diff --git a/genomix/genomix-hadoop/data/webmap/RemoveBridge.txt b/genomix/genomix-hadoop/data/webmap/RemoveBridge.txt
new file mode 100644
index 0000000..472a7dc
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/RemoveBridge.txt
@@ -0,0 +1,2 @@
+1	AATAG
+2	CACGC
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
index d630b5f..e92eaed 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
@@ -11,63 +11,27 @@
 import edu.uci.ics.genomix.type.KmerBytesWritableFactory;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.client.Client;
 import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MergeBubbleMessageWritable;
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
 import edu.uci.ics.genomix.pregelix.type.AdjMessage;
+import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
 
-/*
- * vertexId: BytesWritable
- * vertexValue: ByteWritable
- * edgeValue: NullWritable
- * message: MessageWritable
- * 
- * DNA:
- * A: 00
- * C: 01
- * G: 10
- * T: 11
- * 
- * succeed node
- *  A 00000001 1
- *  G 00000010 2
- *  C 00000100 4
- *  T 00001000 8
- * precursor node
- *  A 00010000 16
- *  G 00100000 32
- *  C 01000000 64
- *  T 10000000 128
- *  
- * For example, ONE LINE in input file: 00,01,10    0001,0010,
- * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
- * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
- * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
- */
 /**
  * Naive Algorithm for path merge graph
  */
 public class BubbleMergeVertex extends
-        Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MergeBubbleMessageWritable> {
-    public static final String KMER_SIZE = "BubbleMergeVertex.kmerSize";
-    public static final String ITERATIONS = "BubbleMergeVertex.iteration";
-    public static int kmerSize = -1;
-    private int maxIteration = -1;
+    BasicGraphCleanVertex {
 
-    private MergeBubbleMessageWritable incomingMsg = new MergeBubbleMessageWritable();
-    private MergeBubbleMessageWritable outgoingMsg = new MergeBubbleMessageWritable();
     private KmerBytesWritableFactory kmerFactory = new KmerBytesWritableFactory(1);
     
-    private Iterator<PositionWritable> iterator;
-    private PositionWritable pos = new PositionWritable();
-    private PositionWritable destVertexId = new PositionWritable();
-    private Iterator<PositionWritable> posIterator;
-    private Map<PositionWritable, ArrayList<MergeBubbleMessageWritable>> receivedMsgMap = new HashMap<PositionWritable, ArrayList<MergeBubbleMessageWritable>>();
-    private ArrayList<MergeBubbleMessageWritable> receivedMsgList = new ArrayList<MergeBubbleMessageWritable>();
+    private Map<KmerBytesWritable, ArrayList<MessageWritable>> receivedMsgMap = new HashMap<KmerBytesWritable, ArrayList<MessageWritable>>();
+    private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
     
     /**
      * initiate kmerSize, maxIteration
@@ -79,188 +43,39 @@
             maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
         outgoingMsg.reset();
     }
-    /**
-     * get destination vertex
-     */
-    public PositionWritable getNextDestVertexId(VertexValueWritable value) {
-        if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
-            posIterator = value.getFFList().iterator();
-        else // #FRList() > 0
-            posIterator = value.getFRList().iterator();
-        return posIterator.next();
-    }
-    
-    public PositionWritable getPrevDestVertexId(VertexValueWritable value) {
-        if(value.getRFList().getCountOfPosition() > 0) // #FFList() > 0
-            posIterator = value.getRFList().iterator();
-        else // #FRList() > 0
-            posIterator = value.getRRList().iterator();
-        return posIterator.next();
-    }
-
-    /**
-     * check if prev/next destination exists
-     */
-    public boolean hasNextDest(VertexValueWritable value){
-        return value.getFFList().getCountOfPosition() > 0 || value.getFRList().getCountOfPosition() > 0;
-    }
-    
-    public boolean hasPrevDest(VertexValueWritable value){
-        return value.getRFList().getCountOfPosition() > 0 || value.getRRList().getCountOfPosition() > 0;
-    }
-    
-    /**
-     * head send message to all next nodes
-     */
-    public void sendMsgToAllNextNodes(VertexValueWritable value) {
-        posIterator = value.getFFList().iterator(); // FFList
-        while(posIterator.hasNext()){
-            outgoingMsg.setMessage(AdjMessage.FROMFF);
-            destVertexId.set(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-        posIterator = value.getFRList().iterator(); // FRList
-        while(posIterator.hasNext()){
-            outgoingMsg.setMessage(AdjMessage.FROMFR);
-            destVertexId.set(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-    }
-    
-    /**
-     * head send message to all next nodes
-     */
-    public void sendMsgToAllPrevNodes(VertexValueWritable value) {
-        posIterator = value.getRFList().iterator(); // FFList
-        while(posIterator.hasNext()){
-            outgoingMsg.setMessage(AdjMessage.FROMRF);
-            destVertexId.set(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-        posIterator = value.getRRList().iterator(); // FRList
-        while(posIterator.hasNext()){
-            outgoingMsg.setMessage(AdjMessage.FROMRR);
-            destVertexId.set(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-    }
-    
-    /**
-     * broadcast kill self to all neighbers  Pre-condition: vertex is a path vertex 
-     */
-    public void broadcaseKillself(){
-        outgoingMsg.setSourceVertexId(getVertexId());
-        
-        if(getVertexValue().getFFList().getCountOfPosition() > 0){//#FFList() > 0
-            outgoingMsg.setMessage(AdjMessage.FROMFF);
-            sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg);
-        }
-        else if(getVertexValue().getFRList().getCountOfPosition() > 0){//#FRList() > 0
-            outgoingMsg.setMessage(AdjMessage.FROMFR);
-            sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg);
-        }
-        
-        
-        if(getVertexValue().getRFList().getCountOfPosition() > 0){//#RFList() > 0
-            outgoingMsg.setMessage(AdjMessage.FROMRF);
-            sendMsg(incomingMsg.getStartVertexId(), outgoingMsg);
-        }
-        else if(getVertexValue().getRRList().getCountOfPosition() > 0){//#RRList() > 0
-            outgoingMsg.setMessage(AdjMessage.FROMRR);
-            sendMsg(incomingMsg.getStartVertexId(), outgoingMsg);
-        }
-        
-        deleteVertex(getVertexId());
-    }
-    
-    /**
-     * do some remove operations on adjMap after receiving the info about dead Vertex
-     */
-    public void responseToDeadVertex(Iterator<MergeBubbleMessageWritable> msgIterator){
-        while (msgIterator.hasNext()) {
-            incomingMsg = msgIterator.next();
-            if(incomingMsg.getMessage() == AdjMessage.FROMFF){
-                //remove incomingMsg.getSourceId from RR positionList
-                iterator = getVertexValue().getRRList().iterator();
-                while(iterator.hasNext()){
-                    pos = iterator.next();
-                    if(pos.equals(incomingMsg.getSourceVertexId())){
-                        iterator.remove();
-                        break;
-                    }
-                }
-            } else if(incomingMsg.getMessage() == AdjMessage.FROMFR){
-                //remove incomingMsg.getSourceId from RF positionList
-                iterator = getVertexValue().getFRList().iterator();
-                while(iterator.hasNext()){
-                    pos = iterator.next();
-                    if(pos.equals(incomingMsg.getSourceVertexId())){
-                        iterator.remove();
-                        break;
-                    }
-                }
-            } else if(incomingMsg.getMessage() == AdjMessage.FROMRF){
-                //remove incomingMsg.getSourceId from FR positionList
-                iterator = getVertexValue().getRFList().iterator();
-                while(iterator.hasNext()){
-                    pos = iterator.next();
-                    if(pos.equals(incomingMsg.getSourceVertexId())){
-                        iterator.remove();
-                        break;
-                    }
-                }
-            } else{ //incomingMsg.getMessage() == AdjMessage.FROMRR
-                //remove incomingMsg.getSourceId from FF positionList
-                iterator = getVertexValue().getFFList().iterator();
-                while(iterator.hasNext()){
-                    pos = iterator.next();
-                    if(pos.equals(incomingMsg.getSourceVertexId())){
-                        iterator.remove();
-                        break;
-                    }
-                }
-            }
-        }
-    }
     
     @SuppressWarnings("unchecked")
     @Override
-    public void compute(Iterator<MergeBubbleMessageWritable> msgIterator) {
+    public void compute(Iterator<MessageWritable> msgIterator) {
         initVertex();
         if (getSuperstep() == 1) {
             if(VertexUtil.isHeadVertexWithIndegree(getVertexValue())
                     || VertexUtil.isHeadWithoutIndegree(getVertexValue())){
-                outgoingMsg.setSourceVertexId(getVertexId());
-                sendMsgToAllNextNodes(getVertexValue());
+                sendSettledMsgToAllNextNodes(getVertexValue());
             }
-//            if(VertexUtil.isRearVertexWithOutdegree(getVertexValue())
-//                    || VertexUtil.isRearWithoutOutdegree(getVertexValue())){
-//                outgoingMsg.setSourceVertexId(getVertexId());
-//                sendMsgToAllPrevNodes(getVertexValue());
-//            }
         } else if (getSuperstep() == 2){
             while (msgIterator.hasNext()) {
                 incomingMsg = msgIterator.next();
                 if(VertexUtil.isPathVertex(getVertexValue())){
-                    switch(incomingMsg.getMessage()){
-                        case AdjMessage.FROMFF:
-                        case AdjMessage.FROMRF:
+                    byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+                    byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+                    switch(neighborToMeDir){
+                        case MessageFlag.DIR_RF:
+                        case MessageFlag.DIR_RR:
                             if(hasNextDest(getVertexValue())){
-                                outgoingMsg.setMessage(AdjMessage.NON);
                                 outgoingMsg.setStartVertexId(incomingMsg.getSourceVertexId());
                                 outgoingMsg.setSourceVertexId(getVertexId());
-                                outgoingMsg.setChainVertexId(getVertexValue().getKmer());
+                                outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
                                 destVertexId.set(getNextDestVertexId(getVertexValue()));
                                 sendMsg(destVertexId, outgoingMsg);
                             }
                             break;
-                        case AdjMessage.FROMFR:
-                        case AdjMessage.FROMRR:
+                        case MessageFlag.DIR_FF:
+                        case MessageFlag.DIR_FR:
                             if(hasPrevDest(getVertexValue())){
-                                outgoingMsg.setMessage(AdjMessage.NON);
                                 outgoingMsg.setStartVertexId(incomingMsg.getSourceVertexId());
                                 outgoingMsg.setSourceVertexId(getVertexId());
-                                outgoingMsg.setChainVertexId(getVertexValue().getKmer());
+                                outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
                                 destVertexId.set(getPrevDestVertexId(getVertexValue()));
                                 sendMsg(destVertexId, outgoingMsg);
                             }
@@ -274,32 +89,23 @@
                 if(!receivedMsgMap.containsKey(incomingMsg.getStartVertexId())){
                     receivedMsgList.clear();
                     receivedMsgList.add(incomingMsg);
-                    receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MergeBubbleMessageWritable>)receivedMsgList.clone());
+                    receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MessageWritable>)receivedMsgList.clone());
                 }
                 else{
                     receivedMsgList.clear();
                     receivedMsgList.addAll(receivedMsgMap.get(incomingMsg.getStartVertexId()));
                     receivedMsgList.add(incomingMsg);
-                    receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MergeBubbleMessageWritable>)receivedMsgList.clone());
+                    receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MessageWritable>)receivedMsgList.clone());
                 }
             }
-            for(PositionWritable prevId : receivedMsgMap.keySet()){
+            for(KmerBytesWritable prevId : receivedMsgMap.keySet()){
                 receivedMsgList = receivedMsgMap.get(prevId);
                 if(receivedMsgList.size() > 1){
-                    //find the node with largest length of Kmer
-                    boolean flag = true; //the same length
-                    int maxLength = receivedMsgList.get(0).getLengthOfChain();
-                    PositionWritable max = receivedMsgList.get(0).getSourceVertexId();
-                    PositionWritable secondMax = receivedMsgList.get(0).getSourceVertexId();
-                    for(int i = 1; i < receivedMsgList.size(); i++){
-                        if(receivedMsgList.get(i).getLengthOfChain() != maxLength)
-                            flag = false;
-                        if(receivedMsgList.get(i).getLengthOfChain() >= maxLength){
-                            maxLength = receivedMsgList.get(i).getLengthOfChain();
-                            secondMax.set(max);
-                            max = receivedMsgList.get(i).getSourceVertexId();
-                        }
-                    }
+                    /** for each startVertex, sort the node by decreasing order of coverage **/
+                    
+                    /** process similarSet, keep the unchanged set and deleted set & add coverage to unchange node **/
+                    
+                    /** send message to the unchanged set for updating coverage & send kill message to the deleted set **/ 
                     //send unchange or merge Message to node with largest length
                     if(flag == true){
                         //1. send unchange Message to node with largest length
@@ -367,7 +173,7 @@
         job.setVertexInputFormatClass(GraphCleanInputFormat.class);
         job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputKeyClass(KmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
index d4a2355..f201fb1 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
@@ -66,10 +66,10 @@
      * get destination vertex
      */
     public KmerBytesWritable getNextDestVertexId(VertexValueWritable value) {
-        if (value.getFFList().getCountOfPosition() > 0){ // #FFList() > 0
+        if (value.getFFList().getCountOfPosition() > 0){ //#FFList() > 0
             kmerIterator = value.getFFList().iterator();
             return kmerIterator.next();
-        } else if (value.getFRList().getCountOfPosition() > 0){ // #FRList() > 0
+        } else if (value.getFRList().getCountOfPosition() > 0){ //#FRList() > 0
             kmerIterator = value.getFRList().iterator();
             return kmerIterator.next();
         } else {
@@ -77,11 +77,11 @@
         }
     }
 
-    public KmerBytesWritable getPreDestVertexId(VertexValueWritable value) {
-        if (value.getRFList().getCountOfPosition() > 0){ // #RFList() > 0
+    public KmerBytesWritable getPrevDestVertexId(VertexValueWritable value) {
+        if (value.getRFList().getCountOfPosition() > 0){ //#RFList() > 0
             kmerIterator = value.getRFList().iterator();
             return kmerIterator.next();
-        } else if (value.getRRList().getCountOfPosition() > 0){ // #RRList() > 0
+        } else if (value.getRRList().getCountOfPosition() > 0){ //#RRList() > 0
             kmerIterator = value.getRRList().iterator();
             return kmerIterator.next();
         } else {
@@ -109,7 +109,7 @@
         
     }
 
-    public KmerBytesWritable getPreDestVertexIdAndSetFlag(VertexValueWritable value) {
+    public KmerBytesWritable getPrevDestVertexIdAndSetFlag(VertexValueWritable value) {
         if (value.getRFList().getCountOfPosition() > 0){ // #RFList() > 0
             kmerIterator = value.getRFList().iterator();
             outFlag &= MessageFlag.DIR_CLEAR;
@@ -189,7 +189,7 @@
         else if(getVertexValue().getRRList().getCountOfPosition() > 0)
             outgoingMsg.setFlag(MessageFlag.DIR_RR);
         outgoingMsg.setSourceVertexId(getVertexId());
-        destVertexId.set(getPreDestVertexId(getVertexValue()));
+        destVertexId.set(getPrevDestVertexId(getVertexValue()));
         sendMsg(destVertexId, outgoingMsg);
     }
     
@@ -350,8 +350,8 @@
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
-                if(getPreDestVertexId(getVertexValue()) != null)
-                    sendMsg(getPreDestVertexId(getVertexValue()), outgoingMsg);
+                if(getPrevDestVertexId(getVertexValue()) != null)
+                    sendMsg(getPrevDestVertexId(getVertexValue()), outgoingMsg);
                 break; 
         }
     }
@@ -494,7 +494,7 @@
                 outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
                 outgoingMsg.setAcutalKmer(getVertexValue().getKmer());
-                sendMsg(getPreDestVertexId(getVertexValue()), outgoingMsg);
+                sendMsg(getPrevDestVertexId(getVertexValue()), outgoingMsg);
                 deleteVertex(getVertexId());
                 break; 
         }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
index 6e3517b..fc78c34 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
@@ -96,7 +96,7 @@
         }
         
         //send wantToMerge to prev
-        tmpKmer = getPreDestVertexIdAndSetFlag(getVertexValue());
+        tmpKmer = getPrevDestVertexIdAndSetFlag(getVertexValue());
         if(tmpKmer != null){
             destVertexId.set(tmpKmer);
             outgoingMsg.setFlag(outFlag);