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 bc4fc2f..df93069 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
@@ -28,6 +28,7 @@
 import edu.uci.ics.genomix.data.Marshal;
 import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
 
+
 /**
  * Variable-length kmer which stores its length internally.
  * Note: `offset` as used in this class is the offset at which the *kmer*
@@ -497,6 +498,11 @@
         clearLeadBit();
         saveHeader(lettersInKmer);
     }
+    
+    public void mergeWithFFKmer(int kmerSize, KmerBytesWritable kmer) {
+        // TODO make this more efficient
+        mergeWithFFKmer(kmerSize, new VKmerBytesWritable(kmer.toString()));
+    }
 
     /**
      * Merge Kmer with the next connected Kmer, when that Kmer needs to be
@@ -538,6 +544,11 @@
         }
         saveHeader(lettersInKmer);
     }
+    
+    public void mergeWithFRKmer(int kmerSize, KmerBytesWritable kmer) {
+        // TODO make this more efficient
+        mergeWithFRKmer(kmerSize, new VKmerBytesWritable(kmer.toString()));
+    }
 
     /**
      * Merge Kmer with the previous connected Kmer, when that kmer needs to be
@@ -550,10 +561,16 @@
      *            : the previous kmer
      */
     public void mergeWithRFKmer(int initialKmerSize, VKmerBytesWritable preKmer) {
+        // TODO make this more efficient
         VKmerBytesWritable reversed = new VKmerBytesWritable(preKmer.lettersInKmer);
         reversed.setByReadReverse(preKmer.toString().getBytes(), 0);
         mergeWithRRKmer(initialKmerSize, reversed);
     }
+    
+    public void mergeWithRFKmer(int kmerSize, KmerBytesWritable kmer) {
+        // TODO make this more efficient
+        mergeWithRFKmer(kmerSize, new VKmerBytesWritable(kmer.toString()));
+    }
 
     /**
      * Merge Kmer with the previous connected Kmer e.g. AACAACC merge with
@@ -590,6 +607,11 @@
                 bytes, kmerStartOffset, bytesUsed);
         clearLeadBit();
     }
+    
+    public void mergeWithRRKmer(int kmerSize, KmerBytesWritable kmer) {
+        // TODO make this more efficient
+        mergeWithRRKmer(kmerSize, new VKmerBytesWritable(kmer.toString()));
+    }
 
     public void mergeWithKmerInDir(byte dir, int initialKmerSize, VKmerBytesWritable kmer) {
         switch (dir & DirectionFlag.DIR_MASK) {
@@ -609,5 +631,16 @@
                 throw new RuntimeException("Direction not recognized: " + dir);
         }
     }
+    public void mergeWithKmerInDir(byte dir, int initialKmerSize, KmerBytesWritable kmer) {
+        // TODO make this more efficient
+        mergeWithKmerInDir(dir, initialKmerSize, new VKmerBytesWritable(kmer.toString()));
+    }
+
+    public KmerBytesWritable asFixedLengthKmer() {
+        if (lettersInKmer != KmerBytesWritable.getKmerLength()) {
+            throw new IllegalArgumentException("VKmer " + this.toString() + " is not of the same length as the fixed length Kmer (" + KmerBytesWritable.getKmerLength() + " )!");
+        }
+        return new KmerBytesWritable(bytes, kmerStartOffset);
+    }
 
 }
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
index 98f561f..833462c 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
@@ -17,6 +17,7 @@
 import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 @SuppressWarnings("deprecation")
 public class GenomixMapper extends MapReduceBase implements
@@ -49,17 +50,18 @@
     @Override
     public void configure(JobConf job) {
         KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
-        preForwardKmer = new KmerBytesWritable(KMER_SIZE);
-        preReverseKmer = new KmerBytesWritable(KMER_SIZE);
-        curForwardKmer = new KmerBytesWritable(KMER_SIZE);
-        curReverseKmer = new KmerBytesWritable(KMER_SIZE);
-        nextForwardKmer = new KmerBytesWritable(KMER_SIZE);
-        nextReverseKmer = new KmerBytesWritable(KMER_SIZE);
+        KmerBytesWritable.setGlobalKmerLength(KMER_SIZE);
+        preForwardKmer = new KmerBytesWritable();
+        preReverseKmer = new KmerBytesWritable();
+        curForwardKmer = new KmerBytesWritable();
+        curReverseKmer = new KmerBytesWritable();
+        nextForwardKmer = new KmerBytesWritable();
+        nextReverseKmer = new KmerBytesWritable();
         nodeId = new PositionWritable();
         nodeIdList = new PositionListWritable();
-        edgeListForPreKmer = new KmerListWritable(KMER_SIZE);
-        edgeListForNextKmer = new KmerListWritable(KMER_SIZE);
-        outputNode = new NodeWritable(KMER_SIZE);
+        edgeListForPreKmer = new KmerListWritable();
+        edgeListForNextKmer = new KmerListWritable();
+        outputNode = new NodeWritable();
         preKmerDir = KmerDir.FORWARD;
         curKmerDir = KmerDir.FORWARD;
         nextKmerDir = KmerDir.FORWARD;
@@ -86,7 +88,7 @@
             }
             
             /** first kmer **/
-            outputNode.reset(KMER_SIZE);
+            outputNode.reset();
             curForwardKmer.setByRead(array, 0);
             curReverseKmer.setByReadReverse(array, 0);
             curKmerDir = curForwardKmer.compareTo(curReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
@@ -100,7 +102,7 @@
             
             /** middle kmer **/
             for (int i = KMER_SIZE + 1; i < array.length; i++) {
-                outputNode.reset(KMER_SIZE);
+                outputNode.reset();
             	setPreKmerByOldCurKmer();
             	setCurKmerByOldNextKmer();
             	setNextKmer(array[i]);
@@ -114,7 +116,7 @@
             }
             
             /** last kmer **/
-            outputNode.reset(KMER_SIZE);
+            outputNode.reset();
         	setPreKmerByOldCurKmer();
         	setCurKmerByOldNextKmer();
         	//set value.nodeId
@@ -138,12 +140,12 @@
     		case FORWARD:
     			switch(preKmerDir){
     				case FORWARD:
-    				    edgeListForPreKmer.reset(KMER_SIZE);
+    				    edgeListForPreKmer.reset();
     				    edgeListForPreKmer.append(preForwardKmer);
     					outputNode.setRRList(edgeListForPreKmer);
     					break;
     				case REVERSE:
-    				    edgeListForPreKmer.reset(KMER_SIZE);
+    				    edgeListForPreKmer.reset();
     				    edgeListForPreKmer.append(preReverseKmer);
     					outputNode.setRFList(edgeListForPreKmer);
     					break;
@@ -152,12 +154,12 @@
     		case REVERSE:
     			switch(preKmerDir){
     				case FORWARD:
-    				    edgeListForPreKmer.reset(KMER_SIZE);
+    				    edgeListForPreKmer.reset();
     				    edgeListForPreKmer.append(preForwardKmer);
     					outputNode.setFRList(edgeListForPreKmer);
     					break;
     				case REVERSE:
-    				    edgeListForPreKmer.reset(KMER_SIZE);
+    				    edgeListForPreKmer.reset();
     				    edgeListForPreKmer.append(preReverseKmer);
     					outputNode.setFFList(edgeListForPreKmer);
     					break;
@@ -171,12 +173,12 @@
     		case FORWARD:
     			switch(nextKmerDir){
     				case FORWARD:
-    					edgeListForNextKmer.reset(KMER_SIZE);
+    					edgeListForNextKmer.reset();
     					edgeListForNextKmer.append(nextForwardKmer);
     					outputNode.setFFList(edgeListForNextKmer);
     					break;
     				case REVERSE:
-    					edgeListForNextKmer.reset(KMER_SIZE);
+    					edgeListForNextKmer.reset();
     					edgeListForNextKmer.append(nextReverseKmer);
     					outputNode.setFRList(edgeListForNextKmer);
     					break;
@@ -185,12 +187,12 @@
     		case REVERSE:
     			switch(nextKmerDir){
     				case FORWARD:
-    					edgeListForNextKmer.reset(KMER_SIZE);
+    					edgeListForNextKmer.reset();
     					edgeListForNextKmer.append(nextForwardKmer);
     					outputNode.setRFList(edgeListForNextKmer);
     					break;
     				case REVERSE:
-    					edgeListForNextKmer.reset(KMER_SIZE);
+    					edgeListForNextKmer.reset();
     					edgeListForNextKmer.append(nextReverseKmer);
     					outputNode.setRRList(edgeListForNextKmer);
     					break;
@@ -201,7 +203,7 @@
     
     //set preKmer by shifting curKmer with preChar
     public void setPreKmer(byte preChar){
-        preForwardKmer.set(curForwardKmer);
+        preForwardKmer.setAsCopy(curForwardKmer);
         preForwardKmer.shiftKmerWithPreChar(preChar);
         preReverseKmer.setByReadReverse(preForwardKmer.toString().getBytes(), preForwardKmer.getOffset());
         preKmerDir = preForwardKmer.compareTo(preReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
@@ -209,7 +211,7 @@
     
     //set nextKmer by shifting curKmer with nextChar
     public void setNextKmer(byte nextChar){
-        nextForwardKmer.set(curForwardKmer);
+        nextForwardKmer.setAsCopy(curForwardKmer);
         nextForwardKmer.shiftKmerWithNextChar(nextChar);
         nextReverseKmer.setByReadReverse(nextForwardKmer.toString().getBytes(), nextForwardKmer.getOffset());
         nextKmerDir = nextForwardKmer.compareTo(nextReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
@@ -218,15 +220,15 @@
     //old curKmer becomes current preKmer
     public void setPreKmerByOldCurKmer(){
     	preKmerDir = curKmerDir;
-    	preForwardKmer.set(curForwardKmer);
-    	preReverseKmer.set(curReverseKmer);
+    	preForwardKmer.setAsCopy(curForwardKmer);
+    	preReverseKmer.setAsCopy(curReverseKmer);
     }
     
     //old nextKmer becomes current curKmer
     public void setCurKmerByOldNextKmer(){
     	curKmerDir = nextKmerDir;
-    	curForwardKmer.set(nextForwardKmer);
-    	curReverseKmer.set(nextReverseKmer);
+    	curForwardKmer.setAsCopy(nextForwardKmer);
+    	curReverseKmer.setAsCopy(nextReverseKmer);
     }
     
     public void setMapperOutput(OutputCollector<KmerBytesWritable, NodeWritable> output) throws IOException{
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
index 1633c26..f39cdcb 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
@@ -23,15 +23,16 @@
     @Override
     public void configure(JobConf job) {
         KMER_SIZE = GenomixMapper.KMER_SIZE;
-        outputNode = new NodeWritable(KMER_SIZE);
-        tmpNode = new NodeWritable(KMER_SIZE);
+        KmerBytesWritable.setGlobalKmerLength(KMER_SIZE);
+        outputNode = new NodeWritable();
+        tmpNode = new NodeWritable();
     }
     
 	@Override
 	public void reduce(KmerBytesWritable key, Iterator<NodeWritable> values,
 			OutputCollector<KmerBytesWritable, NodeWritable> output,
 			Reporter reporter) throws IOException {
-		outputNode.reset(KMER_SIZE);
+		outputNode.reset();
 		
 		while (values.hasNext()) {
 		    tmpNode.set(values.next());
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
index 8736fe3..b28328f 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
@@ -27,6 +27,7 @@
 import edu.uci.ics.genomix.hadoop.pmcommon.PathNodeInitial.PathNodeFlag;
 import edu.uci.ics.genomix.oldtype.NodeWritable;
 import edu.uci.ics.genomix.oldtype.PositionWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 
 @SuppressWarnings("deprecation")
 public class MergePathsH3 extends Configured implements Tool {
@@ -58,12 +59,14 @@
         private boolean finalMerge;
 
         public void configure(JobConf conf) {
+            KMER_SIZE = conf.getInt("sizeKmer", 0);
+            KmerBytesWritable.setGlobalKmerLength(KMER_SIZE);
+            
             randSeed = conf.getLong("randomSeed", 0);
             randGenerator = new Random(randSeed);
             probBeingRandomHead = conf.getFloat("probBeingRandomHead", 0.5f);
             finalMerge = conf.getBoolean("finalMerge", false);
 
-            KMER_SIZE = conf.getInt("sizeKmer", 0);
             outputValue = new NodeWithFlagWritable(KMER_SIZE);
             outputKey = new PositionWritable();
             curNode = new NodeWritable(KMER_SIZE);
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java
index 83fe200..f1bfec6 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java
@@ -60,7 +60,7 @@
                 // kill this node by NOT mapping it.  Update my neighbors with a suicide note
                 //TODO: update neighbors by removing me from its list
             } else {
-                outputValue.set(MergeMessageFlag.MSG_SELF, curNode);
+                outputValue.setAsCopy(MergeMessageFlag.MSG_SELF, curNode);
                 output.collect(key, value);
             }
         }
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
index 943b505..550cc7c 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
@@ -54,12 +54,12 @@
     public void set(PositionListAndKmerWritable right) {
         this.countOfKmer = right.countOfKmer;
         this.vertexIDList.set(right.vertexIDList);
-        this.kmer.set(right.kmer);
+        this.kmer.setAsCopy(right.kmer);
     }
 
     public void set(PositionListWritable list, KmerBytesWritable kmer) {
         this.vertexIDList.set(list);
-        this.kmer.set(kmer);
+        this.kmer.setAsCopy(kmer);
     }
     
     @Override
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
index 841f9f8..84f9fe0 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
@@ -79,7 +79,7 @@
             private KmerListWritable edgeListForPreKmer = new KmerListWritable();
             private KmerListWritable edgeListForNextKmer = new KmerListWritable();
             private NodeWritable outputNode = new NodeWritable();
-            private NodeWritable outputNode2 = new NodeWritable();
+//            private NodeWritable outputNode2 = new NodeWritable();
 
             private KmerBytesWritable preForwardKmer = new KmerBytesWritable();           
             private KmerBytesWritable preReverseKmer = new KmerBytesWritable();
@@ -148,64 +148,12 @@
                 }
                 
                 /*last kmer*/
-/*                outputNode.reset();
+                outputNode.reset();
                 setPreKmerByOldCurKmer();
                 setCurKmerByOldNextKmer();
                 setnodeId(mateId, readID, 0);//array.length - kmerSize + 1
                 setEdgeListForPreKmer();
-                writeToFrame(writer);*/
-                preKmerDir = curKmerDir;
-                preForwardKmer.setAsCopy(curForwardKmer);
-                preReverseKmer.setAsCopy(curReverseKmer);
-                
-                curKmerDir = nextKmerDir;
-                curForwardKmer.setAsCopy(nextForwardKmer);
-                curReverseKmer.setAsCopy(nextReverseKmer);
-                
-                nodeId.set(mateId, readID, 0);
-                nodeIdList.reset();
-                nodeIdList.append(nodeId);
-                outputNode2.setNodeIdList(nodeIdList);
-                
-                switch(curKmerDir){
-                    case FORWARD:
-                        switch(preKmerDir){
-                            case FORWARD:
-                                edgeListForPreKmer.reset();
-                                edgeListForPreKmer.append(preForwardKmer);
-                                outputNode2.setRRList(edgeListForPreKmer);
-                                break;
-                            case REVERSE:
-                                edgeListForPreKmer.reset();
-                                edgeListForPreKmer.append(preReverseKmer);
-                                outputNode2.setRFList(edgeListForPreKmer);
-                                break;
-                        }
-                        break;
-                    case REVERSE:
-                        switch(preKmerDir){
-                            case FORWARD:
-                                edgeListForPreKmer.reset();
-                                edgeListForPreKmer.append(preForwardKmer);
-                                outputNode2.setFRList(edgeListForPreKmer);
-                                break;
-                            case REVERSE:
-                                edgeListForPreKmer.reset();
-                                edgeListForPreKmer.append(preReverseKmer);
-                                outputNode2.setFFList(edgeListForPreKmer);
-                                break;
-                        }
-                        break;
-                }
-                
-                switch(curKmerDir){
-                    case FORWARD:
-                        InsertToFrame(curForwardKmer, outputNode2, writer);
-                        break;
-                    case REVERSE:
-                        InsertToFrame(curReverseKmer, outputNode2, writer);
-                        break;
-                }
+                writeToFrame(writer);
             }
             
             public void setnodeId(byte mateId, long readID, int posId){
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
index e36e344..e8a72ce 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
@@ -60,7 +60,7 @@
             /**
              * set the src vertex id
              */
-            vertexId.set(getRecordReader().getCurrentKey());
+            vertexId.setAsCopy(getRecordReader().getCurrentKey());
             vertex.setVertexId(vertexId);
             /**
              * set the vertex value
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
index 0d685de..4dfff11 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
@@ -11,6 +11,7 @@
 import edu.uci.ics.pregelix.api.io.VertexReader;
 import edu.uci.ics.pregelix.api.util.BspUtils;
 import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
@@ -64,19 +65,20 @@
             /**
              * set the src vertex id
              */
-            vertexId.set(getRecordReader().getCurrentKey());
+            vertexId.setAsCopy(getRecordReader().getCurrentKey());
             vertex.setVertexId(vertexId);
             /**
              * set the vertex value
              */
             node.set(getRecordReader().getCurrentValue());
-            vertexValue.setKmerlength(node.getKmerlength());
+            vertexValue.setKmerlength(node.getKmerLength());
             vertexValue.setNodeIdList(node.getNodeIdList());
             vertexValue.setFFList(node.getFFList());
             vertexValue.setFRList(node.getFRList());
             vertexValue.setRFList(node.getRFList());
             vertexValue.setRRList(node.getRRList());
-            vertexValue.setKmer(getRecordReader().getCurrentKey());
+            // TODO make this more efficient (don't use toString)
+            vertexValue.setKmer(new VKmerBytesWritable(getRecordReader().getCurrentKey().toString()));
             vertexValue.setState(State.IS_NON);
             vertex.setVertexValue(vertexValue);
         }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
index c35ad7f..b19a0cf 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
@@ -19,13 +19,13 @@
     }
     
     public AdjacencyListWritable(int kmerSize){
-        forwardList = new KmerListWritable(kmerSize);
-        reverseList = new KmerListWritable(kmerSize);
+        forwardList = new KmerListWritable();
+        reverseList = new KmerListWritable();
     }
 
     public void set(AdjacencyListWritable adjacencyList){
-        forwardList.set(adjacencyList.getForwardList());
-        reverseList.set(adjacencyList.getReverseList());
+        forwardList.setCopy(adjacencyList.getForwardList());
+        reverseList.setCopy(adjacencyList.getReverseList());
     }
     
     public void reset(){
@@ -34,8 +34,8 @@
     }
     
     public void reset(int kmerSize){
-        forwardList.reset(kmerSize);
-        reverseList.reset(kmerSize);
+        forwardList.reset();
+        reverseList.reset();
     }
     
     public int getCountOfPosition(){
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
index c3b4710..9fd15dd 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
@@ -27,7 +27,7 @@
 
     public MergeBubbleMessageWritable() {
         sourceVertexId = new PositionWritable();
-        chainVertexId = new KmerBytesWritable(0);
+        chainVertexId = new KmerBytesWritable();
         neighberNode = new AdjacencyListWritable();
         startVertexId = new PositionWritable();
         message = Message.NON;
@@ -42,7 +42,7 @@
         }
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.CHAIN;
-            this.chainVertexId.set(msg.getChainVertexId());
+            this.chainVertexId.setAsCopy(msg.getChainVertexId());
         }
         if (neighberNode != null) {
             checkMessage |= CheckMessage.NEIGHBER;
@@ -63,7 +63,7 @@
         }
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.CHAIN;
-            this.chainVertexId.set(chainVertexId);
+            this.chainVertexId.setAsCopy(chainVertexId);
         }
         if (neighberNode != null) {
             checkMessage |= CheckMessage.NEIGHBER;
@@ -78,7 +78,7 @@
 
     public void reset() {
         checkMessage = 0;
-        chainVertexId.reset(1);
+//        chainVertexId.reset();
         neighberNode.reset();
         message = Message.NON;
     }
@@ -101,7 +101,7 @@
     public void setChainVertexId(KmerBytesWritable chainVertexId) {
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.CHAIN;
-            this.chainVertexId.set(chainVertexId);
+            this.chainVertexId.setAsCopy(chainVertexId);
         }
     }
     
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
index 6356715..d9177e2 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
@@ -28,7 +28,7 @@
 
     public MessageWritable() {
         sourceVertexId = new KmerBytesWritable();
-        kmer = new KmerBytesWritable(0);
+        kmer = new KmerBytesWritable();
         neighberNode = new AdjacencyListWritable();
         flag = Message.NON;
         isFlip = false;
@@ -38,7 +38,7 @@
     public MessageWritable(int kmerSize) {
         kmerlength = kmerSize;
         sourceVertexId = new KmerBytesWritable();
-        kmer = new KmerBytesWritable(0);
+        kmer = new KmerBytesWritable();
         neighberNode = new AdjacencyListWritable(kmerSize);
         flag = Message.NON;
         isFlip = false;
@@ -50,11 +50,11 @@
         checkMessage = 0;
         if (sourceVertexId != null) {
             checkMessage |= CheckMessage.SOURCE;
-            this.sourceVertexId.set(msg.getSourceVertexId());
+            this.sourceVertexId.setAsCopy(msg.getSourceVertexId());
         }
         if (kmer != null) {
             checkMessage |= CheckMessage.CHAIN;
-            this.kmer.set(msg.getKmer());
+            this.kmer.setAsCopy(msg.getKmer());
         }
         if (neighberNode != null) {
             checkMessage |= CheckMessage.NEIGHBER;
@@ -70,11 +70,11 @@
         checkMessage = 0;
         if (sourceVertexId != null) {
             checkMessage |= CheckMessage.SOURCE;
-            this.sourceVertexId.set(sourceVertexId);
+            this.sourceVertexId.setAsCopy(sourceVertexId);
         }
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.CHAIN;
-            this.kmer.set(chainVertexId);
+            this.kmer.setAsCopy(chainVertexId);
         }
         if (neighberNode != null) {
             checkMessage |= CheckMessage.NEIGHBER;
@@ -90,7 +90,7 @@
     public void reset(int kmerSize) {
         checkMessage = (byte) 0;
         kmerlength = kmerSize;
-        kmer.reset(1);
+//        kmer.reset();
         neighberNode.reset(kmerSize);
         flag = Message.NON;
         isFlip = false;
@@ -103,7 +103,7 @@
     public void setSourceVertexId(KmerBytesWritable sourceVertexId) {
         if (sourceVertexId != null) {
             checkMessage |= CheckMessage.SOURCE;
-            this.sourceVertexId.set(sourceVertexId);
+            this.sourceVertexId.setAsCopy(sourceVertexId);
         }
     }
     
@@ -114,7 +114,7 @@
     public void setChainVertexId(KmerBytesWritable chainVertexId) {
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.CHAIN;
-            this.kmer.set(chainVertexId);
+            this.kmer.setAsCopy(chainVertexId);
         }
     }
     
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index 065bfd5..60ad003 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -7,6 +7,7 @@
 import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.genomix.type.KmerListWritable;
 
 public class VertexValueWritable implements WritableComparable<VertexValueWritable> {
@@ -39,8 +40,8 @@
     private AdjacencyListWritable incomingList;
     private AdjacencyListWritable outgoingList;
     private byte state;
-    private KmerBytesWritable kmer;
-    private KmerBytesWritable mergeDest;
+    private VKmerBytesWritable kmer;
+    private VKmerBytesWritable mergeDest;
     private int kmerlength = 0;
 
     public VertexValueWritable() {
@@ -53,13 +54,13 @@
         incomingList = new AdjacencyListWritable();
         outgoingList = new AdjacencyListWritable();
         state = State.IS_NON;
-        kmer = new KmerBytesWritable(kmerSize);
-        mergeDest = new KmerBytesWritable(kmerSize);
+        kmer = new VKmerBytesWritable();
+        mergeDest = new VKmerBytesWritable();
     }
 
     public VertexValueWritable(PositionListWritable nodeIdList, KmerListWritable forwardForwardList, KmerListWritable forwardReverseList,
             KmerListWritable reverseForwardList, KmerListWritable reverseReverseList,
-            byte state, KmerBytesWritable kmer) {
+            byte state, VKmerBytesWritable kmer) {
         set(nodeIdList, forwardForwardList, forwardReverseList, 
                 reverseForwardList, reverseReverseList,
                 state, kmer);
@@ -67,14 +68,14 @@
     
     public void set(PositionListWritable nodeIdList, KmerListWritable forwardForwardList, KmerListWritable forwardReverseList,
             KmerListWritable reverseForwardList, KmerListWritable reverseReverseList, 
-            byte state, KmerBytesWritable kmer) {
-        this.kmerlength = kmer.kmerByteSize;
+            byte state, VKmerBytesWritable kmer) {
+        this.kmerlength = kmer.getKmerLetterLength();
         this.incomingList.setForwardList(reverseForwardList);
         this.incomingList.setReverseList(reverseReverseList);
         this.outgoingList.setForwardList(forwardForwardList);
         this.outgoingList.setReverseList(forwardReverseList);
         this.state = state;
-        this.kmer.set(kmer);
+        this.kmer.setAsCopy(kmer);
     }
     
     public void set(VertexValueWritable value) {
@@ -149,22 +150,22 @@
     }
 
     public int getLengthOfKmer() {
-        return kmer.getKmerLength();
+        return kmer.getKmerLetterLength();
     }
 
-    public KmerBytesWritable getKmer() {
+    public VKmerBytesWritable getKmer() {
         return kmer;
     }
 
-    public void setKmer(KmerBytesWritable kmer) {
-        this.kmer.set(kmer);
+    public void setKmer(VKmerBytesWritable kmer) {
+        this.kmer.setAsCopy(kmer);
     }
     
-    public KmerBytesWritable getMergeDest() {
+    public VKmerBytesWritable getMergeDest() {
         return mergeDest;
     }
 
-    public void setMergeDest(KmerBytesWritable mergeDest) {
+    public void setMergeDest(VKmerBytesWritable mergeDest) {
         this.mergeDest = mergeDest;
     }
     
@@ -180,11 +181,11 @@
     public void reset(int kmerSize) {
         this.kmerlength = kmerSize;
         this.nodeIdList.reset();
-        this.incomingList.getForwardList().reset(kmerSize);
-        this.incomingList.getReverseList().reset(kmerSize);
-        this.outgoingList.getForwardList().reset(kmerSize);
-        this.outgoingList.getReverseList().reset(kmerSize);
-        this.kmer.reset(0);
+        this.incomingList.getForwardList().reset();
+        this.incomingList.getReverseList().reset();
+        this.outgoingList.getForwardList().reset();
+        this.outgoingList.getReverseList().reset();
+//        this.kmer.reset(0);
     }
     
     @Override
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java
index bb60a25..95e070f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java
@@ -4,7 +4,7 @@
 import java.util.logging.Handler;
 import java.util.logging.LogRecord;
 
-import edu.uci.ics.genomix.oldtype.NodeWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
 
 public class DataLoadLogFormatter extends Formatter {
     private NodeWritable key;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
index 5f6440f..7d6a1b9 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
@@ -12,11 +12,11 @@
     // Create a DateFormat to format the logger timestamp.
     //
     private long step;
-    private KmerBytesWritable sourceVertexId = new KmerBytesWritable(1);
-    private KmerBytesWritable destVertexId = new KmerBytesWritable(1);
+    private KmerBytesWritable sourceVertexId = new KmerBytesWritable();
+    private KmerBytesWritable destVertexId = new KmerBytesWritable();
     private MessageWritable msg = new MessageWritable();
     private byte state;
-    private KmerBytesWritable mergeChain = new KmerBytesWritable(1);;
+    private KmerBytesWritable mergeChain = new KmerBytesWritable();
     //private boolean testDelete = false;
     /**
      * 0: general operation
@@ -32,8 +32,8 @@
     public void set(long step, KmerBytesWritable sourceVertexId, KmerBytesWritable destVertexId,
             MessageWritable msg, byte state) {
         this.step = step;
-        this.sourceVertexId.set(sourceVertexId);
-        this.destVertexId.set(destVertexId);
+        this.sourceVertexId.setAsCopy(sourceVertexId);
+        this.destVertexId.setAsCopy(destVertexId);
         this.msg = msg;
         this.state = state;
         this.operation = 0;
@@ -42,24 +42,24 @@
     public void setMergeChain(long step, KmerBytesWritable sourceVertexId, KmerBytesWritable mergeChain) {
         this.reset();
         this.step = step;
-        this.sourceVertexId.set(sourceVertexId);
-        this.mergeChain.set(mergeChain);
+        this.sourceVertexId.setAsCopy(sourceVertexId);
+        this.mergeChain.setAsCopy(mergeChain);
         this.operation = 2;
     }
 
     public void setVotoToHalt(long step, KmerBytesWritable sourceVertexId) {
         this.reset();
         this.step = step;
-        this.sourceVertexId.set(sourceVertexId);
+        this.sourceVertexId.setAsCopy(sourceVertexId);
         this.operation = 3;
     }
 
     public void reset() {
-        this.sourceVertexId = new KmerBytesWritable(1);
-        this.destVertexId = new KmerBytesWritable(1);
+        this.sourceVertexId = new KmerBytesWritable();
+        this.destVertexId = new KmerBytesWritable();
         this.msg = new MessageWritable();
         this.state = 0;
-        this.mergeChain = new KmerBytesWritable(1);
+        this.mergeChain = new KmerBytesWritable();
     }
 
     public String format(LogRecord record) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
index 4a5850a..6b23074 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
@@ -15,8 +15,8 @@
 
     public void set(long step, KmerBytesWritable sourceVertexId, KmerBytesWritable destVertexId) {
         this.step = step;
-        this.sourceVertexId.set(sourceVertexId);
-        this.destVertexId.set(destVertexId);
+        this.sourceVertexId.setAsCopy(sourceVertexId);
+        this.destVertexId.setAsCopy(destVertexId);
     }
 
     public String format(LogRecord record) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
index ec608c5..1beee03 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
@@ -30,7 +30,7 @@
     protected MessageWritable outgoingMsg = null; 
     protected KmerBytesWritable destVertexId = new KmerBytesWritable();
     protected Iterator<KmerBytesWritable> posIterator;
-    private KmerBytesWritable kmer = new KmerBytesWritable(kmerSize);
+    private KmerBytesWritable kmer = new KmerBytesWritable();
     byte headFlag;
     protected byte outFlag;
     protected byte inFlag;
@@ -133,12 +133,12 @@
     public void sendMsgToAllNextNodes(VertexValueWritable value) {
         posIterator = value.getFFList().iterator(); // FFList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         posIterator = value.getFRList().iterator(); // FRList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -149,12 +149,12 @@
     public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
         posIterator = value.getRFList().iterator(); // RFList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         posIterator = value.getRRList().iterator(); // RRList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -165,22 +165,22 @@
     public void sendMsgToAllNeighborNodes(VertexValueWritable value){
         posIterator = value.getFFList().iterator(); // FFList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         posIterator = value.getFRList().iterator(); // FRList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         posIterator = value.getFFList().iterator(); // FFList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         posIterator = value.getFRList().iterator(); // FRList
         while(posIterator.hasNext()){
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -193,14 +193,14 @@
         while(posIterator.hasNext()){
             outgoingMsg.setFlag(AdjMessage.FROMFF);
             outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         posIterator = value.getFRList().iterator(); // FRList
         while(posIterator.hasNext()){
             outgoingMsg.setFlag(AdjMessage.FROMFR);
             outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -213,14 +213,14 @@
         while(posIterator.hasNext()){
             outgoingMsg.setFlag(AdjMessage.FROMRF);
             outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
         posIterator = value.getRRList().iterator(); // RRList
         while(posIterator.hasNext()){
             outgoingMsg.setFlag(AdjMessage.FROMRR);
             outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.set(posIterator.next());
+            destVertexId.setAsCopy(posIterator.next());
             sendMsg(destVertexId, outgoingMsg);
         }
     }
@@ -397,7 +397,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setChainVertexId(getVertexValue().getKmer());
+                outgoingMsg.setChainVertexId(getVertexValue().getKmer().asFixedLengthKmer());
                 sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getNextDestVertexId(getVertexValue())
                 break;
             case MessageFlag.DIR_RF:
@@ -410,7 +410,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setChainVertexId(getVertexValue().getKmer());
+                outgoingMsg.setChainVertexId(getVertexValue().getKmer().asFixedLengthKmer());
                 sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getPreDestVertexId(getVertexValue())
                 break; 
         }
@@ -437,7 +437,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setChainVertexId(getVertexValue().getKmer());
+                outgoingMsg.setChainVertexId(getVertexValue().getKmer().asFixedLengthKmer());
                 sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getNextDestVertexId(getVertexValue())
                 break;
             case MessageFlag.DIR_RF:
@@ -450,7 +450,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setChainVertexId(getVertexValue().getKmer());
+                outgoingMsg.setChainVertexId(getVertexValue().getKmer().asFixedLengthKmer());
                 sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getPreDestVertexId(getVertexValue())
                 break; 
         }
@@ -473,7 +473,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setChainVertexId(getVertexValue().getKmer());
+                outgoingMsg.setChainVertexId(getVertexValue().getKmer().asFixedLengthKmer());
                 sendMsg(getNextDestVertexId(getVertexValue()), outgoingMsg);
                 deleteVertex(getVertexId());
                 break;
@@ -486,7 +486,7 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                outgoingMsg.setChainVertexId(getVertexValue().getKmer());
+                outgoingMsg.setChainVertexId(getVertexValue().getKmer().asFixedLengthKmer());
                 sendMsg(getPreDestVertexId(getVertexValue()), outgoingMsg);
                 deleteVertex(getVertexId());
                 break; 
@@ -646,7 +646,7 @@
                 match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
                 msgString = msg.getKmer().toString();
                 index = msgString.indexOf(match);
-                kmer.reset(msgString.length() - index);
+//                kmer.reset(msgString.length() - index);
                 kmer.setByRead(msgString.substring(index).getBytes(), 0);
                 break;
             case MessageFlag.DIR_FR:
@@ -654,7 +654,7 @@
                 match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
                 msgString = GeneCode.reverseComplement(msg.getKmer().toString());
                 index = msgString.indexOf(match);
-                kmer.reset(msgString.length() - index);
+//                kmer.reset(msgString.length() - index);
                 kmer.setByReadReverse(msgString.substring(index).getBytes(), 0);
                 break;
             case MessageFlag.DIR_RF:
@@ -662,7 +662,7 @@
                 match = selfString.substring(0,kmerSize - 1); 
                 msgString = GeneCode.reverseComplement(msg.getKmer().toString());
                 index = msgString.lastIndexOf(match) + kmerSize - 2;
-                kmer.reset(index + 1);
+//                kmer.reset(index + 1);
                 kmer.setByReadReverse(msgString.substring(0, index + 1).getBytes(), 0);
                 break;
             case MessageFlag.DIR_RR:
@@ -670,7 +670,7 @@
                 match = selfString.substring(0,kmerSize - 1); 
                 msgString = msg.getKmer().toString();
                 index = msgString.lastIndexOf(match) + kmerSize - 2;
-                kmer.reset(index + 1);
+//                kmer.reset(index + 1);
                 kmer.setByRead(msgString.substring(0, index + 1).getBytes(), 0);
                 System.out.println(kmer.toString());
                 break;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
index 3b5a782..b6f2164 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
@@ -73,7 +73,7 @@
         //send wantToMerge to next
         tmpKmer = getNextDestVertexIdAndSetFlag(getVertexValue());
         if(tmpKmer != null){
-            destVertexId.set(tmpKmer);
+            destVertexId.setAsCopy(tmpKmer);
             outgoingMsg.setFlag(outFlag);
             outgoingMsg.setSourceVertexId(getVertexId());
             sendMsg(destVertexId, outgoingMsg);
@@ -82,7 +82,7 @@
         //send wantToMerge to prev
         tmpKmer = getPreDestVertexIdAndSetFlag(getVertexValue());
         if(tmpKmer != null){
-            destVertexId.set(tmpKmer);
+            destVertexId.setAsCopy(tmpKmer);
             outgoingMsg.setFlag(outFlag);
             outgoingMsg.setSourceVertexId(getVertexId());
             sendMsg(destVertexId, outgoingMsg);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
index a65f556..53e46af 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
@@ -60,7 +60,7 @@
     private MessageWritable outgoingMsg = new MessageWritable();
   
     private KmerBytesWritableFactory kmerFactory = new KmerBytesWritableFactory(1);
-    private KmerBytesWritable lastKmer = new KmerBytesWritable(1);
+    private KmerBytesWritable lastKmer = new KmerBytesWritable();
     
     private PositionWritable destVertexId = new PositionWritable();
     private Iterator<PositionWritable> posIterator;
@@ -184,7 +184,7 @@
      */
     public void mergeChainVertex() {
         //merge chain
-        lastKmer.set(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
+        lastKmer.setAsCopy(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
                 incomingMsg.getKmer()));
         getVertexValue().setKmer(kmerFactory.mergeTwoKmer(getVertexValue().getKmer(), lastKmer));
         getVertexValue().setOutgoingList(incomingMsg.getNeighberNode());
@@ -225,7 +225,7 @@
         outgoingMsg.setChainVertexId(getVertexValue().getKmer());
         if (getVertexValue().getState() == State.IS_HEAD)//is_tail
             outgoingMsg.setFlag(Message.STOP);
-        destVertexId.set(incomingMsg.getSourceVertexId());
+        destVertexId.setAsCopy(incomingMsg.getSourceVertexId());
         sendMsg(destVertexId, outgoingMsg);
     }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
index f2bb3db..fd3a1db 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
@@ -230,7 +230,7 @@
      * merge chain vertex
      */
     public void mergeChainVertex(){
-        lastKmer.set(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
+        lastKmer.setAsCopy(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
                 incomingMsg.getKmer()));
         getVertexValue().setKmer(
                 kmerFactory.mergeTwoKmer(getVertexValue().getKmer(), 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
index c473867..7a22d25 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
@@ -111,12 +111,12 @@
      */
     protected boolean setNextInfo(VertexValueWritable value) {
         if (value.getFFList().getCountOfPosition() > 0) {
-            nextKmer.set(value.getFFList().getPosition(0));
+            nextKmer.setAsCopy(value.getFFList().getPosition(0));
             nextHead = isNodeRandomHead(nextKmer);
             return true;
         }
         if (value.getFRList().getCountOfPosition() > 0) {
-            nextKmer.set(value.getFRList().getPosition(0));
+            nextKmer.setAsCopy(value.getFRList().getPosition(0));
             nextHead = isNodeRandomHead(nextKmer);
             return true;
         }
@@ -128,12 +128,12 @@
      */
     protected boolean setPrevInfo(VertexValueWritable value) {
         if (value.getRRList().getCountOfPosition() > 0) {
-            prevKmer.set(value.getRRList().getPosition(0));
+            prevKmer.setAsCopy(value.getRRList().getPosition(0));
             prevHead = isNodeRandomHead(prevKmer);
             return true;
         }
         if (value.getRFList().getCountOfPosition() > 0) {
-            prevKmer.set(value.getRFList().getPosition(0));
+            prevKmer.setAsCopy(value.getRFList().getPosition(0));
             prevHead = isNodeRandomHead(prevKmer);
             return true;
         }
@@ -156,7 +156,7 @@
             setStateAsNoMerge();
             
             // only PATH vertices are present. Find the ID's for my neighbors
-            curKmer.set(getVertexId());
+            curKmer.setAsCopy(getVertexId());
             
             curHead = isNodeRandomHead(curKmer);
             
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
index 8a2a301..7f8a832 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
@@ -113,12 +113,12 @@
      */
     protected boolean setNextInfo(VertexValueWritable value) {
         if (value.getFFList().getCountOfPosition() > 0) {
-            nextID.set(value.getFFList().getPosition(0));
+            nextID.setAsCopy(value.getFFList().getPosition(0));
             nextHead = isNodeRandomHead(nextID);
             return true;
         }
         if (value.getFRList().getCountOfPosition() > 0) {
-            nextID.set(value.getFRList().getPosition(0));
+            nextID.setAsCopy(value.getFRList().getPosition(0));
             nextHead = isNodeRandomHead(nextID);
             return true;
         }
@@ -130,12 +130,12 @@
      */
     protected boolean setPrevInfo(VertexValueWritable value) {
         if (value.getRRList().getCountOfPosition() > 0) {
-            prevID.set(value.getRRList().getPosition(0));
+            prevID.setAsCopy(value.getRRList().getPosition(0));
             prevHead = isNodeRandomHead(prevID);
             return true;
         }
         if (value.getRFList().getCountOfPosition() > 0) {
-            prevID.set(value.getRFList().getPosition(0));
+            prevID.setAsCopy(value.getRFList().getPosition(0));
             prevHead = isNodeRandomHead(prevID);
             return true;
         }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
index 7141ae7..9b83d19 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
@@ -71,7 +71,7 @@
             		else if(getVertexValue().getFRList().getCountOfPosition() > 0)
             			outgoingMsg.setFlag(AdjMessage.FROMFR);
             		outgoingMsg.setSourceVertexId(getVertexId());
-            		destVertexId.set(getNextDestVertexId(getVertexValue()));
+            		destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
             		sendMsg(destVertexId, outgoingMsg);
             		deleteVertex(getVertexId());
             	}
@@ -83,7 +83,7 @@
                     else if(getVertexValue().getRRList().getCountOfPosition() > 0)
                         outgoingMsg.setFlag(AdjMessage.FROMRR);
                     outgoingMsg.setSourceVertexId(getVertexId());
-                    destVertexId.set(getPreDestVertexId(getVertexValue()));
+                    destVertexId.setAsCopy(getPreDestVertexId(getVertexValue()));
                     sendMsg(destVertexId, outgoingMsg);
                     deleteVertex(getVertexId());
                 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
index 6b9eb4e..d3180c8 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
@@ -28,7 +28,8 @@
         SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
         SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf, outFile, KmerBytesWritable.class,
                 NullWritable.class, CompressionType.NONE);
-        KmerBytesWritable outKey = new KmerBytesWritable(55);
+        KmerBytesWritable.setGlobalKmerLength(55);
+        KmerBytesWritable outKey = new KmerBytesWritable();
         int i = 0;
 
         for (i = 0; i < numOfLines; i++) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
index bc08600..8618237 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
@@ -19,6 +19,7 @@
 public class GenerateTextFile {
 
     public static void generateFromPathmergeResult(int kmerSize, String strSrcDir, String outPutDir) throws IOException {
+        KmerBytesWritable.setGlobalKmerLength(kmerSize);
         Configuration conf = new Configuration();
         FileSystem fileSys = FileSystem.getLocal(conf);
 
@@ -44,13 +45,14 @@
     }
 
     public static void generateSpecificLengthChainFromNaivePathmergeResult(int maxLength) throws IOException {
+        KmerBytesWritable.setGlobalKmerLength(55);
         BufferedWriter bw = new BufferedWriter(new FileWriter("naive_text_" + maxLength));
         Configuration conf = new Configuration();
         FileSystem fileSys = FileSystem.get(conf);
         for (int i = 0; i < 2; i++) {
             Path path = new Path("/home/anbangx/genomix_result/final_naive/part-" + i);
             SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
-            KmerBytesWritable key = new KmerBytesWritable(55);
+            KmerBytesWritable key = new KmerBytesWritable();
             VertexValueWritable value = new VertexValueWritable();
 
             while (reader.next(key, value)) {
@@ -68,13 +70,14 @@
     }
 
     public static void generateSpecificLengthChainFromLogPathmergeResult(int maxLength) throws IOException {
+        KmerBytesWritable.setGlobalKmerLength(55);
         BufferedWriter bw = new BufferedWriter(new FileWriter("log_text_" + maxLength));
         Configuration conf = new Configuration();
         FileSystem fileSys = FileSystem.get(conf);
         for (int i = 0; i < 2; i++) {
             Path path = new Path("/home/anbangx/genomix_result/improvelog2/part-" + i);
             SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
-            KmerBytesWritable key = new KmerBytesWritable(55);
+            KmerBytesWritable key = new KmerBytesWritable();
             VertexValueWritable value = new VertexValueWritable();
 
             while (reader.next(key, value)) {
@@ -93,12 +96,13 @@
     }
 
     public static void generateFromGraphbuildResult() throws IOException {
+        KmerBytesWritable.setGlobalKmerLength(55);
         BufferedWriter bw = new BufferedWriter(new FileWriter("textfile"));
         Configuration conf = new Configuration();
         FileSystem fileSys = FileSystem.get(conf);
         Path path = new Path("data/input/part-0-out-3000000");
         SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
-        KmerBytesWritable key = new KmerBytesWritable(55);
+        KmerBytesWritable key = new KmerBytesWritable();
 
         while (reader.next(key, null)) {
             if (key == null) {