMBOL[i]);
-			}
-		}
-		str.append('|');
-		for (int i = A; i <= T; i++) {
-			if ((right & (1 << i)) != 0) {
-				str.append((char) GENE_SYMBOL[i]);
-			}
-		}
-		return str.toString();
-	}
+    public static int outDegree(byte bitmap) {
+        return countNumberOfBitSet(bitmap & 0x0f);
+    }
+
+    public static byte mergePreNextAdj(byte pre, byte next) {
+        return (byte) (pre << 4 | (next & 0x0f));
+    }
+
+    public static String getSymbolFromBitMap(byte code) {
+        int left = (code >> 4) & 0x0F;
+        int right = code & 0x0F;
+        StringBuilder str = new StringBuilder();
+        for (int i = A; i <= T; i++) {
+            if ((left & (1 << i)) != 0) {
+                str.append((char) GENE_SYMBOL[i]);
+            }
+        }
+        str.append('|');
+        for (int i = A; i <= T; i++) {
+            if ((right & (1 << i)) != 0) {
+                str.append((char) GENE_SYMBOL[i]);
+            }
+        }
+        return str.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 e8d3e67..ded9f36 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
@@ -26,225 +26,228 @@
  * 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
-		WritableComparable<BinaryComparable> {
-	protected int size;
-	protected byte[] bytes;
-	protected int kmerlength;
+public class KmerBytesWritable extends BinaryComparable implements WritableComparable<BinaryComparable> {
+    protected int size;
+    protected byte[] bytes;
+    protected int kmerlength;
 
-	/**
-	 * Initial Kmer space by kmerlength
-	 * 
-	 * @param k
-	 *            kmerlength
-	 */
-	public KmerBytesWritable(int k) {
-		this.kmerlength = k;
-		this.size = KmerUtil.getByteNumFromK(kmerlength);
-		this.bytes = new byte[this.size];
-	}
+    /**
+     * Initial Kmer space by kmerlength
+     * 
+     * @param k
+     *            kmerlength
+     */
+    public KmerBytesWritable(int k) {
+        this.kmerlength = k;
+        this.size = KmerUtil.getByteNumFromK(kmerlength);
+        this.bytes = new byte[this.size];
+    }
 
-	public KmerBytesWritable(KmerBytesWritable right) {
-		this.kmerlength = right.kmerlength;
-		this.size =  right.size;
-		this.bytes = new byte[right.size];
-		set(right);
-	}
+    public KmerBytesWritable(KmerBytesWritable right) {
+        this.kmerlength = right.kmerlength;
+        this.size = right.size;
+        this.bytes = new byte[right.size];
+        set(right);
+    }
 
-	public byte getGeneCodeAtPosition(int pos) {
-		if (pos >= kmerlength) {
-			return -1;
-		}
-		int posByte = pos / 4;
-		int shift = (pos % 4) << 1;
-		return (byte) ((bytes[size - 1 - posByte] >> shift) & 0x3);
-	}
+    public byte getGeneCodeAtPosition(int pos) {
+        if (pos >= kmerlength) {
+            return -1;
+        }
+        int posByte = pos / 4;
+        int shift = (pos % 4) << 1;
+        return (byte) ((bytes[size - 1 - posByte] >> shift) & 0x3);
+    }
 
-	public int getKmerLength() {
-		return this.kmerlength;
-	}
+    public int getKmerLength() {
+        return this.kmerlength;
+    }
 
-	@Override
-	public byte[] getBytes() {
-		return bytes;
-	}
+    @Override
+    public byte[] getBytes() {
+        return bytes;
+    }
 
-	@Override
-	public int getLength() {
-		return size;
-	}
+    @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++) {
-			byte code = GeneCode.getCodeFromSymbol(array[i]);
-			l |= (byte) (code << bytecount);
-			bytecount += 2;
-			if (bytecount == 8) {
-				bytes[bcount--] = l;
-				l = 0;
-				bytecount = 0;
-			}
-		}
-		if (bcount >= 0) {
-			bytes[0] = l;
-		}
-	}
+    /**
+     * 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++) {
+            byte code = GeneCode.getCodeFromSymbol(array[i]);
+            l |= (byte) (code << bytecount);
+            bytecount += 2;
+            if (bytecount == 8) {
+                bytes[bcount--] = l;
+                l = 0;
+                bytecount = 0;
+            }
+        }
+        if (bcount >= 0) {
+            bytes[0] = l;
+        }
+    }
 
-	/**
-	 * Compress Reversed Kmer into bytes array AATAG will compress as
-	 * [0x000A,0xATAG]
-	 * 
-	 * @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--) {
-			byte code = GeneCode.getCodeFromSymbol(array[i]);
-			l |= (byte) (code << bytecount);
-			bytecount += 2;
-			if (bytecount == 8) {
-				bytes[bcount--] = l;
-				l = 0;
-				bytecount = 0;
-			}
-		}
-		if (bcount >= 0) {
-			bytes[0] = l;
-		}
-	}
+    /**
+     * Compress Reversed Kmer into bytes array AATAG will compress as
+     * [0x000A,0xATAG]
+     * 
+     * @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--) {
+            byte code = GeneCode.getCodeFromSymbol(array[i]);
+            l |= (byte) (code << bytecount);
+            bytecount += 2;
+            if (bytecount == 8) {
+                bytes[bcount--] = l;
+                l = 0;
+                bytecount = 0;
+            }
+        }
+        if (bcount >= 0) {
+            bytes[0] = l;
+        }
+    }
 
-	/**
-	 * 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 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[size - 1] & 0x03);
-		for (int i = size - 1; i > 0; i--) {
-			byte in = (byte) (bytes[i - 1] & 0x03);
-			bytes[i] = (byte) (((bytes[i] >>> 2) & 0x3f) | (in << 6));
-		}
-		int pos = ((kmerlength - 1) % 4) << 1;
-		byte code = (byte) (c << pos);
-		bytes[0] = (byte) (((bytes[0] >>> 2) & 0x3f) | code);
-		return (byte) (1 << output);
-	}
+    /**
+     * 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[size - 1] & 0x03);
+        for (int i = size - 1; i > 0; i--) {
+            byte in = (byte) (bytes[i - 1] & 0x03);
+            bytes[i] = (byte) (((bytes[i] >>> 2) & 0x3f) | (in << 6));
+        }
+        int pos = ((kmerlength - 1) % 4) << 1;
+        byte code = (byte) (c << pos);
+        bytes[0] = (byte) (((bytes[0] >>> 2) & 0x3f) | code);
+        return (byte) (1 << 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 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[0] >> pos) & 0x03);
-		for (int i = 0; i < size - 1; i++) {
-			byte in = (byte) ((bytes[i + 1] >> 6) & 0x03);
-			bytes[i] = (byte) ((bytes[i] << 2) | in);
-		}
-		// (k%4) * 2
-		if (kmerlength % 4 != 0) {
-			bytes[0] &= (1 << ((kmerlength % 4) << 1)) - 1;
-		}
-		bytes[size - 1] = (byte) ((bytes[size - 1] << 2) | c);
-		return (byte) (1 << output);
-	}
+    /**
+     * 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[0] >> pos) & 0x03);
+        for (int i = 0; i < size - 1; i++) {
+            byte in = (byte) ((bytes[i + 1] >> 6) & 0x03);
+            bytes[i] = (byte) ((bytes[i] << 2) | in);
+        }
+        // (k%4) * 2
+        if (kmerlength % 4 != 0) {
+            bytes[0] &= (1 << ((kmerlength % 4) << 1)) - 1;
+        }
+        bytes[size - 1] = (byte) ((bytes[size - 1] << 2) | c);
+        return (byte) (1 << output);
+    }
 
-	public void set(KmerBytesWritable newData) {
-		set(newData.bytes, 0, newData.size);
-	}
+    public void set(KmerBytesWritable newData) {
+        set(newData.bytes, 0, newData.size);
+    }
 
-	public void set(byte[] newData, int offset, int length) {
-		System.arraycopy(newData, offset, bytes, 0, size);
-	}
+    public void set(byte[] newData, int offset, int length) {
+        System.arraycopy(newData, offset, bytes, 0, size);
+    }
 
-	/**
-	 * Don't read the kmerlength from datastream, 
-	 * Read it from configuration
-	 */
-	@Override
-	public void readFields(DataInput in) throws IOException {
-		in.readFully(bytes, 0, size);
-	}
+    /**
+     * Don't read the kmerlength from datastream,
+     * Read it from configuration
+     */
+    @Override
+    public void readFields(DataInput in) throws IOException {
+        this.kmerlength = in.readInt();
+        this.size = KmerUtil.getByteNumFromK(kmerlength);
+        if ( this.bytes.length < this.size){
+            this.bytes = new byte[this.size];
+        }
+        in.readFully(bytes, 0, size);
+    }
 
-	@Override
-	public void write(DataOutput out) throws IOException {
-		out.write(bytes, 0, size);
-	}
+    @Override
+    public void write(DataOutput out) throws IOException {
+        out.writeInt(kmerlength);
+        out.write(bytes, 0, size);
+    }
 
-	@Override
-	public int hashCode() {
-		return super.hashCode() * this.kmerlength;
-	}
+    @Override
+    public int hashCode() {
+        return super.hashCode() * 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 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(), 0,
-				this.getLength());
-	}
+    @Override
+    public String toString() {
+        return KmerUtil.recoverKmerFrom(this.kmerlength, this.getBytes(), 0, this.getLength());
+    }
 
-	public static class Comparator extends WritableComparator {
-		public Comparator() {
-			super(KmerBytesWritable.class);
-		}
+    public static class Comparator extends WritableComparator {
+        public Comparator() {
+            super(KmerBytesWritable.class);
+        }
 
-		public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) {
-			return compareBytes(b1, s1, l1, b2, s2, l2);
-		}
-	}
+        public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) {
+            return compareBytes(b1, s1, l1, b2, s2, l2);
+        }
+    }
 
-	static { // register this comparator
-		WritableComparator.define(KmerBytesWritable.class, new Comparator());
-	}
+    static { // register this comparator
+        WritableComparator.define(KmerBytesWritable.class, new Comparator());
+    }
 
 }
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerCountValue.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerCountValue.java
index 60ad5a3..fab7001 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerCountValue.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerCountValue.java
@@ -21,50 +21,49 @@
 import org.apache.hadoop.io.Writable;
 
 public class KmerCountValue implements Writable {
-	private byte adjBitMap;
-	private byte count;
+    private byte adjBitMap;
+    private byte count;
 
-	public KmerCountValue(byte bitmap, byte count) {
-		set(bitmap, count);
-	}
+    public KmerCountValue(byte bitmap, byte count) {
+        set(bitmap, count);
+    }
 
-	public KmerCountValue() {
-		adjBitMap = 0;
-		count = 0;
-	}
+    public KmerCountValue() {
+        adjBitMap = 0;
+        count = 0;
+    }
 
-	@Override
-	public void readFields(DataInput arg0) throws IOException {
-		adjBitMap = arg0.readByte();
-		count = arg0.readByte();
-	}
+    @Override
+    public void readFields(DataInput arg0) throws IOException {
+        adjBitMap = arg0.readByte();
+        count = arg0.readByte();
+    }
 
-	@Override
-	public void write(DataOutput arg0) throws IOException {
-		arg0.writeByte(adjBitMap);
-		arg0.writeByte(count);
-	}
+    @Override
+    public void write(DataOutput arg0) throws IOException {
+        arg0.writeByte(adjBitMap);
+        arg0.writeByte(count);
+    }
 
-	@Override
-	public String toString() {
-		return GeneCode.getSymbolFromBitMap(adjBitMap) + '\t'
-				+ String.valueOf(count);
-	}
+    @Override
+    public String toString() {
+        return GeneCode.getSymbolFromBitMap(adjBitMap) + '\t' + String.valueOf(count);
+    }
 
-	public void set(byte bitmap, byte count) {
-		this.adjBitMap = bitmap;
-		this.count = count;
-	}
+    public void set(byte bitmap, byte count) {
+        this.adjBitMap = bitmap;
+        this.count = count;
+    }
 
-	public byte getAdjBitMap() {
-		return adjBitMap;
-	}
+    public byte getAdjBitMap() {
+        return adjBitMap;
+    }
 
-	public void setAdjBitMap(byte adjBitMap) {
-		this.adjBitMap = adjBitMap;
-	}
+    public void setAdjBitMap(byte adjBitMap) {
+        this.adjBitMap = adjBitMap;
+    }
 
-	public byte getCount() {
-		return count;
-	}
+    public byte getCount() {
+        return count;
+    }
 }
\ No newline at end of file
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerUtil.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerUtil.java
index 82fe1a1..9dc1dde 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerUtil.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerUtil.java
@@ -1,33 +1,31 @@
 package edu.uci.ics.genomix.type;
 
-
 public class KmerUtil {
 
-	public static int getByteNumFromK(int k) {
-		int x = k / 4;
-		if (k % 4 != 0) {
-			x += 1;
-		}
-		return x;
-	}
-	
-	public static byte reverseKmerByte(byte k) {
-		int x = (((k >> 2) & 0x33) | ((k << 2) & 0xcc));
-		return (byte) (((x >> 4) & 0x0f) | ((x << 4) & 0xf0));
-	}
-	
-	public static String recoverKmerFrom(int k, byte[] keyData, int keyStart,
-			int keyLength) {
-		StringBuilder strKmer = new StringBuilder();
-		int byteId = keyStart + keyLength - 1;
-		byte currentbyte = keyData[byteId];
-		for (int geneCount = 0; geneCount < k; geneCount++) {
-			if (geneCount % 4 == 0 && geneCount > 0) {
-				currentbyte = keyData[--byteId];
-			}
-			strKmer.append((char) GeneCode.GENE_SYMBOL[(currentbyte >> ((geneCount % 4) * 2)) & 0x03]);
-		}
-		return strKmer.toString();
-	}
-	
+    public static int getByteNumFromK(int k) {
+        int x = k / 4;
+        if (k % 4 != 0) {
+            x += 1;
+        }
+        return x;
+    }
+
+    public static byte reverseKmerByte(byte k) {
+        int x = (((k >> 2) & 0x33) | ((k << 2) & 0xcc));
+        return (byte) (((x >> 4) & 0x0f) | ((x << 4) & 0xf0));
+    }
+
+    public static String recoverKmerFrom(int k, byte[] keyData, int keyStart, int keyLength) {
+        StringBuilder strKmer = new StringBuilder();
+        int byteId = keyStart + keyLength - 1;
+        byte currentbyte = keyData[byteId];
+        for (int geneCount = 0; geneCount < k; geneCount++) {
+            if (geneCount % 4 == 0 && geneCount > 0) {
+                currentbyte = keyData[--byteId];
+            }
+            strKmer.append((char) GeneCode.GENE_SYMBOL[(currentbyte >> ((geneCount % 4) * 2)) & 0x03]);
+        }
+        return strKmer.toString();
+    }
+
 }
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
index 67de889..b2af5ee 100644
--- 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
@@ -6,119 +6,110 @@
 
 import org.apache.hadoop.io.WritableComparator;
 
-public class VKmerBytesWritable extends KmerBytesWritable{
+public class VKmerBytesWritable extends KmerBytesWritable {
+    public static final int DEFAULT_KMER_LENGTH = 21;
+    
+    public VKmerBytesWritable(){
+        this(DEFAULT_KMER_LENGTH);
+    }
+    
+    public VKmerBytesWritable(int k) {
+        super(k);
+    }
 
-	public VKmerBytesWritable(int k) {
-		super(k);
-	}
-	
-	public VKmerBytesWritable(KmerBytesWritable other){
-		super(other);
-	}
+    public VKmerBytesWritable(KmerBytesWritable other) {
+        super(other);
+    }
 
-	public void setSize(int size) {
-		if (size > getCapacity()) {
-			setCapacity( (size * 3 / 2));
-		}
-		this.size = size;
-	}
+    public void setSize(int size) {
+        if (size > getCapacity()) {
+            setCapacity((size * 3 / 2));
+        }
+        this.size = size;
+    }
 
-	public int getCapacity() {
-		return bytes.length;
-	}
+    public int getCapacity() {
+        return bytes.length;
+    }
 
-	public 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, 0, new_data, 0, size);
-			}
-			bytes = new_data;
-		}
-	}
-	
-	/**
-	 * 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(int k, byte[] array, int start) {
-		reset(k);
-		super.setByRead(array, start);
-	}
+    public 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, 0, new_data, 0, size);
+            }
+            bytes = new_data;
+        }
+    }
 
-	/**
-	 * Compress Reversed Kmer into bytes array AATAG will compress as
-	 * [0x000A,0xATAG]
-	 * 
-	 * @param input
-	 *            array
-	 * @param start
-	 *            position
-	 */
-	public void setByReadReverse(int k, byte[] array, int start) {
-		reset(k);
-		super.setByReadReverse(array, start);
-	}
+    /**
+     * 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(int k, byte[] array, int start) {
+        reset(k);
+        super.setByRead(array, start);
+    }
 
-	public void set(KmerBytesWritable newData) {
-		set(newData.kmerlength, newData.bytes, 0, newData.size);
-	}
+    /**
+     * Compress Reversed Kmer into bytes array AATAG will compress as
+     * [0x000A,0xATAG]
+     * 
+     * @param input
+     *            array
+     * @param start
+     *            position
+     */
+    public void setByReadReverse(int k, byte[] array, int start) {
+        reset(k);
+        super.setByReadReverse(array, start);
+    }
 
-	public void set(int k, byte[] newData, int offset, int length) {
-		reset(k);
-		System.arraycopy(newData, offset, bytes, 0, size);
-	}
+    public void set(KmerBytesWritable newData) {
+        set(newData.kmerlength, newData.bytes, 0, newData.size);
+    }
 
-	/**
-	 * Reset array by kmerlength
-	 * @param k
-	 */
-	public void reset(int k) {
-		this.kmerlength = k;
-		setSize( 0);
-		setSize( KmerUtil.getByteNumFromK(k));
-	}
+    public void set(int k, byte[] newData, int offset, int length) {
+        reset(k);
+        System.arraycopy(newData, offset, bytes, 0, size);
+    }
 
-	@Override
-	public void readFields(DataInput in) throws IOException {
-		reset(in.readInt());
-		in.readFully(bytes, 0, size);
-	}
+    /**
+     * Reset array by kmerlength
+     * 
+     * @param k
+     */
+    public void reset(int k) {
+        this.kmerlength = k;
+        setSize(0);
+        setSize(KmerUtil.getByteNumFromK(k));
+    }
 
-	/**
-	 * Write the kmer to output
-	 *  we don't need to output size, since size is related to kmerlength
-	 */
-	@Override
-	public void write(DataOutput out) throws IOException {
-		out.writeInt(this.kmerlength);
-		out.write(bytes, 0, size);
-	}
+    public static class Comparator extends WritableComparator {
+        public final int LEAD_BYTES = 4;
 
-	public static class Comparator extends WritableComparator {
-		public final int LEAD_BYTES = 4; 
-		public Comparator() {
-			super(KmerBytesWritable.class);
-		}
+        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){
-				compareBytes(b1, s1 + LEAD_BYTES, l1-LEAD_BYTES, b2, s2+LEAD_BYTES, l2-LEAD_BYTES);
-			}
-			return kmerlength1 - kmerlength2 ;
-		}
-	}
+        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) {
+                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());
-	}
+    static { // register this comparator
+        WritableComparator.define(KmerBytesWritable.class, new Comparator());
+    }
 }
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritableFactory.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritableFactory.java
index a7bcc8b..dfc0ee3 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritableFactory.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritableFactory.java
@@ -1,241 +1,263 @@
 package edu.uci.ics.genomix.type;
 
 public class VKmerBytesWritableFactory {
-	private VKmerBytesWritable kmer;
-	
-	public VKmerBytesWritableFactory(int k){
-		kmer = new VKmerBytesWritable(k);
-	}
+    private VKmerBytesWritable kmer;
 
-	/**
-	 * Read Kmer from read text into bytes array e.g. AATAG will compress as
-	 * [0x000G, 0xATAA]
-	 * 
-	 * @param k
-	 * @param array
-	 * @param start
-	 */
-	public VKmerBytesWritable getKmerByRead(int k, byte[] array, int start) {
-		kmer.setByRead(k, array, start);
-		return kmer;
-	}
+    public VKmerBytesWritableFactory(int k) {
+        kmer = new VKmerBytesWritable(k);
+    }
 
-	/**
-	 * Compress Reversed Kmer into bytes array AATAG will compress as
-	 * [0x000A,0xATAG]
-	 * 
-	 * @param array
-	 * @param start
-	 */
-	public VKmerBytesWritable getKmerByReadReverse(int k, byte[] array, int start) {
-		kmer.setByReadReverse(k, 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 VKmerBytesWritable getLastKmerFromChain(int lastK, final KmerBytesWritable kmerChain) {
-		if (lastK > kmerChain.getKmerLength()) {
-			return null;
-		}
-		if (lastK == kmerChain.getKmerLength()) {
-			kmer.set(kmerChain);
-			return kmer;
-		}
-		kmer.reset(lastK);
+    /**
+     * Read Kmer from read text into bytes array e.g. AATAG will compress as
+     * [0x000G, 0xATAA]
+     * 
+     * @param k
+     * @param array
+     * @param start
+     */
+    public VKmerBytesWritable getKmerByRead(int k, byte[] array, int start) {
+        kmer.setByRead(k, array, start);
+        return kmer;
+    }
 
-		/** 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)));
-		}
+    /**
+     * Compress Reversed Kmer into bytes array AATAG will compress as
+     * [0x000A,0xATAG]
+     * 
+     * @param array
+     * @param start
+     */
+    public VKmerBytesWritable getKmerByReadReverse(int k, byte[] array, int start) {
+        kmer.setByReadReverse(k, array, start);
+        return kmer;
+    }
 
-		/** last kmer byte */
-		if (byteInKmer == 0) {
-			kmer.getBytes()[0] = (byte) ((kmerChain.getBytes()[0] & 0xff) >> posInByteOfChain);
-		}
-		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 VKmerBytesWritable getFirstKmerFromChain(int firstK, final KmerBytesWritable kmerChain) {
-		if (firstK > kmerChain.getKmerLength()) {
-			return null;
-		}
-		if (firstK == kmerChain.getKmerLength()) {
-			kmer.set(kmerChain);
-			return kmer;
-		}
-		kmer.reset(firstK);
+    /**
+     * 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 VKmerBytesWritable getLastKmerFromChain(int lastK, final KmerBytesWritable kmerChain) {
+        if (lastK > kmerChain.getKmerLength()) {
+            return null;
+        }
+        if (lastK == kmerChain.getKmerLength()) {
+            kmer.set(kmerChain);
+            return kmer;
+        }
+        kmer.reset(lastK);
 
-		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));
-		}
-		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 VKmerBytesWritable 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)));
-		}
-		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 VKmerBytesWritable 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));
-		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 VKmerBytesWritable 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));
-			}
-		}
-		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 VKmerBytesWritable 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 VKmerBytesWritable 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 VKmerBytesWritable reverse(final KmerBytesWritable kmer) {
-		this.kmer.reset(kmer.getKmerLength());
+        /** 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)));
+        }
 
-		int curPosAtKmer = ((kmer.getKmerLength() - 1) % 4) << 1;
-		int curByteAtKmer = 0;
+        /** last kmer byte */
+        if (byteInKmer == 0) {
+            kmer.getBytes()[0] = (byte) ((kmerChain.getBytes()[0] & 0xff) >> posInByteOfChain);
+        }
+        return kmer;
+    }
 
-		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++;
-			}
-		}
-		return this.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 VKmerBytesWritable 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));
+        }
+        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 VKmerBytesWritable 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)));
+        }
+        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 VKmerBytesWritable 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));
+        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 VKmerBytesWritable 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));
+            }
+        }
+        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 VKmerBytesWritable 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 VKmerBytesWritable 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 VKmerBytesWritable 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++;
+            }
+        }
+        return this.kmer;
+    }
 }
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerBytesWritableTest.java
index ea1d0c2..f21da91 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerBytesWritableTest.java
@@ -8,73 +8,71 @@
 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 kmer = new KmerBytesWritable(k);
-		kmer.setByRead( array, 0);
-		Assert.assertEquals(kmer.toString(), "AATAGAA");
-		
-		kmer.setByRead( array, 1);
-		Assert.assertEquals(kmer.toString(), "ATAGAAG");
-	}
-	
-	@Test
-	public void TestMoveKmer(){
-		KmerBytesWritable kmer = new KmerBytesWritable(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);
-		}
+    static byte[] array = { 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'G' };
+    static int k = 7;
 
-		byte out = kmer.shiftKmerWithNextChar( array[array.length - 1]);
-		Assert.assertEquals(out, GeneCode.getAdjBit((byte) 'A'));
-		Assert.assertEquals(kmer.toString(), "ATAGAAG");
-	}
-	
-	
-	@Test
-	public void TestCompressKmerReverse() {
-		KmerBytesWritable kmer = new KmerBytesWritable(k);
-		kmer.setByRead( array, 0);
-		Assert.assertEquals(kmer.toString(), "AATAGAA");
-		
-		kmer.setByReadReverse( array, 1);
-		Assert.assertEquals(kmer.toString(), "GAAGATA");
-	}
-	
-	@Test
-	public void TestMoveKmerReverse(){
-		KmerBytesWritable kmer = new KmerBytesWritable(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);
-		}
+    @Test
+    public void TestCompressKmer() {
+        KmerBytesWritable kmer = new KmerBytesWritable(k);
+        kmer.setByRead(array, 0);
+        Assert.assertEquals(kmer.toString(), "AATAGAA");
 
-		byte out = kmer.shiftKmerWithPreChar(array[array.length - 1]);
-		Assert.assertEquals(out, GeneCode.getAdjBit((byte) 'A'));
-		Assert.assertEquals(kmer.toString(), "GAATAGA");
-	}
+        kmer.setByRead(array, 1);
+        Assert.assertEquals(kmer.toString(), "ATAGAAG");
+    }
 
-	@Test
-	public void TestGetGene(){
-		KmerBytesWritable kmer = new KmerBytesWritable(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 TestMoveKmer() {
+        KmerBytesWritable kmer = new KmerBytesWritable(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.getAdjBit((byte) 'A'));
+        Assert.assertEquals(kmer.toString(), "ATAGAAG");
+    }
+
+    @Test
+    public void TestCompressKmerReverse() {
+        KmerBytesWritable kmer = new KmerBytesWritable(k);
+        kmer.setByRead(array, 0);
+        Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+        kmer.setByReadReverse(array, 1);
+        Assert.assertEquals(kmer.toString(), "GAAGATA");
+    }
+
+    @Test
+    public void TestMoveKmerReverse() {
+        KmerBytesWritable kmer = new KmerBytesWritable(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.getAdjBit((byte) 'A'));
+        Assert.assertEquals(kmer.toString(), "GAATAGA");
+    }
+
+    @Test
+    public void TestGetGene() {
+        KmerBytesWritable kmer = new KmerBytesWritable(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))));
+        }
+    }
 
 }
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/VKmerBytesWritableFactoryTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/VKmerBytesWritableFactoryTest.java
index a0b8845..c40729c 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/VKmerBytesWritableFactoryTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/VKmerBytesWritableFactoryTest.java
@@ -9,150 +9,150 @@
 import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
 
 public class VKmerBytesWritableFactoryTest {
-	static byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C','G','T'};
-	
-	VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(8);
-	
-	@Test
-	public void TestDegree(){
-		Assert.assertTrue(GeneCode.inDegree((byte) 0xff) == 4); 
-		Assert.assertTrue(GeneCode.outDegree((byte) 0xff) == 4);
-		Assert.assertTrue(GeneCode.inDegree((byte) 0x3f) == 2);
-		Assert.assertTrue(GeneCode.outDegree((byte) 0x01) == 1);
-		Assert.assertTrue(GeneCode.inDegree((byte) 0x01) == 0);
-	}
-	
-	@Test
-	public void TestGetLastKmer(){
-		KmerBytesWritable kmer = new KmerBytesWritable(9);
-		kmer.setByRead( array, 0);
-		Assert.assertEquals("AGCTGACCG", kmer.toString());
-		KmerBytesWritable lastKmer ;
-		for(int i = 8; i>0 ; i--){
-			lastKmer = kmerFactory.getLastKmerFromChain(i, kmer);
-			Assert.assertEquals("AGCTGACCG".substring(9-i), lastKmer.toString());
-		}
-		VKmerBytesWritable vlastKmer ;
-		for(int i = 8; i>0 ; i--){
-			vlastKmer = kmerFactory.getLastKmerFromChain(i, kmer);
-			Assert.assertEquals("AGCTGACCG".substring(9-i), vlastKmer.toString());
-		}
-	}
-	
-	@Test
-	public void TestMergeNext(){
-		KmerBytesWritable kmer = new KmerBytesWritable(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);
-			text = text + (char)GeneCode.GENE_SYMBOL[x];
-			Assert.assertEquals(text, newkmer.toString());
-			kmer = new KmerBytesWritable(newkmer);
-		}
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			KmerBytesWritable newkmer = kmerFactory.mergeKmerWithNextCode(kmer, x);
-			text = text + (char)GeneCode.GENE_SYMBOL[x];
-			Assert.assertEquals(text, newkmer.toString());
-			kmer = new KmerBytesWritable(newkmer);
-		}
-	}
-	
-	@Test
-	public void TestMergePre(){
-		KmerBytesWritable kmer = new KmerBytesWritable(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);
-			text = (char)GeneCode.GENE_SYMBOL[x] + text;
-			Assert.assertEquals(text , newkmer.toString());
-			kmer = new KmerBytesWritable(newkmer);
-		}
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			KmerBytesWritable newkmer = kmerFactory.mergeKmerWithPreCode(kmer, x);
-			text = (char)GeneCode.GENE_SYMBOL[x] + text;
-			Assert.assertEquals(text , newkmer.toString());
-			kmer = new KmerBytesWritable(newkmer);
-		}
-	}
-	
-	@Test
-	public void TestMergeTwoKmer(){
-		KmerBytesWritable kmer1 = new KmerBytesWritable(9);
-		kmer1.setByRead( array, 0);
-		String text1 = "AGCTGACCG";
-		KmerBytesWritable kmer2 = new KmerBytesWritable(9);
-		kmer2.setByRead(array, 1);
-		String text2 = "GCTGACCGT";
-		Assert.assertEquals(text1, kmer1.toString());
-		Assert.assertEquals(text2, kmer2.toString());
-		
-		KmerBytesWritable merged = kmerFactory.mergeTwoKmer(kmer1, kmer2);
-		Assert.assertEquals(text1+text2, merged.toString());
-		
-		KmerBytesWritable kmer3 =  new KmerBytesWritable(3);
-		kmer3.setByRead(array, 1);
-		String text3 = "GCT";
-		Assert.assertEquals(text3, kmer3.toString());
-		
-		merged = kmerFactory.mergeTwoKmer(kmer1, kmer3);
-		Assert.assertEquals(text1+text3, merged.toString());
-		merged = kmerFactory.mergeTwoKmer( kmer3,  kmer1);
-		Assert.assertEquals(text3+text1, merged.toString());
-		
-		KmerBytesWritable kmer4 = new KmerBytesWritable(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);
-		kmer5.setByRead( array, 0);
-		String text5 = "AGCTGAC";
-		VKmerBytesWritable kmer6 = new VKmerBytesWritable(9);
-		kmer6.setByRead(9, array, 1);
-		String text6 = "GCTGACCGT";
-		merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
-		Assert.assertEquals(text5+text6,  merged.toString());
-		
-		kmer6.setByRead(6, array, 1);
-		String text7 = "GCTGAC";
-		merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
-		Assert.assertEquals(text5+text7,  merged.toString());
-		
-		kmer6.setByRead(4, array, 1);
-		String text8 = "GCTG";
-		merged = kmerFactory.mergeTwoKmer( kmer5, kmer6);
-		Assert.assertEquals(text5+text8, merged.toString());
+    static byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
 
-	}
-	@Test 
-	public void TestShift(){
-		VKmerBytesWritable kmer = new VKmerBytesWritable(kmerFactory.getKmerByRead(9, array, 0));
-		String text = "AGCTGACCG";
-		Assert.assertEquals(text, kmer.toString());
-		
-		VKmerBytesWritable kmerForward = kmerFactory.shiftKmerWithNextCode(kmer,GeneCode.A);
-		Assert.assertEquals(text,  kmer.toString());
-		Assert.assertEquals("GCTGACCGA", kmerForward.toString());
-		VKmerBytesWritable kmerBackward = kmerFactory.shiftKmerWithPreCode(kmer,GeneCode.C);
-		Assert.assertEquals(text, kmer.toString());
-		Assert.assertEquals("CAGCTGACC", kmerBackward.toString());
-		
-	}
+    VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(8);
 
-	
-	@Test
-	public void TestReverseKmer(){
-		KmerBytesWritable kmer = new KmerBytesWritable(7);
-		kmer.setByRead( array, 0);
-		Assert.assertEquals(kmer.toString(), "AGCTGAC");
-		KmerBytesWritable reversed = kmerFactory.reverse(kmer);
-		Assert.assertEquals(reversed.toString(), "CAGTCGA");
-	}
+    @Test
+    public void TestDegree() {
+        Assert.assertTrue(GeneCode.inDegree((byte) 0xff) == 4);
+        Assert.assertTrue(GeneCode.outDegree((byte) 0xff) == 4);
+        Assert.assertTrue(GeneCode.inDegree((byte) 0x3f) == 2);
+        Assert.assertTrue(GeneCode.outDegree((byte) 0x01) == 1);
+        Assert.assertTrue(GeneCode.inDegree((byte) 0x01) == 0);
+    }
+
+    @Test
+    public void TestGetLastKmer() {
+        KmerBytesWritable kmer = new KmerBytesWritable(9);
+        kmer.setByRead(array, 0);
+        Assert.assertEquals("AGCTGACCG", kmer.toString());
+        KmerBytesWritable lastKmer;
+        for (int i = 8; i > 0; i--) {
+            lastKmer = kmerFactory.getLastKmerFromChain(i, kmer);
+            Assert.assertEquals("AGCTGACCG".substring(9 - i), lastKmer.toString());
+        }
+        VKmerBytesWritable vlastKmer;
+        for (int i = 8; i > 0; i--) {
+            vlastKmer = kmerFactory.getLastKmerFromChain(i, kmer);
+            Assert.assertEquals("AGCTGACCG".substring(9 - i), vlastKmer.toString());
+        }
+    }
+
+    @Test
+    public void TestMergeNext() {
+        KmerBytesWritable kmer = new KmerBytesWritable(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);
+            text = text + (char) GeneCode.GENE_SYMBOL[x];
+            Assert.assertEquals(text, newkmer.toString());
+            kmer = new KmerBytesWritable(newkmer);
+        }
+        for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
+            KmerBytesWritable newkmer = kmerFactory.mergeKmerWithNextCode(kmer, x);
+            text = text + (char) GeneCode.GENE_SYMBOL[x];
+            Assert.assertEquals(text, newkmer.toString());
+            kmer = new KmerBytesWritable(newkmer);
+        }
+    }
+
+    @Test
+    public void TestMergePre() {
+        KmerBytesWritable kmer = new KmerBytesWritable(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);
+            text = (char) GeneCode.GENE_SYMBOL[x] + text;
+            Assert.assertEquals(text, newkmer.toString());
+            kmer = new KmerBytesWritable(newkmer);
+        }
+        for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
+            KmerBytesWritable newkmer = kmerFactory.mergeKmerWithPreCode(kmer, x);
+            text = (char) GeneCode.GENE_SYMBOL[x] + text;
+            Assert.assertEquals(text, newkmer.toString());
+            kmer = new KmerBytesWritable(newkmer);
+        }
+    }
+
+    @Test
+    public void TestMergeTwoKmer() {
+        KmerBytesWritable kmer1 = new KmerBytesWritable(9);
+        kmer1.setByRead(array, 0);
+        String text1 = "AGCTGACCG";
+        KmerBytesWritable kmer2 = new KmerBytesWritable(9);
+        kmer2.setByRead(array, 1);
+        String text2 = "GCTGACCGT";
+        Assert.assertEquals(text1, kmer1.toString());
+        Assert.assertEquals(text2, kmer2.toString());
+
+        KmerBytesWritable merged = kmerFactory.mergeTwoKmer(kmer1, kmer2);
+        Assert.assertEquals(text1 + text2, merged.toString());
+
+        KmerBytesWritable kmer3 = new KmerBytesWritable(3);
+        kmer3.setByRead(array, 1);
+        String text3 = "GCT";
+        Assert.assertEquals(text3, kmer3.toString());
+
+        merged = kmerFactory.mergeTwoKmer(kmer1, kmer3);
+        Assert.assertEquals(text1 + text3, merged.toString());
+        merged = kmerFactory.mergeTwoKmer(kmer3, kmer1);
+        Assert.assertEquals(text3 + text1, merged.toString());
+
+        KmerBytesWritable kmer4 = new KmerBytesWritable(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);
+        kmer5.setByRead(array, 0);
+        String text5 = "AGCTGAC";
+        VKmerBytesWritable kmer6 = new VKmerBytesWritable(9);
+        kmer6.setByRead(9, array, 1);
+        String text6 = "GCTGACCGT";
+        merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
+        Assert.assertEquals(text5 + text6, merged.toString());
+
+        kmer6.setByRead(6, array, 1);
+        String text7 = "GCTGAC";
+        merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
+        Assert.assertEquals(text5 + text7, merged.toString());
+
+        kmer6.setByRead(4, array, 1);
+        String text8 = "GCTG";
+        merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
+        Assert.assertEquals(text5 + text8, merged.toString());
+
+    }
+
+    @Test
+    public void TestShift() {
+        VKmerBytesWritable kmer = new VKmerBytesWritable(kmerFactory.getKmerByRead(9, array, 0));
+        String text = "AGCTGACCG";
+        Assert.assertEquals(text, kmer.toString());
+
+        VKmerBytesWritable kmerForward = kmerFactory.shiftKmerWithNextCode(kmer, GeneCode.A);
+        Assert.assertEquals(text, kmer.toString());
+        Assert.assertEquals("GCTGACCGA", kmerForward.toString());
+        VKmerBytesWritable kmerBackward = kmerFactory.shiftKmerWithPreCode(kmer, GeneCode.C);
+        Assert.assertEquals(text, kmer.toString());
+        Assert.assertEquals("CAGCTGACC", kmerBackward.toString());
+
+    }
+
+    @Test
+    public void TestReverseKmer() {
+        KmerBytesWritable kmer = new KmerBytesWritable(7);
+        kmer.setByRead(array, 0);
+        Assert.assertEquals(kmer.toString(), "AGCTGAC");
+        KmerBytesWritable reversed = kmerFactory.reverse(kmer);
+        Assert.assertEquals(reversed.toString(), "CAGTCGA");
+    }
 }
diff --git a/genomix/genomix-data/src/test/resources/hadoop/conf/core-site.xml b/genomix/genomix-data/src/test/resources/hadoop/conf/core-site.xml
index 47dfac5..3e5bacb 100644
--- a/genomix/genomix-data/src/test/resources/hadoop/conf/core-site.xml
+++ b/genomix/genomix-data/src/test/resources/hadoop/conf/core-site.xml
@@ -5,14 +5,14 @@
 
 <configuration>
 
-<property>
-    <name>fs.default.name</name>
-    <value>hdfs://127.0.0.1:31888</value>
-</property>
-<property>
-    <name>hadoop.tmp.dir</name>
-    <value>/tmp/hadoop</value>
-</property>
+	<property>
+		<name>fs.default.name</name>
+		<value>hdfs://127.0.0.1:31888</value>
+	</property>
+	<property>
+		<name>hadoop.tmp.dir</name>
+		<value>/tmp/hadoop</value>
+	</property>
 
 
 </configuration>
diff --git a/genomix/genomix-data/src/test/resources/hadoop/conf/hdfs-site.xml b/genomix/genomix-data/src/test/resources/hadoop/conf/hdfs-site.xml
index 8d29b1d..b1b1902 100644
--- a/genomix/genomix-data/src/test/resources/hadoop/conf/hdfs-site.xml
+++ b/genomix/genomix-data/src/test/resources/hadoop/conf/hdfs-site.xml
@@ -5,14 +5,14 @@
 
 <configuration>
 
-<property>
-   <name>dfs.replication</name>
-   <value>1</value>
-</property>
+	<property>
+		<name>dfs.replication</name>
+		<value>1</value>
+	</property>
 
-<property>
-	<name>dfs.block.size</name>
-	<value>65536</value>
-</property>
+	<property>
+		<name>dfs.block.size</name>
+		<value>65536</value>
+	</property>
 
 </configuration>
diff --git a/genomix/genomix-data/src/test/resources/hadoop/conf/mapred-site.xml b/genomix/genomix-data/src/test/resources/hadoop/conf/mapred-site.xml
index 39b6505..525e7d5 100644
--- a/genomix/genomix-data/src/test/resources/hadoop/conf/mapred-site.xml
+++ b/genomix/genomix-data/src/test/resources/hadoop/conf/mapred-site.xml
@@ -5,21 +5,21 @@
 
 <configuration>
 
-  <property>
-    <name>mapred.job.tracker</name>
-    <value>localhost:29007</value>
-  </property>
-  <property>
-     <name>mapred.tasktracker.map.tasks.maximum</name>
-     <value>20</value>
-  </property>
-   <property>
-      <name>mapred.tasktracker.reduce.tasks.maximum</name>
-      <value>20</value>
-   </property>
-   <property>
-      <name>mapred.max.split.size</name>
-      <value>2048</value>
-   </property>
+	<property>
+		<name>mapred.job.tracker</name>
+		<value>localhost:29007</value>
+	</property>
+	<property>
+		<name>mapred.tasktracker.map.tasks.maximum</name>
+		<value>20</value>
+	</property>
+	<property>
+		<name>mapred.tasktracker.reduce.tasks.maximum</name>
+		<value>20</value>
+	</property>
+	<property>
+		<name>mapred.max.split.size</name>
+		<value>2048</value>
+	</property>
 
 </configuration>