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 d796d19..c4d6401 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
@@ -1,5 +1,7 @@
 package edu.uci.ics.genomix.type;
 
+import java.util.Arrays;
+
 public class KmerUtil {
 
 	public static int countNumberOfBitSet(int i) {
@@ -28,7 +30,7 @@
 	 * @return LastKmer bytes array
 	 */
 	public static byte[] getLastKmerFromChain(int k, int kInChain,
-			byte[] kmerChain) {
+			byte[] kmerChain, int offset, int length) {
 		if (k > kInChain) {
 			return null;
 		}
@@ -39,17 +41,17 @@
 		byte[] kmer = new byte[byteNum];
 
 		/** from end to start */
-		int byteInChain = kmerChain.length - 1 - (kInChain - k) / 4;
+		int byteInChain = length - 1 - (kInChain - k) / 4;
 		int posInByteOfChain = ((kInChain - k) % 4) << 1; // *2
 		int byteInKmer = byteNum - 1;
 		for (; byteInKmer >= 0 && byteInChain > 0; byteInKmer--, byteInChain--) {
-			kmer[byteInKmer] = (byte) ((0xff & kmerChain[byteInChain]) >> posInByteOfChain);
-			kmer[byteInKmer] |= ((kmerChain[byteInChain - 1] << (8 - posInByteOfChain)));
+			kmer[byteInKmer] = (byte) ((0xff & kmerChain[offset + byteInChain]) >> posInByteOfChain);
+			kmer[byteInKmer] |= ((kmerChain[offset + byteInChain - 1] << (8 - posInByteOfChain)));
 		}
 
 		/** last kmer byte */
 		if (byteInKmer == 0) {
-			kmer[0] = (byte) ((kmerChain[0] & 0xff) >> posInByteOfChain);
+			kmer[0] = (byte) ((kmerChain[offset] & 0xff) >> posInByteOfChain);
 		}
 		return kmer;
 	}
@@ -64,7 +66,7 @@
 	 * @return FirstKmer bytes array
 	 */
 	public static byte[] getFirstKmerFromChain(int k, int kInChain,
-			byte[] kmerChain) {
+			byte[] kmerChain, int offset, int length) {
 		if (k > kInChain) {
 			return null;
 		}
@@ -76,13 +78,13 @@
 
 		int i = 1;
 		for (; i < kmer.length; i++) {
-			kmer[kmer.length - i] = kmerChain[kmerChain.length - i];
+			kmer[kmer.length - i] = kmerChain[offset + length - i];
 		}
 		int posInByteOfChain = (k % 4) << 1; // *2
 		if (posInByteOfChain == 0) {
-			kmer[0] = kmerChain[kmerChain.length - i];
+			kmer[0] = kmerChain[offset + length - i];
 		} else {
-			kmer[0] = (byte) (kmerChain[kmerChain.length - i] & ((1 << posInByteOfChain) - 1));
+			kmer[0] = (byte) (kmerChain[offset + length - i] & ((1 << posInByteOfChain) - 1));
 		}
 		return kmer;
 	}
@@ -96,19 +98,19 @@
 	 * @param nextCode: next neighbor in gene-code format
 	 * @return the merged Kmer, this K of this Kmer is k+1
 	 */
-	public static byte[] mergeKmerWithNextCode(int k, byte[] kmer, byte nextCode) {
-		int byteNum = kmer.length;
+	public static byte[] mergeKmerWithNextCode(int k, byte[] kmer, int offset, int length, byte nextCode) {
+		int byteNum = length;
 		if (k % 4 == 0) {
 			byteNum++;
 		}
 		byte[] mergedKmer = new byte[byteNum];
-		for (int i = 1; i <= kmer.length; i++) {
-			mergedKmer[mergedKmer.length - i] = kmer[kmer.length - i];
+		for (int i = 1; i <= length; i++) {
+			mergedKmer[mergedKmer.length - i] = kmer[offset + length - i];
 		}
-		if (mergedKmer.length > kmer.length) {
+		if (mergedKmer.length > length) {
 			mergedKmer[0] = (byte) (nextCode & 0x3);
 		} else {
-			mergedKmer[0] = (byte) (kmer[0] | ((nextCode & 0x3) << ((k % 4) << 1)));
+			mergedKmer[0] = (byte) (kmer[offset] | ((nextCode & 0x3) << ((k % 4) << 1)));
 		}
 		return mergedKmer;
 	}
@@ -122,22 +124,22 @@
 	 * @param preCode: next neighbor in gene-code format
 	 * @return the merged Kmer,this K of this Kmer is k+1
 	 */
-	public static byte[] mergeKmerWithPreCode(int k, byte[] kmer, byte preCode) {
-		int byteNum = kmer.length;
+	public static byte[] mergeKmerWithPreCode(int k, byte[] kmer, int offset, int length, byte preCode) {
+		int byteNum = length;
 		byte[] mergedKmer = null;
 		int byteInMergedKmer = 0;
 		if (k % 4 == 0) {
 			byteNum++;
 			mergedKmer = new byte[byteNum];
-			mergedKmer[0] = (byte) ((kmer[0] >> 6) & 0x3);
+			mergedKmer[0] = (byte) ((kmer[offset] >> 6) & 0x3);
 			byteInMergedKmer++;
 		} else {
 			mergedKmer = new byte[byteNum];
 		}
-		for (int i = 0; i < kmer.length - 1; i++, byteInMergedKmer++) {
-			mergedKmer[byteInMergedKmer] = (byte) ((kmer[i] << 2) | ((kmer[i + 1] >> 6) & 0x3));
+		for (int i = 0; i < length - 1; i++, byteInMergedKmer++) {
+			mergedKmer[byteInMergedKmer] = (byte) ((kmer[offset + i] << 2) | ((kmer[offset + i + 1] >> 6) & 0x3));
 		}
-		mergedKmer[byteInMergedKmer] = (byte) ((kmer[kmer.length - 1] << 2) | (preCode & 0x3));
+		mergedKmer[byteInMergedKmer] = (byte) ((kmer[offset + length - 1] << 2) | (preCode & 0x3));
 		return mergedKmer;
 	}
 
@@ -150,31 +152,31 @@
 	 * @param kmerNext : bytes array of next kmer
 	 * @return merged kmer, the new k is @preK + @nextK
 	 */
-	public static byte[] mergeTwoKmer(int preK, byte[] kmerPre, int nextK,
-			byte[] kmerNext) {
+	public static byte[] mergeTwoKmer(int preK, byte[] kmerPre, int offsetPre, int lengthPre, int nextK,
+			byte[] kmerNext, int offsetNext, int lengthNext) {
 		int byteNum = Kmer.getByteNumFromK(preK + nextK);
 		byte[] mergedKmer = new byte[byteNum];
 		int i = 1;
-		for (; i <= kmerPre.length; i++) {
-			mergedKmer[byteNum - i] = kmerPre[kmerPre.length - i];
+		for (; i <= lengthPre; i++) {
+			mergedKmer[byteNum - i] = kmerPre[offsetPre + lengthPre - i];
 		}
 		if ( i > 1){
 			i--;
 		}
 		if (preK % 4 == 0) {
-			for (int j = 1; j <= kmerNext.length; j++) {
-				mergedKmer[byteNum - i - j] = kmerNext[kmerNext.length - j];
+			for (int j = 1; j <= lengthNext; j++) {
+				mergedKmer[byteNum - i - j] = kmerNext[offsetNext + lengthNext - j];
 			}
 		} else {
 			int posNeedToMove = ((preK % 4) << 1);
-			mergedKmer[byteNum - i] |= kmerNext[kmerNext.length - 1] << posNeedToMove;
-			for (int j = 1; j < kmerNext.length; j++) {
-				mergedKmer[byteNum - i - j] = (byte) (((kmerNext[kmerNext.length
-						- j] & 0xff) >> (8 - posNeedToMove)) | (kmerNext[kmerNext.length
+			mergedKmer[byteNum - i] |= kmerNext[offsetNext + lengthNext - 1] << posNeedToMove;
+			for (int j = 1; j < lengthNext; j++) {
+				mergedKmer[byteNum - i - j] = (byte) (((kmerNext[offsetNext + lengthNext
+						- j] & 0xff) >> (8 - posNeedToMove)) | (kmerNext[offsetNext + lengthNext
 						- j - 1] << posNeedToMove));
 			}
 			if ( (nextK % 4) * 2 + posNeedToMove > 8) {
-				mergedKmer[0] = (byte) (kmerNext[0] >> (8 - posNeedToMove));
+				mergedKmer[0] = (byte) (kmerNext[offsetNext] >> (8 - posNeedToMove));
 			}
 		}
 		return mergedKmer;
@@ -188,8 +190,8 @@
 	 * @param afterCode: input genecode 
 	 * @return new created kmer that shifted by afterCode, the K will not change
 	 */
-	public static byte[] shiftKmerWithNextCode(int k, final byte[] kmer, byte afterCode){
-		byte[] shifted = kmer.clone();
+	public static byte[] shiftKmerWithNextCode(int k, final byte[] kmer, int offset, int length, byte afterCode){
+		byte[] shifted = Arrays.copyOfRange(kmer, offset, offset+length);
 		Kmer.moveKmer(k, shifted, Kmer.GENE_CODE.getSymbolFromCode(afterCode));
 		return shifted;
 	}
@@ -202,10 +204,19 @@
 	 * @param preCode: input genecode 
 	 * @return new created kmer that shifted by preCode, the K will not change
 	 */
-	public static byte[] shiftKmerWithPreCode(int k, final byte[] kmer, byte preCode){
-		byte[] shifted = kmer.clone();
+	public static byte[] shiftKmerWithPreCode(int k, final byte[] kmer, int offset, int length, byte preCode){
+		byte[] shifted = Arrays.copyOfRange(kmer, offset, offset+length);
 		Kmer.moveKmerReverse(k, shifted, Kmer.GENE_CODE.getSymbolFromCode(preCode));
 		return shifted;
 	}
 
+	public static byte getGeneCodeAtPosition(int pos, int k, final byte[] kmer,
+			int offset, int length) {
+		if (pos >= k) {
+			return -1;
+		}
+		int posByte = pos / 4;
+		int shift = (pos  % 4) << 1;
+		return (byte) ((kmer[offset + length - 1 - posByte] >> shift) & 0x3);
+	}
 }
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerUtilTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerUtilTest.java
index 206e279..4b6e180 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerUtilTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerUtilTest.java
@@ -24,7 +24,7 @@
 		Assert.assertEquals("AGCTGACCG", Kmer.recoverKmerFrom(9, kmerChain, 0, kmerChain.length));
 		byte[] lastKmer ;
 		for(int i = 8; i>0 ; i--){
-			lastKmer = KmerUtil.getLastKmerFromChain(i, 9, kmerChain);
+			lastKmer = KmerUtil.getLastKmerFromChain(i, 9, kmerChain, 0, kmerChain.length);
 //			System.out.println(Kmer.recoverKmerFrom(i, lastKmer, 0, lastKmer.length));
 			Assert.assertEquals("AGCTGACCG".substring(9-i), Kmer.recoverKmerFrom(i, lastKmer, 0, lastKmer.length));
 		}
@@ -36,13 +36,13 @@
 		String text = "AGCTGACCG";
 		Assert.assertEquals(text, Kmer.recoverKmerFrom(9, kmer, 0, kmer.length));
 		for(byte x = Kmer.GENE_CODE.A; x<= Kmer.GENE_CODE.T ; x++){
-			kmer = KmerUtil.mergeKmerWithNextCode(9+x, kmer, x);
+			kmer = KmerUtil.mergeKmerWithNextCode(9+x, kmer, 0, kmer.length, x);
 //			System.out.println(Kmer.recoverKmerFrom(9+x+1, kmer, 0, kmer.length));
 			text = text + (char)Kmer.GENE_SYMBOL[x];
 			Assert.assertEquals(text, Kmer.recoverKmerFrom(9+x+1, kmer, 0, kmer.length));
 		}
 		for(byte x = Kmer.GENE_CODE.A; x<= Kmer.GENE_CODE.T ; x++){
-			kmer = KmerUtil.mergeKmerWithNextCode(13+x, kmer, x);
+			kmer = KmerUtil.mergeKmerWithNextCode(13+x, kmer,0, kmer.length, x);
 //			System.out.println(Kmer.recoverKmerFrom(13+x+1, kmer, 0, kmer.length));
 			text = text + (char)Kmer.GENE_SYMBOL[x];
 			Assert.assertEquals(text, Kmer.recoverKmerFrom(13+x+1, kmer, 0, kmer.length));
@@ -55,13 +55,13 @@
 		String text = "AGCTGACCG";
 		Assert.assertEquals(text, Kmer.recoverKmerFrom(9, kmer, 0, kmer.length));
 		for(byte x = Kmer.GENE_CODE.A; x<= Kmer.GENE_CODE.T ; x++){
-			kmer = KmerUtil.mergeKmerWithPreCode(9+x, kmer, x);
+			kmer = KmerUtil.mergeKmerWithPreCode(9+x, kmer, 0, kmer.length,x);
 //			System.out.println(Kmer.recoverKmerFrom(9+x+1, kmer, 0, kmer.length));
 			text = (char)Kmer.GENE_SYMBOL[x] + text;
 			Assert.assertEquals(text , Kmer.recoverKmerFrom(9+x+1, kmer, 0, kmer.length));
 		}
 		for(byte x = Kmer.GENE_CODE.A; x<= Kmer.GENE_CODE.T ; x++){
-			kmer = KmerUtil.mergeKmerWithPreCode(13+x, kmer, x);
+			kmer = KmerUtil.mergeKmerWithPreCode(13+x, kmer,0, kmer.length, x);
 //			System.out.println(Kmer.recoverKmerFrom(13+x+1, kmer, 0, kmer.length));
 			text = (char)Kmer.GENE_SYMBOL[x] + text;
 			Assert.assertEquals(text , Kmer.recoverKmerFrom(13+x+1, kmer, 0, kmer.length));
@@ -77,33 +77,33 @@
 		Assert.assertEquals(text1, Kmer.recoverKmerFrom(9, kmer1, 0, kmer1.length));
 		Assert.assertEquals(text2, Kmer.recoverKmerFrom(9, kmer2, 0, kmer2.length));
 		
-		byte[] merged = KmerUtil.mergeTwoKmer(9, kmer1, 9, kmer2);
+		byte[] merged = KmerUtil.mergeTwoKmer(9, kmer1,0,kmer1.length, 9, kmer2,0,kmer2.length);
 		Assert.assertEquals(text1+text2, Kmer.recoverKmerFrom(9+9, merged, 0, merged.length));
 		
 		byte[] kmer3 = Kmer.compressKmer(3, array, 1);
 		String text3 = "GCT";
 		Assert.assertEquals(text3, Kmer.recoverKmerFrom(3, kmer3, 0, kmer3.length));
-		merged = KmerUtil.mergeTwoKmer(9, kmer1, 3, kmer3);
+		merged = KmerUtil.mergeTwoKmer(9, kmer1, 0 , kmer1.length, 3, kmer3, 0, kmer3.length);
 		Assert.assertEquals(text1+text3, Kmer.recoverKmerFrom(9+3, merged, 0, merged.length));
-		merged = KmerUtil.mergeTwoKmer(3, kmer3, 9, kmer1);
+		merged = KmerUtil.mergeTwoKmer(3, kmer3, 0 , kmer3.length, 9, kmer1, 0, kmer1.length);
 		Assert.assertEquals(text3+text1, Kmer.recoverKmerFrom(9+3, merged, 0, merged.length));
 		
 		byte[] kmer4 = Kmer.compressKmer(8, array, 0);
 		String text4 = "AGCTGACC";
 		Assert.assertEquals(text4, Kmer.recoverKmerFrom(8, kmer4, 0, kmer4.length));
-		merged = KmerUtil.mergeTwoKmer(8, kmer4, 3, kmer3);
+		merged = KmerUtil.mergeTwoKmer(8, kmer4, 0, kmer4.length, 3, kmer3, 0, kmer3.length);
 		Assert.assertEquals(text4+text3, Kmer.recoverKmerFrom(8+3, merged, 0, merged.length));
 		
 		byte[] kmer5 = Kmer.compressKmer(7, array, 0);
 		String text5 = "AGCTGAC";
 		byte[] kmer6 = Kmer.compressKmer(9, array, 1);
 		String text6 = "GCTGACCGT";
-		merged = KmerUtil.mergeTwoKmer(7, kmer5, 9, kmer6);
+		merged = KmerUtil.mergeTwoKmer(7, kmer5, 0, kmer5.length,9, kmer6, 0, kmer6.length);
 		Assert.assertEquals(text5+text6, Kmer.recoverKmerFrom(7+9, merged, 0, merged.length));
 		
 		byte[] kmer7 = Kmer.compressKmer(6, array, 1);
 		String text7 = "GCTGAC";
-		merged = KmerUtil.mergeTwoKmer(7, kmer5, 6, kmer7);
+		merged = KmerUtil.mergeTwoKmer(7, kmer5, 0, kmer5.length, 6, kmer7, 0, kmer7.length);
 		Assert.assertEquals(text5+text7, Kmer.recoverKmerFrom(7+6, merged, 0, merged.length));
 
 	}
@@ -113,12 +113,21 @@
 		String text = "AGCTGACCG";
 		Assert.assertEquals(text, Kmer.recoverKmerFrom(9, kmer, 0, kmer.length));
 		
-		byte [] kmerForward = KmerUtil.shiftKmerWithNextCode(9, kmer, Kmer.GENE_CODE.A);
+		byte [] kmerForward = KmerUtil.shiftKmerWithNextCode(9, kmer,0, kmer.length, Kmer.GENE_CODE.A);
 		Assert.assertEquals(text, Kmer.recoverKmerFrom(9, kmer, 0, kmer.length));
 		Assert.assertEquals("GCTGACCGA", Kmer.recoverKmerFrom(9, kmerForward, 0, kmerForward.length));
-		byte [] kmerBackward = KmerUtil.shiftKmerWithPreCode(9, kmer, Kmer.GENE_CODE.C);
+		byte [] kmerBackward = KmerUtil.shiftKmerWithPreCode(9, kmer,0, kmer.length,Kmer.GENE_CODE.C);
 		Assert.assertEquals(text, Kmer.recoverKmerFrom(9, kmer, 0, kmer.length));
 		Assert.assertEquals("CAGCTGACC", Kmer.recoverKmerFrom(9, kmerBackward, 0, kmerBackward.length));
 		
 	}
+	@Test
+	public void TestGetGene(){
+		byte[] kmer = Kmer.compressKmer(9, array, 0);
+		String text = "AGCTGACCG";
+		for(int i =0; i < 9; i++){
+			Assert.assertEquals(text.charAt(i), 
+					(char)(Kmer.GENE_CODE.getSymbolFromCode(KmerUtil.getGeneCodeAtPosition(i, 9, kmer, 0, kmer.length))));
+		}
+	}
 }
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java
index 50146ad..1d772b2 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java
@@ -49,20 +49,18 @@
         precursor = (byte) ((precursor & 0xff) >> 4);
         succeed = (byte) (succeed & adjBitMap);
 
-        byte[] kmerValue = new byte[key.getLength()];
-        for (int i = 0; i < kmerValue.length; i++) {
-            kmerValue[i] = key.getBytes()[i];
-        }
+        byte[] kmerValue = key.getBytes();
+        int kmerLength = key.getLength();
         if (bitFlag == 1) {
             byte succeedCode = GENE_CODE.getGeneCodeFromBitMap(succeed);
             int originalByteNum = Kmer.getByteNumFromK(KMER_SIZE);
-            byte[] tmpKmer = KmerUtil.getLastKmerFromChain(KMER_SIZE, value.getKmerSize(), kmerValue);
-            byte[] newKmer = KmerUtil.shiftKmerWithNextCode(KMER_SIZE, tmpKmer, succeedCode);
+            byte[] tmpKmer = KmerUtil.getLastKmerFromChain(KMER_SIZE, value.getKmerSize(), kmerValue, 0, kmerLength);
+            byte[] newKmer = KmerUtil.shiftKmerWithNextCode(KMER_SIZE, tmpKmer,0, tmpKmer.length, succeedCode);
             outputKmer.set(newKmer, 0, originalByteNum);
 
             int mergeByteNum = Kmer.getByteNumFromK(value.getKmerSize() - (KMER_SIZE - 1));
             byte[] mergeKmer = KmerUtil.getFirstKmerFromChain(value.getKmerSize() - (KMER_SIZE - 1),
-                    value.getKmerSize(), kmerValue);
+                    value.getKmerSize(), kmerValue, 0, kmerLength);
             outputAdjList.set(mergeKmer, 0, mergeByteNum, adjBitMap, bitFlag, value.getKmerSize() - (KMER_SIZE - 1));
             output.collect(outputKmer, outputAdjList);
         } else {
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java
index 0ffc6e0..2397a98 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java
@@ -50,20 +50,18 @@
 
         if (values.hasNext() == true) {
 
-            byte[] keyBytes = new byte[key.getLength()];
-            for (int i = 0; i < keyBytes.length; i++) {
-                keyBytes[i] = key.getBytes()[i];
-            }
+            byte[] keyBytes = key.getBytes();
+            int keyLength = key.getLength();
             if (outputAdjList.getFlag() == 1) {
                 byte adjBitMap = outputAdjList.getAdjBitMap();
                 byte bitFlag = outputAdjList.getFlag();
                 int kmerSize = outputAdjList.getKmerSize();
                 int mergeByteNum = Kmer.getByteNumFromK(KMER_SIZE + kmerSize);
-                byte[] valueBytes = new byte[outputAdjList.getLength()];
-                for (int i = 0; i < valueBytes.length; i++) {
-                    valueBytes[i] = outputAdjList.getBytes()[i];
-                }
-                byte[] mergeKmer = KmerUtil.mergeTwoKmer(outputAdjList.getKmerSize(), valueBytes, KMER_SIZE, keyBytes);
+                byte[] valueBytes = outputAdjList.getBytes();
+                int valueLength = outputAdjList.getLength();
+                
+                byte[] mergeKmer = KmerUtil.mergeTwoKmer(outputAdjList.getKmerSize(), valueBytes,0, valueLength, 
+                		KMER_SIZE, keyBytes, 0, keyLength);
                 outputKmer.set(mergeKmer, 0, mergeByteNum);
 
                 outputAdjList = values.next();
@@ -84,11 +82,10 @@
                 byte flag = outputAdjList.getFlag();
                 int kmerSize = outputAdjList.getKmerSize();
                 int mergeByteNum = Kmer.getByteNumFromK(KMER_SIZE + kmerSize);
-                byte[] valueBytes = new byte[outputAdjList.getLength()];
-                for (int i = 0; i < valueBytes.length; i++) {
-                    valueBytes[i] = outputAdjList.getBytes()[i];
-                }
-                byte[] mergeKmer = KmerUtil.mergeTwoKmer(outputAdjList.getKmerSize(), valueBytes, KMER_SIZE, keyBytes);
+                byte[] valueBytes = outputAdjList.getBytes();
+                int valueLength =outputAdjList.getLength();
+                byte[] mergeKmer = KmerUtil.mergeTwoKmer(outputAdjList.getKmerSize(), valueBytes, 0, valueLength,
+                		KMER_SIZE, keyBytes, 0, keyLength);
                 outputKmer.set(mergeKmer, 0, mergeByteNum);
 
                 adjBitMap = (byte) (adjBitMap & 0xF0);
@@ -98,22 +95,18 @@
                 mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputAdjList);
             }
         } else {
-            byte[] keyBytes = new byte[key.getLength()];
-            for (int i = 0; i < keyBytes.length; i++) {
-                keyBytes[i] = key.getBytes()[i];
-            }
+            byte[] keyBytes = key.getBytes();
+            int keyLength = key.getLength();
             if (outputAdjList.getFlag() != 0) {
                 byte adjBitMap = outputAdjList.getAdjBitMap();
                 byte flag = outputAdjList.getFlag();
                 int kmerSize = outputAdjList.getKmerSize();
                 int mergeByteNum = Kmer.getByteNumFromK(KMER_SIZE - 1 + kmerSize);
-                byte[] tmpKmer = KmerUtil.getFirstKmerFromChain(KMER_SIZE - 1, KMER_SIZE, keyBytes);
-                byte[] valueBytes = new byte[outputAdjList.getLength()];
-                for (int i = 0; i < valueBytes.length; i++) {
-                    valueBytes[i] = outputAdjList.getBytes()[i];
-                }
-                byte[] mergeKmer = KmerUtil.mergeTwoKmer(outputAdjList.getKmerSize(), valueBytes, KMER_SIZE - 1,
-                        tmpKmer);
+                byte[] tmpKmer = KmerUtil.getFirstKmerFromChain(KMER_SIZE - 1, KMER_SIZE, keyBytes,0,keyLength);
+                byte[] valueBytes = outputAdjList.getBytes();
+                int valueLength = outputAdjList.getLength();
+                byte[] mergeKmer = KmerUtil.mergeTwoKmer(outputAdjList.getKmerSize(), valueBytes,0, valueLength,
+                		KMER_SIZE - 1, tmpKmer,0,tmpKmer.length);
                 outputKmer.set(mergeKmer, 0, mergeByteNum);
                 outputAdjList.set(null, 0, 0, adjBitMap, flag, KMER_SIZE + kmerSize);
                 mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputAdjList);
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java
index 3552681..2e25c0d 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java
@@ -105,10 +105,8 @@
         boolean inDegree = measureDegree(precursor);
         boolean outDegree = measureDegree(succeed);
         byte initial = 0;
-        byte[] kmerValue = new byte[key.getLength()];
-        for (int i = 0; i < kmerValue.length; i++) {
-            kmerValue[i] = key.getBytes()[i];
-        }
+        byte[] kmerValue = key.getBytes();
+        int kmerLength = key.getLength();
         if (inDegree == true && outDegree == false) {
             flag = (byte) 2;
             switch (succeed) {
@@ -125,7 +123,7 @@
                     initial = (byte) 0x03;
                     break;
             }
-            byte[] newKmer = KmerUtil.shiftKmerWithNextCode(KMER_SIZE, kmerValue, initial);
+            byte[] newKmer = KmerUtil.shiftKmerWithNextCode(KMER_SIZE, kmerValue,0, kmerLength, initial);
             outputKmer.set(newKmer, 0, kmerValue.length);
             adjBitMap = (byte) (adjBitMap & 0xF0);
             outputAdjList.set(null, 0, 0, adjBitMap, flag, KMER_SIZE);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LogAlgorithmForMergeGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LogAlgorithmForMergeGraphVertex.java
index 19a8fcb..2264301 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LogAlgorithmForMergeGraphVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LogAlgorithmForMergeGraphVertex.java
@@ -70,7 +70,7 @@
 				tmpMsg.setMessage(Message.START);
 				for(byte x = Kmer.GENE_CODE.A; x<= Kmer.GENE_CODE.T ; x++){
 					if((tmpVal.getValue() & (1 << x)) != 0){
-						tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(GraphVertexOperation.k, tmpVertexId, x);
+						tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(GraphVertexOperation.k, tmpVertexId, 0, tmpVertexId.length,x);
 						destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
 						sendMsg(destVertexId,tmpMsg);
 					}
@@ -82,7 +82,7 @@
 				
 				for(byte x = Kmer.GENE_CODE.A; x<= Kmer.GENE_CODE.T ; x++){
 					if(((tmpVal.getValue()>> 4) & (1 << x)) != 0){
-						tmpDestVertexId = KmerUtil.shiftKmerWithPreCode(GraphVertexOperation.k, tmpVertexId, x);
+						tmpDestVertexId = KmerUtil.shiftKmerWithPreCode(GraphVertexOperation.k, tmpVertexId, 0, tmpVertexId.length, x);
 						destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
 						sendMsg(destVertexId,tmpMsg);
 					}
@@ -120,7 +120,7 @@
 		else if(getSuperstep()%3 == 0){
 			if(getSuperstep() == 3){
 				tmpMsg = new LogAlgorithmMessageWritable();
-				tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(GraphVertexOperation.k, tmpVertexId, 
+				tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(GraphVertexOperation.k, tmpVertexId, 0, tmpVertexId.length,
 						Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpVal.getValue() & 0x0F)));
 				destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
 				if(tmpVal.getState() == State.START_VERTEX){
@@ -141,8 +141,8 @@
 					tmpMsg = msgIterator.next();
 					byte[] lastKmer = KmerUtil.getLastKmerFromChain(GraphVertexOperation.k,
 							tmpVal.getLengthOfMergeChain(),
-							tmpVal.getMergeChain());
-					tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(GraphVertexOperation.k, lastKmer, 
+							tmpVal.getMergeChain(),0,tmpVal.getMergeChain().length);
+					tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(GraphVertexOperation.k, lastKmer, 0, lastKmer.length,
 							Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpVal.getValue() & 0x0F))); //tmpMsg.getNeighberInfo()
 					destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
 					if(tmpVal.getState() == State.START_VERTEX){
@@ -222,11 +222,13 @@
 						lengthOfMergeChainVertex = tmpVal.getLengthOfMergeChain(); 
 						mergeChainVertexId = tmpVal.getMergeChain(); 
 					}
+					byte[] tmplastKmer = KmerUtil.getLastKmerFromChain(tmpMsg.getLengthOfChain() - GraphVertexOperation.k + 1,
+							tmpMsg.getLengthOfChain(), tmpMsg.getChainVertexId(),0, tmpMsg.getChainVertexId().length);
 					mergeChainVertexId = KmerUtil.mergeTwoKmer(lengthOfMergeChainVertex, 
-							mergeChainVertexId,
+							mergeChainVertexId, 0, mergeChainVertexId.length,
 							tmpMsg.getLengthOfChain() - GraphVertexOperation.k + 1, 
-							KmerUtil.getLastKmerFromChain(tmpMsg.getLengthOfChain() - GraphVertexOperation.k + 1,
-									tmpMsg.getLengthOfChain(), tmpMsg.getChainVertexId()));
+							tmplastKmer, 0 , tmplastKmer.length
+							);
 					lengthOfMergeChainVertex = lengthOfMergeChainVertex + tmpMsg.getLengthOfChain()
 							- GraphVertexOperation.k + 1;
 					tmpVal.setLengthOfMergeChain(lengthOfMergeChainVertex);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java
index 36dc8a1..7f2cc43 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java
@@ -71,7 +71,7 @@
 				tmpMsg.setChainVertexId(tmpChainVertexId.getBytes());
 				for(byte x = Kmer.GENE_CODE.A; x<= Kmer.GENE_CODE.T ; x++){
 					if((getVertexValue().getValue() & (1 << x)) != 0){
-						tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(GraphVertexOperation.k, tmpVertexId, x);
+						tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(GraphVertexOperation.k, tmpVertexId, 0, tmpVertexId.length, x);
 						destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
 						sendMsg(destVertexId,tmpMsg);
 					}
@@ -99,7 +99,7 @@
 							String source = Kmer.recoverKmerFrom(GraphVertexOperation.k, tmpVertexId, 0, tmpVertexId.length);
 							tmpMsg.setChainVertexId(KmerUtil.mergeKmerWithNextCode(
 									tmpMsg.getLengthOfChain(),
-									tmpMsg.getChainVertexId(),
+									tmpMsg.getChainVertexId(),0, tmpMsg.getChainVertexId().length,
 									Kmer.GENE_CODE.getCodeFromSymbol((byte)source.charAt(source.length() - 1))));
 							tmpMsg.incrementLength();
 							deleteVertex(getVertexId());
@@ -141,8 +141,8 @@
 				if(!tmpMsg.isRear()){
 					byte[] lastKmer = KmerUtil.getLastKmerFromChain(GraphVertexOperation.k,
 							tmpMsg.getLengthOfChain(),
-							tmpMsg.getChainVertexId());
-					tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(GraphVertexOperation.k, lastKmer, 
+							tmpMsg.getChainVertexId(), 0 , tmpMsg.getChainVertexId().length);
+					tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(GraphVertexOperation.k, lastKmer, 0, lastKmer.length,
 							Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpMsg.getNeighberInfo() & 0x0F)));
 
 					tmpMsg.setSourceVertexId(tmpVertexId);