diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java
index 3349aaf..de27f30 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java
@@ -98,6 +98,10 @@
         }
     }
     
+    public void reset() {
+        this.reset(0);
+    }
+    
     public void reset(int kmerSize) {
         kmerlength = kmerSize;
         kmerByteSize = KmerUtil.getByteNumFromK(kmerlength);
@@ -156,6 +160,26 @@
         };
         return it;
     }
+    
+    /*
+     * remove the first instance of @toRemove. Uses a linear scan.  Throws an exception if not in this list.
+     */
+    public void remove(KmerBytesWritable toRemove, boolean ignoreMissing) {
+        Iterator<KmerBytesWritable> posIterator = this.iterator();
+        while (posIterator.hasNext()) {
+            if(toRemove.equals(posIterator.next())) {
+                posIterator.remove();
+                return;
+            }
+        }
+        if (!ignoreMissing) {
+            throw new ArrayIndexOutOfBoundsException("the KmerBytesWritable `" + toRemove.toString() + "` was not found in this list.");
+        }
+    }
+    
+    public void remove(KmerBytesWritable toRemove) {
+        remove(toRemove, false);
+    }
 
     @Override
     public void readFields(DataInput in) throws IOException {
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 2f66bbc..396d5ec 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
@@ -13,8 +13,8 @@
 
 import edu.uci.ics.pregelix.api.io.VertexInputFormat;
 import edu.uci.ics.pregelix.api.io.VertexReader;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 
 public class BinaryDataCleanVertexInputFormat<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
         extends VertexInputFormat<I, V, E, M> {
@@ -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, VertexValueWritable> lineRecordReader;
+        private final RecordReader<KmerBytesWritable, VertexValueWritable> lineRecordReader;
         /** Context passed to initialize */
         private TaskAttemptContext context;
 
@@ -48,7 +48,7 @@
          * @param recordReader
          *            Line record reader from SequenceFileInputFormat
          */
-        public BinaryDataCleanVertexReader(RecordReader<PositionWritable, VertexValueWritable> recordReader) {
+        public BinaryDataCleanVertexReader(RecordReader<KmerBytesWritable, VertexValueWritable> recordReader) {
             this.lineRecordReader = recordReader;
         }
 
@@ -74,7 +74,7 @@
          * 
          * @return Record reader to be used for reading.
          */
-        protected RecordReader<PositionWritable, VertexValueWritable> getRecordReader() {
+        protected RecordReader<KmerBytesWritable, 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 c23ceeb..c07d076 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
@@ -10,8 +10,8 @@
 import org.apache.hadoop.mapreduce.TaskAttemptContext;
 import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
 
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 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, VertexValueWritable> lineRecordWriter;
+        private final RecordWriter<KmerBytesWritable, VertexValueWritable> lineRecordWriter;
 
         /**
          * Initialize with the LineRecordWriter.
@@ -57,7 +57,7 @@
          * @param lineRecordWriter
          *            Line record writer from SequenceFileOutputFormat
          */
-        public BinaryVertexWriter(RecordWriter<PositionWritable, VertexValueWritable> lineRecordWriter) {
+        public BinaryVertexWriter(RecordWriter<KmerBytesWritable, VertexValueWritable> lineRecordWriter) {
             this.lineRecordWriter = lineRecordWriter;
         }
 
@@ -76,7 +76,7 @@
          * 
          * @return Record writer to be used for writing.
          */
-        public RecordWriter<PositionWritable, VertexValueWritable> getRecordWriter() {
+        public RecordWriter<KmerBytesWritable, VertexValueWritable> getRecordWriter() {
             return lineRecordWriter;
         }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexOutputFormat.java
deleted file mode 100644
index a147e2f..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexOutputFormat.java
+++ /dev/null
@@ -1,102 +0,0 @@
-package edu.uci.ics.genomix.pregelix.api.io.binary;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.io.Writable;
-import org.apache.hadoop.io.WritableComparable;
-import org.apache.hadoop.mapreduce.JobContext;
-import org.apache.hadoop.mapreduce.OutputCommitter;
-import org.apache.hadoop.mapreduce.RecordWriter;
-import org.apache.hadoop.mapreduce.TaskAttemptContext;
-import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
-
-import edu.uci.ics.genomix.oldtype.NodeWritable;
-import edu.uci.ics.pregelix.api.io.VertexOutputFormat;
-import edu.uci.ics.pregelix.api.io.VertexWriter;
-
-/**
- * Abstract class that users should subclass to use their own text based vertex
- * output format.
- * 
- * @param <I>
- *            Vertex index value
- * @param <V>
- *            Vertex value
- * @param <E>
- *            Edge value
- */
-@SuppressWarnings("rawtypes")
-public abstract class BinaryVertexOutputFormat<I extends WritableComparable, V extends Writable, E extends Writable>
-        extends VertexOutputFormat<I, V, E> {
-    /** Uses the SequenceFileOutputFormat to do everything */
-    protected SequenceFileOutputFormat binaryOutputFormat = new SequenceFileOutputFormat();
-
-    /**
-     * Abstract class to be implemented by the user based on their specific
-     * vertex output. Easiest to ignore the key value separator and only use key
-     * instead.
-     * 
-     * @param <I>
-     *            Vertex index value
-     * @param <V>
-     *            Vertex value
-     * @param <E>
-     *            Edge value
-     */
-    public static abstract class BinaryVertexWriter<I extends WritableComparable, V extends Writable, E extends Writable>
-            implements VertexWriter<I, V, E> {
-        /** Context passed to initialize */
-        private TaskAttemptContext context;
-        /** Internal line record writer */
-        private final RecordWriter<NodeWritable, NullWritable> lineRecordWriter;
-
-        /**
-         * Initialize with the LineRecordWriter.
-         * 
-         * @param lineRecordWriter
-         *            Line record writer from SequenceFileOutputFormat
-         */
-        public BinaryVertexWriter(RecordWriter<NodeWritable, NullWritable> lineRecordWriter) {
-            this.lineRecordWriter = lineRecordWriter;
-        }
-
-        @Override
-        public void initialize(TaskAttemptContext context) throws IOException {
-            this.context = context;
-        }
-
-        @Override
-        public void close(TaskAttemptContext context) throws IOException, InterruptedException {
-            lineRecordWriter.close(context);
-        }
-
-        /**
-         * Get the line record writer.
-         * 
-         * @return Record writer to be used for writing.
-         */
-        public RecordWriter<NodeWritable, NullWritable> getRecordWriter() {
-            return lineRecordWriter;
-        }
-
-        /**
-         * Get the context.
-         * 
-         * @return Context passed to initialize.
-         */
-        public TaskAttemptContext getContext() {
-            return context;
-        }
-    }
-
-    @Override
-    public void checkOutputSpecs(JobContext context) throws IOException, InterruptedException {
-        binaryOutputFormat.checkOutputSpecs(context);
-    }
-
-    @Override
-    public OutputCommitter getOutputCommitter(TaskAttemptContext context) throws IOException, InterruptedException {
-        return binaryOutputFormat.getOutputCommitter(context);
-    }
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/InitialGraphCleanVertexInputFormat.java
similarity index 86%
rename from genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexInputFormat.java
rename to genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/InitialGraphCleanVertexInputFormat.java
index f9a3068..d6be23b 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/InitialGraphCleanVertexInputFormat.java
@@ -3,7 +3,6 @@
 import java.io.IOException;
 import java.util.List;
 
-import org.apache.hadoop.io.NullWritable;
 import org.apache.hadoop.io.Writable;
 import org.apache.hadoop.io.WritableComparable;
 import org.apache.hadoop.mapreduce.InputSplit;
@@ -14,9 +13,10 @@
 
 import edu.uci.ics.pregelix.api.io.VertexInputFormat;
 import edu.uci.ics.pregelix.api.io.VertexReader;
-import edu.uci.ics.genomix.oldtype.NodeWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 
-public class BinaryVertexInputFormat<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
+public class InitialGraphCleanVertexInputFormat<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
         extends VertexInputFormat<I, V, E, M> {
 
     /** Uses the SequenceFileInputFormat to do everything */
@@ -38,7 +38,7 @@
     public static abstract class BinaryVertexReader<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<NodeWritable, NullWritable> lineRecordReader;
+        private final RecordReader<KmerBytesWritable, NodeWritable> lineRecordReader;
         /** Context passed to initialize */
         private TaskAttemptContext context;
 
@@ -48,7 +48,7 @@
          * @param recordReader
          *            Line record reader from SequenceFileInputFormat
          */
-        public BinaryVertexReader(RecordReader<NodeWritable, NullWritable> recordReader) {
+        public BinaryVertexReader(RecordReader<KmerBytesWritable, NodeWritable> recordReader) {
             this.lineRecordReader = recordReader;
         }
 
@@ -74,7 +74,7 @@
          * 
          * @return Record reader to be used for reading.
          */
-        protected RecordReader<NodeWritable, NullWritable> getRecordReader() {
+        protected RecordReader<KmerBytesWritable, NodeWritable> getRecordReader() {
             return lineRecordReader;
         }
 
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 23a53f9..1d7bf4b 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
@@ -10,20 +10,20 @@
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.io.VertexReader;
 import edu.uci.ics.pregelix.api.util.BspUtils;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 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;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 
 public class DataCleanInputFormat extends
-    BinaryDataCleanVertexInputFormat<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
+    BinaryDataCleanVertexInputFormat<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
     /**
      * Format INPUT
      */
     @SuppressWarnings("unchecked")
     @Override
-    public VertexReader<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> createVertexReader(
+    public VertexReader<KmerBytesWritable, 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, VertexValueWritable, NullWritable, MessageWritable> {
+    BinaryDataCleanVertexReader<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
     private Vertex vertex;
-    private PositionWritable vertexId = new PositionWritable();
+    private KmerBytesWritable vertexId = new KmerBytesWritable();
     private VertexValueWritable vertexValue = new VertexValueWritable();
 
-    public BinaryDataCleanLoadGraphReader(RecordReader<PositionWritable, VertexValueWritable> recordReader) {
+    public BinaryDataCleanLoadGraphReader(RecordReader<KmerBytesWritable, VertexValueWritable> recordReader) {
         super(recordReader);
     }
 
@@ -47,7 +47,7 @@
 
     @SuppressWarnings("unchecked")
     @Override
-    public Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> getCurrentVertex()
+    public Vertex<KmerBytesWritable, 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 11606db..cbbdd9a 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
@@ -6,20 +6,20 @@
 import org.apache.hadoop.mapreduce.RecordWriter;
 import org.apache.hadoop.mapreduce.TaskAttemptContext;
 
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.io.VertexWriter;
 
 public class DataCleanOutputFormat extends
-    BinaryDataCleanVertexOutputFormat<PositionWritable, VertexValueWritable, NullWritable> {
+    BinaryDataCleanVertexOutputFormat<KmerBytesWritable, VertexValueWritable, NullWritable> {
 
     @Override
-    public VertexWriter<PositionWritable, VertexValueWritable, NullWritable> createVertexWriter(
+    public VertexWriter<KmerBytesWritable, VertexValueWritable, NullWritable> createVertexWriter(
             TaskAttemptContext context) throws IOException, InterruptedException {
         @SuppressWarnings("unchecked")
-        RecordWriter<PositionWritable, VertexValueWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
+        RecordWriter<KmerBytesWritable, VertexValueWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
         return new BinaryLoadGraphVertexWriter(recordWriter);
     }
 
@@ -27,15 +27,14 @@
      * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
      */
     public static class BinaryLoadGraphVertexWriter extends
-            BinaryVertexWriter<PositionWritable, VertexValueWritable, NullWritable> {
-        public BinaryLoadGraphVertexWriter(RecordWriter<PositionWritable, VertexValueWritable> lineRecordWriter) {
+            BinaryVertexWriter<KmerBytesWritable, VertexValueWritable, NullWritable> {
+        public BinaryLoadGraphVertexWriter(RecordWriter<KmerBytesWritable, VertexValueWritable> lineRecordWriter) {
             super(lineRecordWriter);
         }
 
         @Override
-        public void writeVertex(Vertex<PositionWritable, VertexValueWritable, NullWritable, ?> vertex)
+        public void writeVertex(Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, ?> vertex)
                 throws IOException, InterruptedException {
-            //if(vertex.getVertexValue().getState() != MessageFlag.IS_OLDHEAD)
             getRecordWriter().write(vertex.getVertexId(), vertex.getVertexValue());
         }
     }
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/InitialGraphCleanInputFormat.java
similarity index 64%
rename from genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeInputFormat.java
rename to genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
index 93781a6..db751a5 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/InitialGraphCleanInputFormat.java
@@ -10,22 +10,22 @@
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.io.VertexReader;
 import edu.uci.ics.pregelix.api.util.BspUtils;
-import edu.uci.ics.genomix.oldtype.NodeWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
-import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexInputFormat;
-import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexInputFormat.BinaryVertexReader;
+import edu.uci.ics.genomix.pregelix.api.io.binary.InitialGraphCleanVertexInputFormat;
+import edu.uci.ics.genomix.pregelix.api.io.binary.InitialGraphCleanVertexInputFormat.BinaryVertexReader;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 
-public class NaiveAlgorithmForPathMergeInputFormat extends
-        BinaryVertexInputFormat<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
+public class InitialGraphCleanInputFormat extends
+        InitialGraphCleanVertexInputFormat<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
     /**
      * Format INPUT
      */
     @SuppressWarnings("unchecked")
     @Override
-    public VertexReader<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> createVertexReader(
+    public VertexReader<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> createVertexReader(
             InputSplit split, TaskAttemptContext context) throws IOException {
         return new BinaryLoadGraphReader(binaryInputFormat.createRecordReader(split, context));
     }
@@ -33,13 +33,14 @@
 
 @SuppressWarnings("rawtypes")
 class BinaryLoadGraphReader extends
-        BinaryVertexReader<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
+        BinaryVertexReader<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
+    
     private Vertex vertex;
+    private KmerBytesWritable vertexId = new KmerBytesWritable();
     private NodeWritable node = new NodeWritable();
-    private PositionWritable vertexId = new PositionWritable();
     private VertexValueWritable vertexValue = new VertexValueWritable();
 
-    public BinaryLoadGraphReader(RecordReader<NodeWritable, NullWritable> recordReader) {
+    public BinaryLoadGraphReader(RecordReader<KmerBytesWritable, NodeWritable> recordReader) {
         super(recordReader);
     }
 
@@ -50,34 +51,35 @@
 
     @SuppressWarnings("unchecked")
     @Override
-    public Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> getCurrentVertex()
+    public Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> getCurrentVertex()
             throws IOException, InterruptedException {
         if (vertex == null)
             vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
-
+    
         vertex.getMsgList().clear();
         vertex.getEdges().clear();
-
+    
         vertex.reset();
         if (getRecordReader() != null) {
             /**
              * set the src vertex id
              */
-            node = getRecordReader().getCurrentKey();
-            vertexId.set(node.getNodeID());
+            vertexId.set(getRecordReader().getCurrentKey());
             vertex.setVertexId(vertexId);
             /**
              * set the vertex value
              */
+            node.set(getRecordReader().getCurrentValue());
+            vertexValue.setNodeIdList(node.getNodeIdList());
             vertexValue.setFFList(node.getFFList());
             vertexValue.setFRList(node.getFRList());
             vertexValue.setRFList(node.getRFList());
             vertexValue.setRRList(node.getRRList());
-            vertexValue.setKmer(node.getKmer());
+            vertexValue.setKmer(getRecordReader().getCurrentKey());
             vertexValue.setState(State.IS_NON);
             vertex.setVertexValue(vertexValue);
         }
-
+    
         return vertex;
     }
 }
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
deleted file mode 100644
index 25c884b..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeInputFormat.java
+++ /dev/null
@@ -1,82 +0,0 @@
-package edu.uci.ics.genomix.pregelix.format;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.mapreduce.InputSplit;
-import org.apache.hadoop.mapreduce.RecordReader;
-import org.apache.hadoop.mapreduce.TaskAttemptContext;
-
-import edu.uci.ics.genomix.oldtype.NodeWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
-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.VertexValueWritable;
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
-import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.pregelix.api.io.VertexReader;
-import edu.uci.ics.pregelix.api.util.BspUtils;
-
-public class LogAlgorithmForPathMergeInputFormat extends
-        BinaryVertexInputFormat<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
-    /**
-     * Format INPUT
-     */
-    @SuppressWarnings("unchecked")
-    @Override
-    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, VertexValueWritable, NullWritable, MessageWritable> {
-        private Vertex vertex = null;
-        private NodeWritable node = new NodeWritable();
-        private PositionWritable vertexId = new PositionWritable(); 
-        private VertexValueWritable vertexValue = new VertexValueWritable();
-
-        public BinaryLoadGraphReader(RecordReader<NodeWritable, NullWritable> recordReader) {
-            super(recordReader);
-        }
-
-        @Override
-        public boolean nextVertex() throws IOException, InterruptedException {
-            return getRecordReader().nextKeyValue();
-        }
-
-        @SuppressWarnings("unchecked")
-        @Override
-        public Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> getCurrentVertex()
-                throws IOException, InterruptedException {
-            if (vertex == null)
-                vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
-
-            vertex.getMsgList().clear();
-            vertex.getEdges().clear();
-
-            if (getRecordReader() != null) {
-                /**
-                 * set the src vertex id
-                 */
-                node = getRecordReader().getCurrentKey();
-                vertexId.set(node.getNodeID());
-                vertex.setVertexId(vertexId);
-                /**
-                 * set the vertex value
-                 */
-                vertexValue.setFFList(node.getFFList());
-                vertexValue.setFRList(node.getFRList());
-                vertexValue.setRFList(node.getRFList());
-                vertexValue.setRRList(node.getRRList());
-                vertexValue.setKmer(node.getKmer());
-                vertexValue.setState(State.IS_NON);
-                vertex.setVertexValue(vertexValue);
-            }
-
-            return vertex;
-        }
-    }
-
-}
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
deleted file mode 100644
index 20a4587..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForPathMergeOutputFormat.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package edu.uci.ics.genomix.pregelix.format;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.mapreduce.RecordWriter;
-import org.apache.hadoop.mapreduce.TaskAttemptContext;
-
-import edu.uci.ics.genomix.oldtype.NodeWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
-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.VertexValueWritable;
-
-public class LogAlgorithmForPathMergeOutputFormat extends
-        BinaryVertexOutputFormat<PositionWritable, VertexValueWritable, NullWritable> {
-
-    @Override
-    public VertexWriter<PositionWritable, VertexValueWritable, NullWritable> createVertexWriter(
-            TaskAttemptContext context) throws IOException, InterruptedException {
-        @SuppressWarnings("unchecked")
-        RecordWriter<NodeWritable, NullWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
-        return new BinaryLoadGraphVertexWriter(recordWriter);
-    }
-
-    /**
-     * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
-     */
-    public static class BinaryLoadGraphVertexWriter extends
-            BinaryVertexWriter<PositionWritable, VertexValueWritable, NullWritable> {
-        private NodeWritable node = new NodeWritable();
-        private NullWritable nul = NullWritable.get();
-        
-        public BinaryLoadGraphVertexWriter(RecordWriter<NodeWritable, NullWritable> lineRecordWriter) {
-            super(lineRecordWriter);
-        }
-
-        @Override
-        public void writeVertex(Vertex<PositionWritable, VertexValueWritable, NullWritable, ?> vertex)
-                throws IOException, InterruptedException {
-            node.set(vertex.getVertexId(), vertex.getVertexValue().getFFList(),
-                    vertex.getVertexValue().getFRList(), vertex.getVertexValue().getRFList(),
-                    vertex.getVertexValue().getRRList(), vertex.getVertexValue().getKmer());
-            getRecordWriter().write(node, nul);
-        }
-    }
-}
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
deleted file mode 100644
index 77a893a..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package edu.uci.ics.genomix.pregelix.format;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.mapreduce.RecordWriter;
-import org.apache.hadoop.mapreduce.TaskAttemptContext;
-
-import edu.uci.ics.genomix.oldtype.NodeWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
-import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.pregelix.api.io.VertexWriter;
-
-public class NaiveAlgorithmForPathMergeOutputFormat extends
-        BinaryVertexOutputFormat<PositionWritable, VertexValueWritable, NullWritable> {
-
-    @Override
-    public VertexWriter<PositionWritable, VertexValueWritable, NullWritable> createVertexWriter(
-            TaskAttemptContext context) throws IOException, InterruptedException {
-        @SuppressWarnings("unchecked")
-        RecordWriter<NodeWritable, NullWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
-        return new BinaryLoadGraphVertexWriter(recordWriter);
-    }
-
-    /**
-     * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
-     */
-    public static class BinaryLoadGraphVertexWriter extends
-            BinaryVertexWriter<PositionWritable, VertexValueWritable, NullWritable> {
-        private NodeWritable node = new NodeWritable();
-        private NullWritable nullWritable = NullWritable.get();
-        
-        public BinaryLoadGraphVertexWriter(RecordWriter<NodeWritable, NullWritable> lineRecordWriter) {
-            super(lineRecordWriter);
-        }
-
-        @Override
-        public void writeVertex(Vertex<PositionWritable, VertexValueWritable, NullWritable, ?> vertex)
-                throws IOException, InterruptedException {
-            node.set(vertex.getVertexId(), vertex.getVertexValue().getFFList(),
-                    vertex.getVertexValue().getFRList(), vertex.getVertexValue().getRFList(),
-                    vertex.getVertexValue().getRRList(), vertex.getVertexValue().getKmer());
-            getRecordWriter().write(node, nullWritable);
-        }
-    }
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
index 4aeffa0..b23edaf 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
@@ -7,14 +7,15 @@
 import org.apache.hadoop.io.WritableComparable;
 
 import edu.uci.ics.genomix.oldtype.PositionListWritable;
+import edu.uci.ics.genomix.type.KmerListWritable;
 
 public class AdjacencyListWritable implements WritableComparable<AdjacencyListWritable>{
-    private PositionListWritable forwardList;
-    private PositionListWritable reverseList;
+    private KmerListWritable forwardList;
+    private KmerListWritable reverseList;
     
     public AdjacencyListWritable(){
-        forwardList = new PositionListWritable();
-        reverseList = new PositionListWritable();
+        forwardList = new KmerListWritable();
+        reverseList = new KmerListWritable();
     }
 
     public void set(AdjacencyListWritable adjacencyList){
@@ -30,20 +31,20 @@
     public int getCountOfPosition(){
     	return forwardList.getCountOfPosition() + reverseList.getCountOfPosition();
     }
-    
-    public PositionListWritable getForwardList() {
+
+    public KmerListWritable getForwardList() {
         return forwardList;
     }
 
-    public void setForwardList(PositionListWritable forwardList) {
+    public void setForwardList(KmerListWritable forwardList) {
         this.forwardList = forwardList;
     }
 
-    public PositionListWritable getReverseList() {
+    public KmerListWritable getReverseList() {
         return reverseList;
     }
 
-    public void setReverseList(PositionListWritable reverseList) {
+    public void setReverseList(KmerListWritable reverseList) {
         this.reverseList = reverseList;
     }
 
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 e1e9a3e..adb1aac 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
@@ -6,7 +6,6 @@
 
 import org.apache.hadoop.io.WritableComparable;
 
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.type.CheckMessage;
 import edu.uci.ics.genomix.pregelix.type.Message;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
@@ -17,7 +16,7 @@
      * stores neighber vertexValue when pathVertex sends the message
      * file stores the point to the file that stores the chains of connected DNA
      */
-    private PositionWritable sourceVertexId;
+    private KmerBytesWritable sourceVertexId;
     private KmerBytesWritable kmer;
     private AdjacencyListWritable neighberNode; //incoming or outgoing
     private byte flag;
@@ -26,7 +25,7 @@
     private byte checkMessage;
 
     public MessageWritable() {
-        sourceVertexId = new PositionWritable();
+        sourceVertexId = new KmerBytesWritable();
         kmer = new KmerBytesWritable(0);
         neighberNode = new AdjacencyListWritable();
         flag = Message.NON;
@@ -52,11 +51,11 @@
         this.flag = msg.getFlag();
     }
 
-    public void set(PositionWritable sourceVertexId, KmerBytesWritable chainVertexId, AdjacencyListWritable neighberNode, byte message) {
+    public void set(KmerBytesWritable sourceVertexId, KmerBytesWritable chainVertexId, AdjacencyListWritable neighberNode, byte message) {
         checkMessage = 0;
         if (sourceVertexId != null) {
             checkMessage |= CheckMessage.SOURCE;
-            this.sourceVertexId.set(sourceVertexId.getReadID(),sourceVertexId.getPosInRead());
+            this.sourceVertexId.set(sourceVertexId);
         }
         if (chainVertexId != null) {
             checkMessage |= CheckMessage.CHAIN;
@@ -76,14 +75,14 @@
         flag = Message.NON;
     }
 
-    public PositionWritable getSourceVertexId() {
+    public KmerBytesWritable getSourceVertexId() {
         return sourceVertexId;
     }
 
-    public void setSourceVertexId(PositionWritable sourceVertexId) {
+    public void setSourceVertexId(KmerBytesWritable sourceVertexId) {
         if (sourceVertexId != null) {
             checkMessage |= CheckMessage.SOURCE;
-            this.sourceVertexId.set(sourceVertexId.getReadID(),sourceVertexId.getPosInRead());
+            this.sourceVertexId.set(sourceVertexId);
         }
     }
     
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index 56cc86b..f2a90d0 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -4,10 +4,10 @@
 
 import org.apache.hadoop.io.WritableComparable;
 
-import edu.uci.ics.genomix.oldtype.PositionListWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
+import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.KmerListWritable;
 
 public class VertexValueWritable implements WritableComparable<VertexValueWritable> {
 
@@ -35,30 +35,32 @@
         public static final byte SHOULD_MERGE_CLEAR = 0b1110011;
     }
     
+    private PositionListWritable nodeIdList;
     private AdjacencyListWritable incomingList;
     private AdjacencyListWritable outgoingList;
     private byte state;
     private KmerBytesWritable kmer;
-    private PositionWritable mergeDest;
+    private KmerBytesWritable mergeDest;
 
     public VertexValueWritable() {
+        nodeIdList = new PositionListWritable();
         incomingList = new AdjacencyListWritable();
         outgoingList = new AdjacencyListWritable();
         state = State.IS_NON;
         kmer = new KmerBytesWritable(0);
-        mergeDest = new PositionWritable();
+        mergeDest = new KmerBytesWritable(0);
     }
 
-    public VertexValueWritable(PositionListWritable forwardForwardList, PositionListWritable forwardReverseList,
-            PositionListWritable reverseForwardList, PositionListWritable reverseReverseList,
+    public VertexValueWritable(PositionListWritable nodeIdList, KmerListWritable forwardForwardList, KmerListWritable forwardReverseList,
+            KmerListWritable reverseForwardList, KmerListWritable reverseReverseList,
             byte state, KmerBytesWritable kmer) {
-        set(forwardForwardList, forwardReverseList, 
+        set(nodeIdList, forwardForwardList, forwardReverseList, 
                 reverseForwardList, reverseReverseList,
                 state, kmer);
     }
     
-    public void set(PositionListWritable forwardForwardList, PositionListWritable forwardReverseList,
-            PositionListWritable reverseForwardList, PositionListWritable reverseReverseList, 
+    public void set(PositionListWritable nodeIdList, KmerListWritable forwardForwardList, KmerListWritable forwardReverseList,
+            KmerListWritable reverseForwardList, KmerListWritable reverseReverseList, 
             byte state, KmerBytesWritable kmer) {
         this.incomingList.setForwardList(reverseForwardList);
         this.incomingList.setReverseList(reverseReverseList);
@@ -69,39 +71,48 @@
     }
     
     public void set(VertexValueWritable value) {
-        set(value.getFFList(),value.getFRList(),value.getRFList(),value.getRRList(),value.getState(),
+        set(value.getNodeIdList(), value.getFFList(),value.getFRList(),value.getRFList(),value.getRRList(),value.getState(),
                 value.getKmer());
     }
     
-    public PositionListWritable getFFList() {
+    
+    public PositionListWritable getNodeIdList() {
+        return nodeIdList;
+    }
+
+    public void setNodeIdList(PositionListWritable nodeIdList) {
+        this.nodeIdList.set(nodeIdList);
+    }
+
+    public KmerListWritable getFFList() {
         return outgoingList.getForwardList();
     }
 
-    public PositionListWritable getFRList() {
+    public KmerListWritable getFRList() {
         return outgoingList.getReverseList();
     }
 
-    public PositionListWritable getRFList() {
+    public KmerListWritable getRFList() {
         return incomingList.getForwardList();
     }
 
-    public PositionListWritable getRRList() {
+    public KmerListWritable getRRList() {
         return incomingList.getReverseList();
     }
     
-    public void setFFList(PositionListWritable forwardForwardList){
+    public void setFFList(KmerListWritable forwardForwardList){
         outgoingList.setForwardList(forwardForwardList);
     }
     
-    public void setFRList(PositionListWritable forwardReverseList){
+    public void setFRList(KmerListWritable forwardReverseList){
         outgoingList.setReverseList(forwardReverseList);
     }
     
-    public void setRFList(PositionListWritable reverseForwardList){
+    public void setRFList(KmerListWritable reverseForwardList){
         incomingList.setForwardList(reverseForwardList);
     }
 
-    public void setRRList(PositionListWritable reverseReverseList){
+    public void setRRList(KmerListWritable reverseReverseList){
         incomingList.setReverseList(reverseReverseList);
     }
     
@@ -141,16 +152,17 @@
         this.kmer.set(kmer);
     }
     
-    public PositionWritable getMergeDest() {
+    public KmerBytesWritable getMergeDest() {
         return mergeDest;
     }
 
-    public void setMergeDest(PositionWritable mergeDest) {
+    public void setMergeDest(KmerBytesWritable mergeDest) {
         this.mergeDest = mergeDest;
     }
 
     @Override
     public void readFields(DataInput in) throws IOException {
+        nodeIdList.readFields(in);
         incomingList.readFields(in);
         outgoingList.readFields(in);
         state = in.readByte();
@@ -160,6 +172,7 @@
 
     @Override
     public void write(DataOutput out) throws IOException {
+        nodeIdList.write(out);
         incomingList.write(out);
         outgoingList.write(out);
         out.writeByte(state);
@@ -175,12 +188,13 @@
     @Override
     public String toString() {
         StringBuilder sbuilder = new StringBuilder();
-        sbuilder.append('(');
+        sbuilder.append('{');
+        sbuilder.append(nodeIdList.toString()).append('\t');
         sbuilder.append(outgoingList.getForwardList().toString()).append('\t');
         sbuilder.append(outgoingList.getReverseList().toString()).append('\t');
         sbuilder.append(incomingList.getForwardList().toString()).append('\t');
         sbuilder.append(incomingList.getReverseList().toString()).append('\t');
-        sbuilder.append(kmer.toString()).append(')');
+        sbuilder.append(kmer.toString()).append('}');
         return sbuilder.toString();
     }
     
@@ -195,8 +209,8 @@
     /*
      * Process any changes to value.  This is for edge updates
      */
-    public void processUpdates(byte neighborToDeleteDir, PositionWritable nodeToDelete,
-            byte neighborToMergeDir, PositionWritable nodeToAdd){
+    public void processUpdates(byte neighborToDeleteDir, KmerBytesWritable nodeToDelete,
+            byte neighborToMergeDir, KmerBytesWritable nodeToAdd){
 //        TODO
 //        this.getListFromDir(neighborToDeleteDir).remove(nodeToDelete);
 //        this.getListFromDir(neighborToMergeDir).append(nodeToDelete);
@@ -234,8 +248,8 @@
     /*
      * Process any changes to value.  This is for merging
      */
-    public void processMerges(byte neighborToDeleteDir, PositionWritable nodeToDelete,
-            byte neighborToMergeDir, PositionWritable nodeToAdd, 
+    public void processMerges(byte neighborToDeleteDir, KmerBytesWritable nodeToDelete,
+            byte neighborToMergeDir, KmerBytesWritable nodeToAdd, 
             int kmerSize, KmerBytesWritable kmer){
         switch (neighborToDeleteDir & MessageFlag.DIR_MASK) {
             case MessageFlag.DIR_FF:
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
index 1a793cd..6b5562a 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
@@ -7,19 +7,19 @@
 
 
 import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
 import edu.uci.ics.genomix.pregelix.type.AdjMessage;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 
 /**
  * Naive Algorithm for path merge graph
  */
 public class BasicPathMergeVertex extends
-        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
+        Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "BasicPathMergeVertex.kmerSize";
     public static final String ITERATIONS = "BasicPathMergeVertex.iteration";
     public static int kmerSize = -1;
@@ -27,9 +27,9 @@
     
     protected MessageWritable incomingMsg = new MessageWritable();
     protected MessageWritable outgoingMsg = new MessageWritable();
-    protected PositionWritable destVertexId = new PositionWritable();
-    protected Iterator<PositionWritable> posIterator;
-    private PositionWritable pos = new PositionWritable();
+    protected KmerBytesWritable destVertexId = new KmerBytesWritable();
+    protected Iterator<KmerBytesWritable> posIterator;
+    private KmerBytesWritable kmer = new KmerBytesWritable();
     byte headFlag;
     protected byte outFlag;
     protected byte inFlag;
@@ -66,7 +66,7 @@
     /**
      * get destination vertex
      */
-    public PositionWritable getNextDestVertexId(VertexValueWritable value) {
+    public KmerBytesWritable getNextDestVertexId(VertexValueWritable value) {
         if (value.getFFList().getCountOfPosition() > 0){ // #FFList() > 0
             posIterator = value.getFFList().iterator();
             return posIterator.next();
@@ -78,7 +78,7 @@
         }
     }
 
-    public PositionWritable getPreDestVertexId(VertexValueWritable value) {
+    public KmerBytesWritable getPreDestVertexId(VertexValueWritable value) {
         if (value.getRFList().getCountOfPosition() > 0){ // #RFList() > 0
             posIterator = value.getRFList().iterator();
             return posIterator.next();
@@ -93,7 +93,7 @@
     /**
      * get destination vertex
      */
-    public PositionWritable getNextDestVertexIdAndSetFlag(VertexValueWritable value) {
+    public KmerBytesWritable getNextDestVertexIdAndSetFlag(VertexValueWritable value) {
         if (value.getFFList().getCountOfPosition() > 0){ // #FFList() > 0
             posIterator = value.getFFList().iterator();
             outFlag |= MessageFlag.DIR_FF;
@@ -108,7 +108,7 @@
         
     }
 
-    public PositionWritable getPreDestVertexIdAndSetFlag(VertexValueWritable value) {
+    public KmerBytesWritable getPreDestVertexIdAndSetFlag(VertexValueWritable value) {
         if (value.getRFList().getCountOfPosition() > 0){ // #RFList() > 0
             posIterator = value.getRFList().iterator();
             outFlag |= MessageFlag.DIR_RF;
@@ -618,8 +618,8 @@
                 //remove incomingMsg.getSourceId from RR positionList
                 posIterator = getVertexValue().getRRList().iterator();
                 while(posIterator.hasNext()){
-                    pos = posIterator.next();
-                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                    kmer = posIterator.next();
+                    if(kmer.equals(incomingMsg.getSourceVertexId())){
                         posIterator.remove();
                         break;
                     }
@@ -628,8 +628,8 @@
                 //remove incomingMsg.getSourceId from FR positionList
                 posIterator = getVertexValue().getFRList().iterator();
                 while(posIterator.hasNext()){
-                    pos = posIterator.next();
-                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                    kmer = posIterator.next();
+                    if(kmer.equals(incomingMsg.getSourceVertexId())){
                         posIterator.remove();
                         break;
                     }
@@ -638,8 +638,8 @@
                 //remove incomingMsg.getSourceId from RF positionList
                 posIterator = getVertexValue().getRFList().iterator();
                 while(posIterator.hasNext()){
-                    pos = posIterator.next();
-                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                    kmer = posIterator.next();
+                    if(kmer.equals(incomingMsg.getSourceVertexId())){
                         posIterator.remove();
                         break;
                     }
@@ -648,8 +648,8 @@
                 //remove incomingMsg.getSourceId from FF positionList
                 posIterator = getVertexValue().getFFList().iterator();
                 while(posIterator.hasNext()){
-                    pos = posIterator.next();
-                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                    kmer = posIterator.next();
+                    if(kmer.equals(incomingMsg.getSourceVertexId())){
                         posIterator.remove();
                         break;
                     }
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 05a4700..01fd71f 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
@@ -7,8 +7,6 @@
 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.NaiveAlgorithmForPathMergeInputFormat;
-import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
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 7b0dfec..b7f6a4f 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
@@ -117,7 +117,7 @@
     /**
      * get nodeId from Ad
      */
-    public static PositionWritable getNodeIdFromAdjacencyList(AdjacencyListWritable adj){
+    public static KmerBytesWritable getNodeIdFromAdjacencyList(AdjacencyListWritable adj){
         if(adj.getForwardList().getCountOfPosition() > 0)
             return adj.getForwardList().getPosition(0);
         else if(adj.getReverseList().getCountOfPosition() > 0)