diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexInputFormat.java
index d3d52f3..65458c0 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexInputFormat.java
@@ -13,7 +13,7 @@
 
 import edu.uci.ics.pregelix.api.io.VertexInputFormat;
 import edu.uci.ics.pregelix.api.io.VertexReader;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
 
 public class BinaryDataCleanVertexInputFormat<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
@@ -38,7 +38,7 @@
     public static abstract class BinaryDataCleanVertexReader<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
             implements VertexReader<I, V, E, M> {
         /** Internal line record reader */
-        private final RecordReader<PositionWritable, ValueStateWritable> lineRecordReader;
+        private final RecordReader<PositionWritable, VertexValueWritable> lineRecordReader;
         /** Context passed to initialize */
         private TaskAttemptContext context;
 
@@ -48,7 +48,7 @@
          * @param recordReader
          *            Line record reader from SequenceFileInputFormat
          */
-        public BinaryDataCleanVertexReader(RecordReader<PositionWritable, ValueStateWritable> recordReader) {
+        public BinaryDataCleanVertexReader(RecordReader<PositionWritable, VertexValueWritable> recordReader) {
             this.lineRecordReader = recordReader;
         }
 
@@ -74,7 +74,7 @@
          * 
          * @return Record reader to be used for reading.
          */
-        protected RecordReader<PositionWritable, ValueStateWritable> getRecordReader() {
+        protected RecordReader<PositionWritable, VertexValueWritable> getRecordReader() {
             return lineRecordReader;
         }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexOutputFormat.java
index efe41d6..65c7d94 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexOutputFormat.java
@@ -10,7 +10,7 @@
 import org.apache.hadoop.mapreduce.TaskAttemptContext;
 import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
 
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
 import edu.uci.ics.pregelix.api.io.VertexOutputFormat;
 import edu.uci.ics.pregelix.api.io.VertexWriter;
@@ -49,7 +49,7 @@
         /** Context passed to initialize */
         private TaskAttemptContext context;
         /** Internal line record writer */
-        private final RecordWriter<PositionWritable, ValueStateWritable> lineRecordWriter;
+        private final RecordWriter<PositionWritable, VertexValueWritable> lineRecordWriter;
 
         /**
          * Initialize with the LineRecordWriter.
@@ -57,7 +57,7 @@
          * @param lineRecordWriter
          *            Line record writer from SequenceFileOutputFormat
          */
-        public BinaryVertexWriter(RecordWriter<PositionWritable, ValueStateWritable> lineRecordWriter) {
+        public BinaryVertexWriter(RecordWriter<PositionWritable, VertexValueWritable> lineRecordWriter) {
             this.lineRecordWriter = lineRecordWriter;
         }
 
@@ -76,7 +76,7 @@
          * 
          * @return Record writer to be used for writing.
          */
-        public RecordWriter<PositionWritable, ValueStateWritable> getRecordWriter() {
+        public RecordWriter<PositionWritable, VertexValueWritable> getRecordWriter() {
             return lineRecordWriter;
         }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanInputFormat.java
index 140a703..c4c1b64 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanInputFormat.java
@@ -12,18 +12,18 @@
 import edu.uci.ics.pregelix.api.io.VertexReader;
 import edu.uci.ics.pregelix.api.util.BspUtils;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexInputFormat;
 import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexInputFormat.BinaryDataCleanVertexReader;
 
 public class DataCleanInputFormat extends
-    BinaryDataCleanVertexInputFormat<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+    BinaryDataCleanVertexInputFormat<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     /**
      * Format INPUT
      */
     @SuppressWarnings("unchecked")
     @Override
-    public VertexReader<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> createVertexReader(
+    public VertexReader<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> createVertexReader(
             InputSplit split, TaskAttemptContext context) throws IOException {
         return new BinaryDataCleanLoadGraphReader(binaryInputFormat.createRecordReader(split, context));
     }
@@ -31,12 +31,12 @@
 
 @SuppressWarnings("rawtypes")
 class BinaryDataCleanLoadGraphReader extends
-    BinaryDataCleanVertexReader<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+    BinaryDataCleanVertexReader<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     private Vertex vertex;
     private PositionWritable vertexId = new PositionWritable();
-    private ValueStateWritable vertexValue = new ValueStateWritable();
+    private VertexValueWritable vertexValue = new VertexValueWritable();
 
-    public BinaryDataCleanLoadGraphReader(RecordReader<PositionWritable, ValueStateWritable> recordReader) {
+    public BinaryDataCleanLoadGraphReader(RecordReader<PositionWritable, VertexValueWritable> recordReader) {
         super(recordReader);
     }
 
@@ -47,7 +47,7 @@
 
     @SuppressWarnings("unchecked")
     @Override
-    public Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> getCurrentVertex()
+    public Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> getCurrentVertex()
             throws IOException, InterruptedException {
         if (vertex == null)
             vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java
index b06dbbe..4c38255 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java
@@ -7,20 +7,20 @@
 import org.apache.hadoop.mapreduce.TaskAttemptContext;
 
 import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.type.PositionWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.io.VertexWriter;
 
 public class DataCleanOutputFormat extends
-    BinaryDataCleanVertexOutputFormat<PositionWritable, ValueStateWritable, NullWritable> {
+    BinaryDataCleanVertexOutputFormat<PositionWritable, VertexValueWritable, NullWritable> {
 
     @Override
-    public VertexWriter<PositionWritable, ValueStateWritable, NullWritable> createVertexWriter(
+    public VertexWriter<PositionWritable, VertexValueWritable, NullWritable> createVertexWriter(
             TaskAttemptContext context) throws IOException, InterruptedException {
         @SuppressWarnings("unchecked")
-        RecordWriter<PositionWritable, ValueStateWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
+        RecordWriter<PositionWritable, VertexValueWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
         return new BinaryLoadGraphVertexWriter(recordWriter);
     }
 
@@ -28,13 +28,13 @@
      * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
      */
     public static class BinaryLoadGraphVertexWriter extends
-            BinaryVertexWriter<PositionWritable, ValueStateWritable, NullWritable> {
-        public BinaryLoadGraphVertexWriter(RecordWriter<PositionWritable, ValueStateWritable> lineRecordWriter) {
+            BinaryVertexWriter<PositionWritable, VertexValueWritable, NullWritable> {
+        public BinaryLoadGraphVertexWriter(RecordWriter<PositionWritable, VertexValueWritable> lineRecordWriter) {
             super(lineRecordWriter);
         }
 
         @Override
-        public void writeVertex(Vertex<PositionWritable, ValueStateWritable, NullWritable, ?> vertex)
+        public void writeVertex(Vertex<PositionWritable, VertexValueWritable, NullWritable, ?> vertex)
                 throws IOException, InterruptedException {
             if(vertex.getVertexValue().getState() != State.END_VERTEX)
                 getRecordWriter().write(vertex.getVertexId(), vertex.getVertexValue());
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeInputFormat.java
index 0b0055b..cf254d1 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeInputFormat.java
@@ -9,7 +9,7 @@
 
 import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexInputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
@@ -18,24 +18,24 @@
 import edu.uci.ics.pregelix.api.util.BspUtils;
 
 public class LogAlgorithmForPathMergeInputFormat extends
-        BinaryVertexInputFormat<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        BinaryVertexInputFormat<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     /**
      * Format INPUT
      */
     @SuppressWarnings("unchecked")
     @Override
-    public VertexReader<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> createVertexReader(
+    public VertexReader<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> createVertexReader(
             InputSplit split, TaskAttemptContext context) throws IOException {
         return new BinaryLoadGraphReader(binaryInputFormat.createRecordReader(split, context));
     }
 
     @SuppressWarnings("rawtypes")
     class BinaryLoadGraphReader extends
-            BinaryVertexReader<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+            BinaryVertexReader<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
         private Vertex vertex = null;
         private NodeWritable node = new NodeWritable();
         private PositionWritable vertexId = new PositionWritable(); 
-        private ValueStateWritable vertexValue = new ValueStateWritable();
+        private VertexValueWritable vertexValue = new VertexValueWritable();
 
         public BinaryLoadGraphReader(RecordReader<NodeWritable, NullWritable> recordReader) {
             super(recordReader);
@@ -48,7 +48,7 @@
 
         @SuppressWarnings("unchecked")
         @Override
-        public Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> getCurrentVertex()
+        public Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> getCurrentVertex()
                 throws IOException, InterruptedException {
             if (vertex == null)
                 vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeOutputFormat.java
index a26c075..95e24be 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeOutputFormat.java
@@ -9,15 +9,15 @@
 import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexOutputFormat;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.io.VertexWriter;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
 
 public class LogAlgorithmForPathMergeOutputFormat extends
-        BinaryVertexOutputFormat<PositionWritable, ValueStateWritable, NullWritable> {
+        BinaryVertexOutputFormat<PositionWritable, VertexValueWritable, NullWritable> {
 
     @Override
-    public VertexWriter<PositionWritable, ValueStateWritable, NullWritable> createVertexWriter(
+    public VertexWriter<PositionWritable, VertexValueWritable, NullWritable> createVertexWriter(
             TaskAttemptContext context) throws IOException, InterruptedException {
         @SuppressWarnings("unchecked")
         RecordWriter<NodeWritable, NullWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
@@ -28,7 +28,7 @@
      * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
      */
     public static class BinaryLoadGraphVertexWriter extends
-            BinaryVertexWriter<PositionWritable, ValueStateWritable, NullWritable> {
+            BinaryVertexWriter<PositionWritable, VertexValueWritable, NullWritable> {
         private NodeWritable node = new NodeWritable();
         private NullWritable nul = NullWritable.get();
         
@@ -37,7 +37,7 @@
         }
 
         @Override
-        public void writeVertex(Vertex<PositionWritable, ValueStateWritable, NullWritable, ?> vertex)
+        public void writeVertex(Vertex<PositionWritable, VertexValueWritable, NullWritable, ?> vertex)
                 throws IOException, InterruptedException {
             node.set(vertex.getVertexId(), vertex.getVertexValue().getFFList(),
                     vertex.getVertexValue().getFRList(), vertex.getVertexValue().getRFList(),
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeInputFormat.java
index 91634d8..d10e625 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeInputFormat.java
@@ -13,19 +13,19 @@
 import edu.uci.ics.pregelix.api.io.VertexReader;
 import edu.uci.ics.pregelix.api.util.BspUtils;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexInputFormat;
 import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexInputFormat.BinaryVertexReader;
 
 public class NaiveAlgorithmForPathMergeInputFormat extends
-        BinaryVertexInputFormat<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        BinaryVertexInputFormat<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     /**
      * Format INPUT
      */
     @SuppressWarnings("unchecked")
     @Override
-    public VertexReader<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> createVertexReader(
+    public VertexReader<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> createVertexReader(
             InputSplit split, TaskAttemptContext context) throws IOException {
         return new BinaryLoadGraphReader(binaryInputFormat.createRecordReader(split, context));
     }
@@ -33,11 +33,11 @@
 
 @SuppressWarnings("rawtypes")
 class BinaryLoadGraphReader extends
-        BinaryVertexReader<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        BinaryVertexReader<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     private Vertex vertex;
     private NodeWritable node = new NodeWritable();
     private PositionWritable vertexId = new PositionWritable();
-    private ValueStateWritable vertexValue = new ValueStateWritable();
+    private VertexValueWritable vertexValue = new VertexValueWritable();
 
     public BinaryLoadGraphReader(RecordReader<NodeWritable, NullWritable> recordReader) {
         super(recordReader);
@@ -50,7 +50,7 @@
 
     @SuppressWarnings("unchecked")
     @Override
-    public Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> getCurrentVertex()
+    public Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> getCurrentVertex()
             throws IOException, InterruptedException {
         if (vertex == null)
             vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java
index 7e157bb..f9f3749 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java
@@ -7,17 +7,17 @@
 import org.apache.hadoop.mapreduce.TaskAttemptContext;
 
 import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.io.VertexWriter;
 
 public class NaiveAlgorithmForPathMergeOutputFormat extends
-        BinaryVertexOutputFormat<PositionWritable, ValueStateWritable, NullWritable> {
+        BinaryVertexOutputFormat<PositionWritable, VertexValueWritable, NullWritable> {
 
     @Override
-    public VertexWriter<PositionWritable, ValueStateWritable, NullWritable> createVertexWriter(
+    public VertexWriter<PositionWritable, VertexValueWritable, NullWritable> createVertexWriter(
             TaskAttemptContext context) throws IOException, InterruptedException {
         @SuppressWarnings("unchecked")
         RecordWriter<NodeWritable, NullWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
@@ -28,7 +28,7 @@
      * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
      */
     public static class BinaryLoadGraphVertexWriter extends
-            BinaryVertexWriter<PositionWritable, ValueStateWritable, NullWritable> {
+            BinaryVertexWriter<PositionWritable, VertexValueWritable, NullWritable> {
         private NodeWritable node = new NodeWritable();
         private NullWritable nullWritable = NullWritable.get();
         
@@ -37,7 +37,7 @@
         }
 
         @Override
-        public void writeVertex(Vertex<PositionWritable, ValueStateWritable, NullWritable, ?> vertex)
+        public void writeVertex(Vertex<PositionWritable, VertexValueWritable, NullWritable, ?> vertex)
                 throws IOException, InterruptedException {
             node.set(vertex.getVertexId(), vertex.getVertexValue().getFFList(),
                     vertex.getVertexValue().getFRList(), vertex.getVertexValue().getRFList(),
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 6a71344..935da50 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
@@ -6,6 +6,7 @@
 
 import org.apache.hadoop.io.WritableComparable;
 
+import edu.uci.ics.genomix.pregelix.type.AdjMessage;
 import edu.uci.ics.genomix.pregelix.type.CheckMessage;
 import edu.uci.ics.genomix.pregelix.type.Message;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
@@ -21,6 +22,7 @@
     private KmerBytesWritable chainVertexId;
     private AdjacencyListWritable neighberNode; //incoming or outgoing
     private byte message;
+    private byte adjMessage;
 
     private byte checkMessage;
 
@@ -29,6 +31,7 @@
         chainVertexId = new KmerBytesWritable(0);
         neighberNode = new AdjacencyListWritable();
         message = Message.NON;
+        adjMessage = AdjMessage.NON;
         checkMessage = (byte) 0;
     }
     
@@ -46,6 +49,8 @@
             checkMessage |= CheckMessage.NEIGHBER;
             this.neighberNode.set(msg.getNeighberNode());
         }
+        checkMessage |= CheckMessage.ADJMSG;
+        this.adjMessage = msg.getAdjMessage();
         this.message = msg.getMessage();
     }
 
@@ -109,6 +114,15 @@
     public int getLengthOfChain() {
         return chainVertexId.getKmerLength();
     }
+    
+    public byte getAdjMessage() {
+        return adjMessage;
+    }
+
+    public void setAdjMessage(byte adjMessage) {
+        checkMessage |= CheckMessage.ADJMSG;
+        this.adjMessage = adjMessage;
+    }
 
     public byte getMessage() {
         return message;
@@ -127,6 +141,8 @@
             chainVertexId.write(out);
         if ((checkMessage & CheckMessage.NEIGHBER) != 0)
             neighberNode.write(out);
+        if ((checkMessage & CheckMessage.ADJMSG) != 0)
+            out.write(adjMessage);
         out.write(message);
     }
 
@@ -140,6 +156,8 @@
             chainVertexId.readFields(in);
         if ((checkMessage & CheckMessage.NEIGHBER) != 0)
             neighberNode.readFields(in);
+        if ((checkMessage & CheckMessage.ADJMSG) != 0)
+            adjMessage = in.readByte();
         message = in.readByte();
     }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
similarity index 86%
rename from genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
rename to genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index 7895da4..de483bc 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -7,22 +7,25 @@
 import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.PositionListWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
 
-public class ValueStateWritable implements WritableComparable<ValueStateWritable> {
+public class VertexValueWritable implements WritableComparable<VertexValueWritable> {
 
     private AdjacencyListWritable incomingList;
     private AdjacencyListWritable outgoingList;
     private byte state;
     private KmerBytesWritable mergeChain;
+    private PositionWritable mergeDest;
 
-    public ValueStateWritable() {
+    public VertexValueWritable() {
         incomingList = new AdjacencyListWritable();
         outgoingList = new AdjacencyListWritable();
         state = State.NON_VERTEX;
         mergeChain = new KmerBytesWritable(0);
+        mergeDest = new PositionWritable();
     }
 
-    public ValueStateWritable(PositionListWritable forwardForwardList, PositionListWritable forwardReverseList,
+    public VertexValueWritable(PositionListWritable forwardForwardList, PositionListWritable forwardReverseList,
             PositionListWritable reverseForwardList, PositionListWritable reverseReverseList,
             byte state, KmerBytesWritable mergeChain) {
         set(forwardForwardList, forwardReverseList, 
@@ -41,7 +44,7 @@
         this.mergeChain.set(mergeChain);
     }
     
-    public void set(ValueStateWritable value) {
+    public void set(VertexValueWritable value) {
         set(value.getFFList(),value.getFRList(),value.getRFList(),value.getRRList(),value.getState(),
                 value.getMergeChain());
     }
@@ -113,6 +116,14 @@
     public void setMergeChain(KmerBytesWritable mergeChain) {
         this.mergeChain.set(mergeChain);
     }
+    
+    public PositionWritable getMergeDest() {
+        return mergeDest;
+    }
+
+    public void setMergeDest(PositionWritable mergeDest) {
+        this.mergeDest = mergeDest;
+    }
 
     @Override
     public void readFields(DataInput in) throws IOException {
@@ -120,6 +131,7 @@
         outgoingList.readFields(in);
         state = in.readByte();
         mergeChain.readFields(in);
+        mergeDest.readFields(in);
     }
 
     @Override
@@ -128,10 +140,11 @@
         outgoingList.write(out);
         out.writeByte(state);
         mergeChain.write(out);
+        mergeDest.write(out);
     }
 
     @Override
-    public int compareTo(ValueStateWritable o) {
+    public int compareTo(VertexValueWritable o) {
         return 0;
     }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
index 6c24aa9..8525a0a 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
@@ -13,7 +13,7 @@
 import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 
 /*
  * vertexId: BytesWritable
@@ -47,7 +47,7 @@
  * Naive Algorithm for path merge graph
  */
 public class BridgeAddVertex extends
-        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "BridgeRemoveVertex.kmerSize";
     public static final String LENGTH = "BridgeRemoveVertex.length";
     public static int kmerSize = -1;
@@ -77,7 +77,7 @@
                 vertex.getMsgList().clear();
                 vertex.getEdges().clear();
                 PositionWritable vertexId = new PositionWritable();
-                ValueStateWritable vertexValue = new ValueStateWritable();
+                VertexValueWritable vertexValue = new VertexValueWritable();
                 /**
                  * set the src vertex id
                  */
@@ -116,7 +116,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
index bc97dbd..2770ab8 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
@@ -11,7 +11,7 @@
 import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.AdjMessage;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
 
@@ -47,7 +47,7 @@
  * Naive Algorithm for path merge graph
  */
 public class BridgeRemoveVertex extends
-        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "BridgeRemoveVertex.kmerSize";
     public static final String LENGTH = "BridgeRemoveVertex.length";
     public static int kmerSize = -1;
@@ -76,7 +76,7 @@
     /**
      * head send message to all next nodes
      */
-    public void sendMsgToAllNextNodes(ValueStateWritable value) {
+    public void sendMsgToAllNextNodes(VertexValueWritable value) {
         posIterator = value.getFFList().iterator(); // FFList
         while(posIterator.hasNext()){
             outgoingMsg.setMessage(AdjMessage.FROMFF);
@@ -96,7 +96,7 @@
     /**
      * head send message to all previous nodes
      */
-    public void sendMsgToAllPreviousNodes(ValueStateWritable value) {
+    public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
         posIterator = value.getRFList().iterator(); // RFList
         while(posIterator.hasNext()){
             outgoingMsg.setMessage(AdjMessage.FROMRF);
@@ -269,7 +269,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
index b02ea06..63ac5b5 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
@@ -13,7 +13,7 @@
 import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 
 /*
  * vertexId: BytesWritable
@@ -47,7 +47,7 @@
  *  Remove tip or single node when l > constant
  */
 public class BubbleAddVertex extends
-        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "BubbleAddVertex.kmerSize";
     public static int kmerSize = -1;
    
@@ -73,7 +73,7 @@
                 vertex.getMsgList().clear();
                 vertex.getEdges().clear();
                 PositionWritable vertexId = new PositionWritable();
-                ValueStateWritable vertexValue = new ValueStateWritable();
+                VertexValueWritable vertexValue = new VertexValueWritable();
                 /**
                  * set the src vertex id
                  */
@@ -112,7 +112,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
index f64c36d..396d43d 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
@@ -15,7 +15,7 @@
 import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MergeBubbleMessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.AdjMessage;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
 
@@ -51,7 +51,7 @@
  * Naive Algorithm for path merge graph
  */
 public class BubbleMergeVertex extends
-        Vertex<PositionWritable, ValueStateWritable, NullWritable, MergeBubbleMessageWritable> {
+        Vertex<PositionWritable, VertexValueWritable, NullWritable, MergeBubbleMessageWritable> {
     public static final String KMER_SIZE = "BubbleMergeVertex.kmerSize";
     public static final String ITERATIONS = "BubbleMergeVertex.iteration";
     public static int kmerSize = -1;
@@ -81,7 +81,7 @@
     /**
      * get destination vertex
      */
-    public PositionWritable getNextDestVertexId(ValueStateWritable value) {
+    public PositionWritable getNextDestVertexId(VertexValueWritable value) {
         if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
             posIterator = value.getFFList().iterator();
         else // #FRList() > 0
@@ -92,7 +92,7 @@
     /**
      * head send message to all next nodes
      */
-    public void sendMsgToAllNextNodes(ValueStateWritable value) {
+    public void sendMsgToAllNextNodes(VertexValueWritable value) {
         posIterator = value.getFFList().iterator(); // FFList
         while(posIterator.hasNext()){
             destVertexId.set(posIterator.next());
@@ -299,7 +299,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.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/LogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
index 87016b7..cff6cd7 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
@@ -10,7 +10,7 @@
 import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeInputFormat;
 import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.Message;
 import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
@@ -19,7 +19,7 @@
 import edu.uci.ics.genomix.type.PositionWritable;
 /*
  * vertexId: BytesWritable
- * vertexValue: ValueStateWritable
+ * vertexValue: VertexValueWritable
  * edgeValue: NullWritable
  * message: MessageWritable
  * 
@@ -46,7 +46,7 @@
  * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
  */
 public class LogAlgorithmForPathMergeVertex extends
-        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "LogAlgorithmForPathMergeVertex.kmerSize";
     public static final String ITERATIONS = "LogAlgorithmForPathMergeVertex.iteration";
     public static int kmerSize = -1;
@@ -74,7 +74,7 @@
     /**
      * get destination vertex
      */
-    public PositionWritable getNextDestVertexId(ValueStateWritable value) {
+    public PositionWritable getNextDestVertexId(VertexValueWritable value) {
         if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
             posIterator = value.getFFList().iterator();
         else // #FRList() > 0
@@ -82,7 +82,7 @@
         return posIterator.next();
     }
 
-    public PositionWritable getPreDestVertexId(ValueStateWritable value) {
+    public PositionWritable getPreDestVertexId(VertexValueWritable value) {
         if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
             posIterator = value.getRFList().iterator();
         else // #RRList() > 0
@@ -93,7 +93,7 @@
     /**
      * head send message to all next nodes
      */
-    public void sendMsgToAllNextNodes(ValueStateWritable value) {
+    public void sendMsgToAllNextNodes(VertexValueWritable value) {
         posIterator = value.getFFList().iterator(); // FFList
         while(posIterator.hasNext()){
             destVertexId.set(posIterator.next());
@@ -109,7 +109,7 @@
     /**
      * head send message to all previous nodes
      */
-    public void sendMsgToAllPreviousNodes(ValueStateWritable value) {
+    public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
         posIterator = value.getRFList().iterator(); // RFList
         while(posIterator.hasNext()){
             destVertexId.set(posIterator.next());
@@ -283,7 +283,7 @@
         job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class);
         job.setVertexOutputFormatClass(LogAlgorithmForPathMergeOutputFormat.class);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         job.setDynamicVertexValueSize(true);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
index f27c140..47ca06e 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
@@ -13,7 +13,7 @@
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.Message;
 import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
@@ -50,7 +50,7 @@
  * Naive Algorithm for path merge graph
  */
 public class NaiveAlgorithmForPathMergeVertex extends
-        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "NaiveAlgorithmForPathMergeVertex.kmerSize";
     public static final String ITERATIONS = "NaiveAlgorithmForPathMergeVertex.iteration";
     public static int kmerSize = -1;
@@ -79,7 +79,7 @@
     /**
      * get destination vertex
      */
-    public PositionWritable getNextDestVertexId(ValueStateWritable value) {
+    public PositionWritable getNextDestVertexId(VertexValueWritable value) {
         if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
             posIterator = value.getFFList().iterator();
         else // #FRList() > 0
@@ -87,7 +87,7 @@
         return posIterator.next();
     }
 
-    public PositionWritable getPreDestVertexId(ValueStateWritable value) {
+    public PositionWritable getPreDestVertexId(VertexValueWritable value) {
         if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
             posIterator = value.getRFList().iterator();
         else // #RRList() > 0
@@ -98,7 +98,7 @@
     /**
      * head send message to all next nodes
      */
-    public void sendMsgToAllNextNodes(ValueStateWritable value) {
+    public void sendMsgToAllNextNodes(VertexValueWritable value) {
         posIterator = value.getFFList().iterator(); // FFList
         while(posIterator.hasNext()){
             destVertexId.set(posIterator.next());
@@ -114,7 +114,7 @@
     /**
      * head send message to all previous nodes
      */
-    public void sendMsgToAllPreviousNodes(ValueStateWritable value) {
+    public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
         posIterator = value.getRFList().iterator(); // RFList
         while(posIterator.hasNext()){
             destVertexId.set(posIterator.next());
@@ -260,7 +260,7 @@
         job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.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/P3ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
index 35e679a..949e8bb 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
@@ -13,7 +13,7 @@
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.Message;
 import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
@@ -50,7 +50,7 @@
  * Naive Algorithm for path merge graph
  */
 public class P3ForPathMergeVertex extends
-        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "P3ForPathMergeVertex.kmerSize";
     public static final String ITERATIONS = "P3ForPathMergeVertex.iteration";
     public static final String PSEUDORATE = "P3ForPathMergeVertex.pseudoRate";
@@ -86,7 +86,7 @@
     /**
      * get destination vertex
      */
-    public PositionWritable getNextDestVertexId(ValueStateWritable value) {
+    public PositionWritable getNextDestVertexId(VertexValueWritable value) {
         if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
             posIterator = value.getFFList().iterator();
         else // #FRList() > 0
@@ -94,7 +94,7 @@
         return posIterator.next();
     }
 
-    public PositionWritable getPreDestVertexId(ValueStateWritable value) {
+    public PositionWritable getPreDestVertexId(VertexValueWritable value) {
         if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
             posIterator = value.getRFList().iterator();
         else // #RRList() > 0
@@ -105,7 +105,7 @@
     /**
      * head send message to all next nodes
      */
-    public void sendMsgToAllNextNodes(ValueStateWritable value) {
+    public void sendMsgToAllNextNodes(VertexValueWritable value) {
         posIterator = value.getFFList().iterator(); // FFList
         while(posIterator.hasNext()){
             destVertexId.set(posIterator.next());
@@ -121,7 +121,7 @@
     /**
      * head send message to all previous nodes
      */
-    public void sendMsgToAllPreviousNodes(ValueStateWritable value) {
+    public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
         posIterator = value.getRFList().iterator(); // RFList
         while(posIterator.hasNext()){
             destVertexId.set(posIterator.next());
@@ -411,7 +411,7 @@
         job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
index 31e0e24..b6c03fb 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
@@ -12,9 +12,9 @@
 import edu.uci.ics.genomix.pregelix.client.Client;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.AdjacencyListWritable;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.type.AdjMessage;
 import edu.uci.ics.genomix.pregelix.type.Message;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.pregelix.type.State;
@@ -52,7 +52,7 @@
  * Naive Algorithm for path merge graph
  */
 public class P4ForPathMergeVertex extends
-        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "P4ForPathMergeVertex.kmerSize";
     public static final String ITERATIONS = "P4ForPathMergeVertex.iteration";
     public static final String RANDSEED = "P4ForPathMergeVertex.randSeed";
@@ -113,7 +113,7 @@
     /**
      * set nextID to the element that's next (in the node's FF or FR list), returning true when there is a next neighbor
      */
-    protected boolean setNextInfo(ValueStateWritable value) {
+    protected boolean setNextInfo(VertexValueWritable value) {
         if (value.getFFList().getCountOfPosition() > 0) {
             nextID.set(value.getFFList().getPosition(0));
             nextHead = isNodeRandomHead(nextID);
@@ -130,7 +130,7 @@
     /**
      * set prevID to the element that's previous (in the node's RR or RF list), returning true when there is a previous neighbor
      */
-    protected boolean setPrevInfo(ValueStateWritable value) {
+    protected boolean setPrevInfo(VertexValueWritable value) {
         if (value.getRRList().getCountOfPosition() > 0) {
             prevID.set(value.getRRList().getPosition(0));
             prevHead = isNodeRandomHead(prevID);
@@ -147,7 +147,7 @@
     /**
      * get destination vertex
      */
-    public PositionWritable getNextDestVertexId(ValueStateWritable value) {
+    public PositionWritable getNextDestVertexId(VertexValueWritable value) {
         if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
             posIterator = value.getFFList().iterator();
         else // #FRList() > 0
@@ -155,7 +155,7 @@
         return posIterator.next();
     }
 
-    public PositionWritable getPreDestVertexId(ValueStateWritable value) {
+    public PositionWritable getPreDestVertexId(VertexValueWritable value) {
         if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
             posIterator = value.getRFList().iterator();
         else // #RRList() > 0
@@ -166,7 +166,7 @@
     /**
      * head send message to all next nodes
      */
-    public void sendMsgToAllNextNodes(ValueStateWritable value) {
+    public void sendMsgToAllNextNodes(VertexValueWritable value) {
         posIterator = value.getFFList().iterator(); // FFList
         while(posIterator.hasNext()){
             destVertexId.set(posIterator.next());
@@ -182,7 +182,7 @@
     /**
      * head send message to all previous nodes
      */
-    public void sendMsgToAllPreviousNodes(ValueStateWritable value) {
+    public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
         posIterator = value.getRFList().iterator(); // RFList
         while(posIterator.hasNext()){
             destVertexId.set(posIterator.next());
@@ -271,46 +271,105 @@
         else
             return false;
     }
+    
     /**
-     * send update message from predecessor
+     * set adjMessage to successor(from predecessor)
      */
-    public void sendUpMsgFromPredecessor(){
+    public void setSuccessorAdjMsg(){
+        if(getVertexValue().getFFList().getLength() > 0)
+            outgoingMsg.setAdjMessage(AdjMessage.FROMFF);
+        else
+            outgoingMsg.setAdjMessage(AdjMessage.FROMFR);
+    }
+    
+    /**
+     * set adjMessage to predecessor(from successor)
+     */
+    public void setPredecessorAdjMsg(){
+        if(getVertexValue().getRFList().getLength() > 0)
+            outgoingMsg.setAdjMessage(AdjMessage.FROMRF);
+        else
+            outgoingMsg.setAdjMessage(AdjMessage.FROMRR);
+    }
+    
+    /**
+     * send update message to neighber
+     */
+    public void broadcastUpdateMsg(){
         outFlag |= MessageFlag.FROM_PREDECESSOR;
         outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
         if(ifFlipWithPredecessor())
             outFlag |= MessageFlag.FLIP;
         outgoingMsg.setMessage(outFlag);
         outgoingMsg.setSourceVertexId(getVertexId());
+        setSuccessorAdjMsg();
         sendMsg(getNextDestVertexId(getVertexValue()), outgoingMsg);
-        outUpFlag = (byte)(MessageFlag.FROM_DEADVERTEX | MessageFlag.FROM_SUCCESSOR);
+        outUpFlag = (byte)(MessageFlag.FROM_SUCCESSOR);
         outgoingUpMsg.setNeighberNode(getVertexValue().getOutgoingList());
         if(ifFilpWithSuccessor())
             outFlag |= MessageFlag.FLIP;
         outgoingUpMsg.setMessage(outUpFlag);
         outgoingUpMsg.setSourceVertexId(getVertexId());
+        setPredecessorAdjMsg();
         sendMsg(getPreDestVertexId(getVertexValue()), outgoingUpMsg);
-        deleteVertex(getVertexId());
+        //remove its own neighbers
+        getVertexValue().setIncomingList(null);
+        getVertexValue().setOutgoingList(null);
     }
     
     /**
-     * send update message from successor
+     * This vertex tries to merge with next vertex and send update msg to neighber
+     */
+    public void sendUpMsgFromPredecessor(){
+        getVertexValue().setState(MessageFlag.SHOULD_MERGEWITHNEXT);
+        if(getVertexValue().getFFList().getLength() > 0)
+            getVertexValue().setMergeDest(getVertexValue().getFFList().getPosition(0));
+        else
+            getVertexValue().setMergeDest(getVertexValue().getFRList().getPosition(0));
+        broadcastUpdateMsg();
+    }
+    
+    /**
+     * This vertex tries to merge with next vertex and send update msg to neighber
      */
     public void sendUpMsgFromSuccessor(){
-        outFlag |= MessageFlag.FROM_SUCCESSOR;
-        outgoingUpMsg.setNeighberNode(getVertexValue().getOutgoingList());
-        if(ifFilpWithSuccessor())
-            outFlag |= MessageFlag.FLIP;
-        outgoingMsg.setMessage(outFlag);
-        outgoingMsg.setSourceVertexId(getVertexId());
-        sendMsg(getPreDestVertexId(getVertexValue()), outgoingMsg);
-        outUpFlag = (byte)(MessageFlag.FROM_DEADVERTEX | MessageFlag.FROM_PREDECESSOR);
-        outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
-        if(ifFlipWithPredecessor())
-            outFlag |= MessageFlag.FLIP;
-        outgoingUpMsg.setMessage(outUpFlag);
-        outgoingUpMsg.setSourceVertexId(getVertexId());
-        sendMsg(getNextDestVertexId(getVertexValue()), outgoingUpMsg);
-        deleteVertex(getVertexId());
+        getVertexValue().setState(MessageFlag.SHOULD_MERGEWITHPREV);
+        if(getVertexValue().getRFList().getLength() > 0)
+            getVertexValue().setMergeDest(getVertexValue().getRFList().getPosition(0));
+        else
+            getVertexValue().setMergeDest(getVertexValue().getRRList().getPosition(0));
+        broadcastUpdateMsg();
+    }
+    
+    /**
+     * updateAdjList
+     */
+    public void updateAdjList(){
+        if(incomingMsg.getAdjMessage() == AdjMessage.FROMFF){
+            getVertexValue().setRRList(null); //may replace setNull with remove 
+            if(incomingMsg.getNeighberNode().getForwardList().getLength() > 0)
+                getVertexValue().setRFList(incomingMsg.getNeighberNode().getForwardList());
+            else
+                getVertexValue().setRFList(incomingMsg.getNeighberNode().getReverseList());
+        } else if(incomingMsg.getAdjMessage() == AdjMessage.FROMFR){
+            getVertexValue().setFRList(null); //may replace setNull with remove 
+            if(incomingMsg.getNeighberNode().getForwardList().getLength() > 0)
+                getVertexValue().setFFList(incomingMsg.getNeighberNode().getForwardList());
+            else
+                getVertexValue().setFFList(incomingMsg.getNeighberNode().getReverseList());
+        } else if(incomingMsg.getAdjMessage() == AdjMessage.FROMRF){
+            getVertexValue().setRFList(null); //may replace setNull with remove 
+            if(incomingMsg.getNeighberNode().getForwardList().getLength() > 0)
+                getVertexValue().setRRList(incomingMsg.getNeighberNode().getForwardList());
+            else
+                getVertexValue().setRRList(incomingMsg.getNeighberNode().getReverseList());
+        } else if(incomingMsg.getAdjMessage() == AdjMessage.FROMRR){
+            getVertexValue().setFFList(null); //may replace setNull with remove 
+            if(incomingMsg.getNeighberNode().getForwardList().getLength() > 0)
+                getVertexValue().setFRList(incomingMsg.getNeighberNode().getForwardList());
+            else
+                getVertexValue().setFRList(incomingMsg.getNeighberNode().getReverseList());
+        }
     }
     
     /**
@@ -318,19 +377,7 @@
      */
     public void updateAdjList_MsgPredecessor(){
         if((outFlag & MessageFlag.FLIP) > 0){
-            if(getVertexValue().getFFList().getLength() > 0){
-                getVertexValue().setFFList(null);
-                if(incomingMsg.getNeighberNode().getForwardList().getLength() > 0)
-                    getVertexValue().setFRList(incomingMsg.getNeighberNode().getForwardList());
-                else
-                    getVertexValue().setFRList(incomingMsg.getNeighberNode().getReverseList());
-            } else {
-                getVertexValue().setFRList(null);
-                if(incomingMsg.getNeighberNode().getForwardList().getLength() > 0)
-                    getVertexValue().setFFList(incomingMsg.getNeighberNode().getForwardList());
-                else
-                    getVertexValue().setFFList(incomingMsg.getNeighberNode().getReverseList());
-            }
+            updateAdjList();
         } else {
             getVertexValue().setIncomingList(incomingMsg.getNeighberNode());
         }
@@ -341,19 +388,7 @@
      */
     public void updateAdjList_MsgSuccessor(){
         if((outFlag & MessageFlag.FLIP) > 0){
-            if(getVertexValue().getRRList().getLength() > 0){
-                getVertexValue().setRRList(null);
-                if(incomingMsg.getNeighberNode().getForwardList().getLength() > 0)
-                    getVertexValue().setRFList(incomingMsg.getNeighberNode().getForwardList());
-                else
-                    getVertexValue().setRFList(incomingMsg.getNeighberNode().getReverseList());
-            } else {
-                getVertexValue().setRFList(null);
-                if(incomingMsg.getNeighberNode().getForwardList().getLength() > 0)
-                    getVertexValue().setRRList(incomingMsg.getNeighberNode().getForwardList());
-                else
-                    getVertexValue().setRRList(incomingMsg.getNeighberNode().getReverseList());
-            }
+            updateAdjList();
         } else {
             getVertexValue().setOutgoingList(incomingMsg.getNeighberNode());
         }
@@ -366,7 +401,7 @@
             startSendMsg();
         else if (getSuperstep() == 2)
             initState(msgIterator);
-        else if (getSuperstep() % 2 == 1){
+        else if (getSuperstep() % 4 == 3){
             // Node may be marked as head b/c it's a real head or a real tail
             headFlag = (byte) (State.START_VERTEX & getVertexValue().getState());
             tailFlag = (byte) (State.END_VERTEX & getVertexValue().getState());
@@ -382,7 +417,6 @@
             hasNext = setNextInfo(getVertexValue()) && tailFlag == 0;
             hasPrev = setPrevInfo(getVertexValue()) && headFlag == 0;
             if ((outFlag & MessageFlag.IS_HEAD) > 0 && (outFlag & MessageFlag.IS_TAIL) > 0) {
-                outFlag |= MessageFlag.FROM_SELF;
                 getVertexValue().setState(outFlag);
                 voteToHalt();
             }
@@ -419,30 +453,47 @@
                 }
             }
         }
-        else if (getSuperstep() % 2 == 0){
+        else if (getSuperstep() % 4 == 0){
+            //update neighber
             while (msgIterator.hasNext()) {
                 incomingMsg = msgIterator.next();
                 outFlag = incomingMsg.getMessage();
-                if((outFlag & MessageFlag.FROM_DEADVERTEX) > 0){
-                    if((outFlag & MessageFlag.FROM_PREDECESSOR) > 0){
-                        updateAdjList_MsgPredecessor();
-                    } 
-                    else {//Message from successor.
-                        updateAdjList_MsgSuccessor();
-                    }
+                if((outFlag & MessageFlag.FROM_PREDECESSOR) > 0){
+                    updateAdjList_MsgPredecessor();
+                } 
+                else {//Message from successor.
+                    updateAdjList_MsgSuccessor();
                 }
-                else {//Not for update, but for merging
-                    if((outFlag & MessageFlag.FROM_PREDECESSOR) > 0){
-                        //B merge with A's reverse
-                        //append A's reverse to B
-                        //
-                        updateAdjList_MsgPredecessor();
-                    } 
-                    else {//Message from successor
-                        //B merge with A's reverse
-                        //append 
-                        updateAdjList_MsgSuccessor();
-                    }
+            }
+        } else if (getSuperstep() % 4 == 1){
+            //send message to the merge object and kill self
+            if((getVertexValue().getState() | MessageFlag.SHOULD_MERGEWITHNEXT) > 0){
+                setSuccessorAdjMsg();
+                outgoingMsg.setChainVertexId(getVertexValue().getMergeChain());
+                sendMsg(getVertexValue().getMergeDest(), outgoingMsg);
+                deleteVertex(getVertexId());
+            } else if((getVertexValue().getState() | MessageFlag.SHOULD_MERGEWITHPREV) > 0){
+                setPredecessorAdjMsg();
+                outgoingMsg.setChainVertexId(getVertexValue().getMergeChain());
+                sendMsg(getVertexValue().getMergeDest(), outgoingMsg);
+                deleteVertex(getVertexId());
+            }
+        } else if (getSuperstep() % 4 == 2){
+            //merge kmer
+            while (msgIterator.hasNext()) {
+                incomingMsg = msgIterator.next();
+                outFlag = incomingMsg.getMessage();
+                if(outFlag == AdjMessage.FROMFF){
+                    //mergeWithRR(incomingMsg.getChain())
+                }
+                else if(outFlag == AdjMessage.FROMFR){
+                  //mergeWithRF(incomingMsg.getChain())
+                }
+                else if(outFlag == AdjMessage.FROMRF){
+                  //mergeWithFR(incomingMsg.getChain())
+                }
+                else if(outFlag == AdjMessage.FROMRR){
+                  //mergeWithFF(incomingMsg.getChain())
                 }
             }
         }
@@ -458,7 +509,7 @@
         job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
index 8c9fdc5..59a5efb 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
@@ -13,7 +13,7 @@
 import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 
 /*
  * vertexId: BytesWritable
@@ -47,7 +47,7 @@
  *  Remove tip or single node when l > constant
  */
 public class TipAddVertex extends
-        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "TipAddVertex.kmerSize";
     public static int kmerSize = -1;
    
@@ -73,7 +73,7 @@
                 vertex.getMsgList().clear();
                 vertex.getEdges().clear();
                 PositionWritable vertexId = new PositionWritable();
-                ValueStateWritable vertexValue = new ValueStateWritable();
+                VertexValueWritable vertexValue = new VertexValueWritable();
                 /**
                  * set the src vertex id
                  */
@@ -107,7 +107,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
index 4901269..61e7ae9 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
@@ -10,7 +10,7 @@
 import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.AdjMessage;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
 
@@ -46,7 +46,7 @@
  *  Remove tip or single node when l > constant
  */
 public class TipRemoveVertex extends
-        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "TipRemoveVertex.kmerSize";
     public static final String LENGTH = "TipRemoveVertex.length";
     public static int kmerSize = -1;
@@ -74,7 +74,7 @@
     /**
      * get destination vertex
      */
-    public PositionWritable getNextDestVertexId(ValueStateWritable value) {
+    public PositionWritable getNextDestVertexId(VertexValueWritable value) {
         if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
             posIterator = value.getFFList().iterator();
         else // #FRList() > 0
@@ -82,7 +82,7 @@
         return posIterator.next();
     }
 
-    public PositionWritable getPreDestVertexId(ValueStateWritable value) {
+    public PositionWritable getPreDestVertexId(VertexValueWritable value) {
         if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
             posIterator = value.getRFList().iterator();
         else // #RRList() > 0
@@ -182,7 +182,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
index 452f72d..8669ecd 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
@@ -11,7 +11,7 @@
 import org.apache.hadoop.io.SequenceFile;
 import org.apache.hadoop.io.SequenceFile.CompressionType;
 
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
@@ -25,11 +25,11 @@
 
         SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
         SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf, outFile, PositionWritable.class,
-                ValueStateWritable.class, CompressionType.NONE);
+                VertexValueWritable.class, CompressionType.NONE);
         NodeWritable node = new NodeWritable();
         NullWritable value = NullWritable.get();
         PositionWritable outputKey = new PositionWritable();
-        ValueStateWritable outputValue = new ValueStateWritable();
+        VertexValueWritable outputValue = new VertexValueWritable();
 
         while(reader.next(node, value)) {
             System.out.println(node.getNodeID().toString());
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 1dd8757..9dd5162 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
@@ -12,7 +12,7 @@
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.SequenceFile;
 
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
@@ -31,7 +31,7 @@
             //NodeWritable key = new NodeWritable(kmerSize);
             //NullWritable value = NullWritable.get();
             PositionWritable key = new PositionWritable();
-            ValueStateWritable value = new ValueStateWritable();
+            VertexValueWritable value = new VertexValueWritable();
 
             while (reader.next(key, value)) {
                 if (key == null) {
@@ -54,7 +54,7 @@
             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);
-            ValueStateWritable value = new ValueStateWritable();
+            VertexValueWritable value = new VertexValueWritable();
 
             while (reader.next(key, value)) {
                 if (key == null || value == null) {
@@ -78,7 +78,7 @@
             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);
-            ValueStateWritable value = new ValueStateWritable();
+            VertexValueWritable value = new VertexValueWritable();
 
             while (reader.next(key, value)) {
                 if (key == null || value == null) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/CheckMessage.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/CheckMessage.java
index c7bcf48..4aee8a0 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/CheckMessage.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/CheckMessage.java
@@ -7,7 +7,7 @@
     public static final byte NEIGHBER = 1 << 2;
     public static final byte MESSAGE = 1 << 3;
     public static final byte STATE = 1 << 4;
-    public static final byte LASTGENECODE = 1 << 5;
+    public static final byte ADJMSG = 1 << 5;
     public static final byte START = 1 << 6;
 
     public final static class CheckMessage_CONTENT {
@@ -30,8 +30,8 @@
                 case STATE:
                     r = "STATE";
                     break;
-                case LASTGENECODE:
-                    r = "LASTGENECODE";
+                case ADJMSG:
+                    r = "ADJMSG";
                     break;
                 case START:
                     r = "START";
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
index 9ef6842..0a5428b 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
@@ -1,26 +1,25 @@
 package edu.uci.ics.genomix.pregelix.type;
 
 public class MessageFlag {
-    public static final byte FROM_SELF = 0;
+    public static final byte FLIP = 0;
     public static final byte IS_HEAD = 1 << 1;
     public static final byte IS_TAIL = 1 << 2;
-    public static final byte FROM_DEADVERTEX = 1 << 3;
-    //public static final byte FROM_FORWARDLIST = 1 << 4;
-    public static final byte FLIP = 1 << 4;
+    public static final byte SHOULD_MERGEWITHNEXT = 1 << 3;
+    public static final byte SHOULD_MERGEWITHPREV = 1 << 4;
     public static final byte FROM_SUCCESSOR = 1 << 5;
     public static final byte FROM_PREDECESSOR = 1 << 6;
     
     public static String getFlagAsString(byte code) {
         // TODO: allow multiple flags to be set
         switch (code) {
-            case FROM_SELF:
-                return "FROM_SELF";
             case IS_HEAD:
                 return "IS_HEAD";
             case IS_TAIL:
                 return "IS_TAIL";
-            case FROM_DEADVERTEX:
-                return "FROM_DEADVERTEX";
+            case SHOULD_MERGEWITHNEXT:
+                return "SHOULD_MERGEWITHNEXT";
+            case SHOULD_MERGEWITHPREV:
+                return "SHOULD_MERGEWITHPREV";
             case FLIP:
                 return "FLIP";
             case FROM_SUCCESSOR:
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
index 7962c67..67c9792 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
@@ -1,6 +1,6 @@
 package edu.uci.ics.genomix.pregelix.util;
 
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
 
 public class VertexUtil {
@@ -9,7 +9,7 @@
      * 
      * @param vertexValue
      */
-    public static boolean isPathVertex(ValueStateWritable value) {
+    public static boolean isPathVertex(VertexValueWritable value) {
         return value.inDegree() == 1 && value.outDegree() == 1;
     }
 
@@ -18,7 +18,7 @@
      * 
      * @param vertexValue
      */
-    public static boolean isHeadVertex(ValueStateWritable value) {
+    public static boolean isHeadVertex(VertexValueWritable value) {
         return value.outDegree() > 0 && !isPathVertex(value) && !isHeadWithoutIndegree(value);
     }
 
@@ -27,21 +27,21 @@
      * 
      * @param vertexValue
      */
-    public static boolean isRearVertex(ValueStateWritable value) {
+    public static boolean isRearVertex(VertexValueWritable value) {
         return value.inDegree() > 0 && !isPathVertex(value) && !isRearWithoutOutdegree(value);
     }
 
     /**
      * Head Vertex without indegree: indegree = 0, outdegree = 1
      */
-    public static boolean isHeadWithoutIndegree(ValueStateWritable value){
+    public static boolean isHeadWithoutIndegree(VertexValueWritable value){
         return value.inDegree() == 0 && value.outDegree() == 1;
     }
     
     /**
      * Rear Vertex without outdegree: indegree = 1, outdegree = 0
      */
-    public static boolean isRearWithoutOutdegree(ValueStateWritable value){
+    public static boolean isRearWithoutOutdegree(VertexValueWritable value){
         return value.inDegree() == 1 && value.outDegree() == 0;
     }
     
@@ -65,32 +65,32 @@
     /**
      * check if vertex is a tip
      */
-    public static boolean isIncomingTipVertex(ValueStateWritable value){
+    public static boolean isIncomingTipVertex(VertexValueWritable value){
     	return value.inDegree() == 0 && value.outDegree() == 1;
     }
     
-    public static boolean isOutgoingTipVertex(ValueStateWritable value){
+    public static boolean isOutgoingTipVertex(VertexValueWritable value){
     	return value.inDegree() == 1 && value.outDegree() == 0;
     }
     
     /**
      * check if vertex is single
      */
-    public static boolean isSingleVertex(ValueStateWritable value){
+    public static boolean isSingleVertex(VertexValueWritable value){
         return value.inDegree() == 0 && value.outDegree() == 0;
     }
     
     /**
      * check if vertex is upbridge
      */
-    public static boolean isUpBridgeVertex(ValueStateWritable value){
+    public static boolean isUpBridgeVertex(VertexValueWritable value){
         return value.inDegree() == 1 && value.outDegree() > 1;
     }
     
     /**
      * check if vertex is downbridge
      */
-    public static boolean isDownBridgeVertex(ValueStateWritable value){
+    public static boolean isDownBridgeVertex(VertexValueWritable value){
         return value.inDegree() > 1 && value.outDegree() == 1;
     }
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index 33955c9..f52957e 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -10,7 +10,7 @@
 import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeOutputFormat;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeAddVertex;
 import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeRemoveVertex;
 import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleAddVertex;
@@ -34,7 +34,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, 3);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
@@ -51,7 +51,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class); //LogAlgorithmForPathMergeOutputFormat
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.KMER_SIZE, 3);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
@@ -67,7 +67,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         job.getConfiguration().setInt(P3ForPathMergeVertex.KMER_SIZE, 3);
         job.getConfiguration().setFloat(P3ForPathMergeVertex.PSEUDORATE, 0.3f);
         job.getConfiguration().setInt(P3ForPathMergeVertex.MAXROUND, 2);
@@ -86,7 +86,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         job.getConfiguration().setInt(TipAddVertex.KMER_SIZE, 3);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
@@ -103,7 +103,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 3);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
@@ -120,7 +120,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         job.getConfiguration().setInt(BridgeAddVertex.KMER_SIZE, 3);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
@@ -137,7 +137,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 3);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
@@ -154,7 +154,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         job.getConfiguration().setInt(BubbleAddVertex.KMER_SIZE, 3);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
@@ -171,7 +171,7 @@
         job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
         job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 3);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
index 8c02547..499abdc 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
@@ -12,7 +12,7 @@
 import org.apache.hadoop.io.SequenceFile;
 import org.junit.Test;
 
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.State;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
 
@@ -51,7 +51,7 @@
             Path path = new Path(input + "/part-" + i);
             SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
             KmerBytesWritable key = new KmerBytesWritable(kmerSize);
-            ValueStateWritable value = new ValueStateWritable();
+            VertexValueWritable value = new VertexValueWritable();
 
             while (reader.next(key, value)) {
                 if (key == null || value == null) {
@@ -91,7 +91,7 @@
             Path path = new Path(input + "/part-" + i);
             SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
             KmerBytesWritable key = new KmerBytesWritable(kmerSize);
-            ValueStateWritable value = new ValueStateWritable();
+            VertexValueWritable value = new VertexValueWritable();
 
             while (reader.next(key, value)) {
                 if (key == null || value == null) {
@@ -116,7 +116,7 @@
             Path path = new Path(input + "/part-" + i);
             SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
             KmerBytesWritable key = new KmerBytesWritable(kmerSize);
-            ValueStateWritable value = new ValueStateWritable();
+            VertexValueWritable value = new VertexValueWritable();
 
             while (reader.next(key, value)) {
                 if (key == null || value == null) {