diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/IntermediateNodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/IntermediateNodeWritable.java
deleted file mode 100644
index 220f45c..0000000
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/IntermediateNodeWritable.java
+++ /dev/null
@@ -1,151 +0,0 @@
-package edu.uci.ics.genomix.oldtype;
-
-import java.io.DataInput;
-import java.io.DataOutput;
-import java.io.IOException;
-import java.io.Serializable;
-
-import org.apache.hadoop.io.WritableComparable;
-
-import edu.uci.ics.genomix.type.KmerListWritable;
-import edu.uci.ics.genomix.type.PositionWritable;
-
-public class IntermediateNodeWritable implements WritableComparable<IntermediateNodeWritable>, Serializable{
-
-    private static final long serialVersionUID = 1L;
-    public static final IntermediateNodeWritable EMPTY_NODE = new IntermediateNodeWritable();
-    
-    private KmerListWritable forwardForwardList;
-    private KmerListWritable forwardReverseList;
-    private KmerListWritable reverseForwardList;
-    private KmerListWritable reverseReverseList;
-    private ReadIDWritable readId;
-    public IntermediateNodeWritable(){
-        forwardForwardList = new KmerListWritable();
-        forwardReverseList = new KmerListWritable();
-        reverseForwardList = new KmerListWritable();
-        reverseReverseList = new KmerListWritable();
-        readId = new ReadIDWritable();
-    }
-    
-    public IntermediateNodeWritable(KmerListWritable FFList, KmerListWritable FRList,
-            KmerListWritable RFList, KmerListWritable RRList, ReadIDWritable uniqueKey) {
-        this();
-        set(FFList, FRList, RFList, RRList, uniqueKey);
-    }
-    
-    public void set(IntermediateNodeWritable node){
-        set(node.forwardForwardList, node.forwardReverseList, node.reverseForwardList, 
-                node.reverseReverseList, node.readId);
-    }
-    
-    public void set(KmerListWritable FFList, KmerListWritable FRList,
-            KmerListWritable RFList, KmerListWritable RRList, ReadIDWritable uniqueKey) {
-        this.forwardForwardList.set(FFList);
-        this.forwardReverseList.set(FRList);
-        this.reverseForwardList.set(RFList);
-        this.reverseReverseList.set(RRList);
-        this.readId.set(uniqueKey);
-    }
-
-    public void reset(int kmerSize) {
-        forwardForwardList.reset();
-        forwardReverseList.reset();
-        reverseForwardList.reset();
-        reverseReverseList.reset();
-        readId.reset();
-    }
-    
-    public KmerListWritable getFFList() {
-        return forwardForwardList;
-    }
-
-    public void setFFList(KmerListWritable forwardForwardList) {
-        this.forwardForwardList.set(forwardForwardList);
-    }
-
-    public KmerListWritable getFRList() {
-        return forwardReverseList;
-    }
-
-    public void setFRList(KmerListWritable forwardReverseList) {
-        this.forwardReverseList.set(forwardReverseList);
-    }
-
-    public KmerListWritable getRFList() {
-        return reverseForwardList;
-    }
-
-    public void setRFList(KmerListWritable reverseForwardList) {
-        this.reverseForwardList.set(reverseForwardList);
-    }
-
-    public KmerListWritable getRRList() {
-        return reverseReverseList;
-    }
-
-    public void setRRList(KmerListWritable reverseReverseList) {
-        this.reverseReverseList.set(reverseReverseList);
-    }
-
-	public ReadIDWritable getreadId() {
-        return readId;
-    }
-
-    public void setreadId(ReadIDWritable readId) {
-        this.readId.set(readId);
-    }
-
-    @Override
-    public void readFields(DataInput in) throws IOException {
-        this.forwardForwardList.readFields(in);
-        this.forwardReverseList.readFields(in);
-        this.reverseForwardList.readFields(in);
-        this.reverseReverseList.readFields(in);
-        this.readId.readFields(in);
-    }
-
-    @Override
-    public void write(DataOutput out) throws IOException {
-        this.forwardForwardList.write(out);
-        this.forwardReverseList.write(out);
-        this.reverseForwardList.write(out);
-        this.reverseReverseList.write(out);
-        this.readId.write(out);
-    }
-
-    @Override
-    public int compareTo(IntermediateNodeWritable other) {
-        // TODO Auto-generated method stub
-        return this.readId.compareTo(other.readId);
-    }
-    
-    @Override
-    public int hashCode() {
-        return this.readId.hashCode();
-    }
-    
-    @Override
-    public boolean equals(Object o) {
-        if (o instanceof IntermediateNodeWritable) {
-            IntermediateNodeWritable nw = (IntermediateNodeWritable) o;
-            return (this.forwardForwardList.equals(nw.forwardForwardList)
-                    && this.forwardReverseList.equals(nw.forwardReverseList)
-                    && this.reverseForwardList.equals(nw.reverseForwardList)
-                    && this.reverseReverseList.equals(nw.reverseReverseList) && (this.readId.equals(nw.readId)));
-        }
-        return false;
-    }
-    
-    @Override
-    public String toString() {
-        StringBuilder sbuilder = new StringBuilder();
-        sbuilder.append('(');
-        sbuilder.append(readId.toString()).append('\t');
-        sbuilder.append(forwardForwardList.toString()).append('\t');
-        sbuilder.append(forwardReverseList.toString()).append('\t');
-        sbuilder.append(reverseForwardList.toString()).append('\t');
-        sbuilder.append(reverseReverseList.toString()).append('\t').append(')');
-        return sbuilder.toString();
-    }
-}
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 eb0bd59..88bb79c 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
@@ -56,11 +56,13 @@
     }
     
     public void append(KmerBytesWritable kmer){
-        kmerByteSize = kmer.kmerByteSize;
-        kmerlength = kmer.kmerlength;
-        setSize((1 + valueCount) * kmerByteSize); 
-        System.arraycopy(kmer.getBytes(), 0, storage, offset + valueCount * kmerByteSize, kmerByteSize);
-        valueCount += 1;
+        if(kmer != null){
+            kmerByteSize = kmer.kmerByteSize;
+            kmerlength = kmer.kmerlength;
+            setSize((1 + valueCount) * kmerByteSize); 
+            System.arraycopy(kmer.getBytes(), 0, storage, offset + valueCount * kmerByteSize, kmerByteSize);
+            valueCount += 1;
+        }
     }
     
     /*
@@ -98,6 +100,10 @@
         }
     }
     
+    public void reset() {
+        this.reset(0);
+    }
+    
     public void reset(int kmerSize) {
         kmerlength = kmerSize;
         kmerByteSize = KmerUtil.getByteNumFromK(kmerlength);
@@ -156,12 +162,32 @@
         };
         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 {
         this.valueCount = in.readInt();
-        setSize(valueCount * kmerByteSize);
-        in.readFully(storage, offset, valueCount * kmerByteSize);
+        setSize(valueCount * kmerByteSize);//kmerByteSize
+        in.readFully(storage, offset, valueCount * kmerByteSize);//kmerByteSize
     }
 
     @Override
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
index 4725e30..efa87f7 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
@@ -10,11 +10,6 @@
 
 public class NodeWritable implements WritableComparable<NodeWritable>, Serializable{
 
-//    public static class KMER{
-//        public static final byte EXIST = 0;
-//        public static final byte NON_EXIST = 1;
-//    }
-    
     private static final long serialVersionUID = 1L;
     public static final NodeWritable EMPTY_NODE = new NodeWritable(0);
     
@@ -24,7 +19,7 @@
     private KmerListWritable reverseForwardList;
     private KmerListWritable reverseReverseList;
     private KmerBytesWritable kmer;
-//    private byte kmerMark;
+    private int kmerlength = 0;
     
     // merge/update directions
     public static class DirectionFlag {
@@ -39,14 +34,14 @@
         this(0);
     }
     
-    public NodeWritable(int kmerSize) {
+    public NodeWritable(int kmerlenth) {
+        this.kmerlength = kmerlenth;
         nodeIdList = new PositionListWritable();
-        forwardForwardList = new KmerListWritable(kmerSize);
-        forwardReverseList = new KmerListWritable(kmerSize);
-        reverseForwardList = new KmerListWritable(kmerSize);
-        reverseReverseList = new KmerListWritable(kmerSize);
-        kmer = new KmerBytesWritable(kmerSize);
-//        kmerMark = KMER.NON_EXIST;
+        forwardForwardList = new KmerListWritable(kmerlenth);
+        forwardReverseList = new KmerListWritable(kmerlenth);
+        reverseForwardList = new KmerListWritable(kmerlenth);
+        reverseReverseList = new KmerListWritable(kmerlenth);
+        kmer = new KmerBytesWritable(); //in graph construction - not set kmerlength Optimization: VKmer
     }
     
     public NodeWritable(PositionListWritable nodeIdList, KmerListWritable FFList, KmerListWritable FRList,
@@ -56,6 +51,7 @@
     }
     
     public void set(NodeWritable node){
+        this.kmerlength = node.kmerlength;
         set(node.nodeIdList, node.forwardForwardList, node.forwardReverseList, node.reverseForwardList, 
                 node.reverseReverseList, node.kmer);
     }
@@ -68,17 +64,16 @@
         this.reverseForwardList.set(RFList);
         this.reverseReverseList.set(RRList);
         this.kmer.set(kmer);
-//        kmerMark = KMER.EXIST;
     }
 
     public void reset(int kmerSize) {
-        nodeIdList.reset();
-        forwardForwardList.reset(kmerSize);
-        forwardReverseList.reset(kmerSize);
-        reverseForwardList.reset(kmerSize);
-        reverseReverseList.reset(kmerSize);
-        kmer.reset(kmerSize);
-//        kmerMark = KMER.NON_EXIST;
+        this.kmerlength = kmerSize;
+        this.nodeIdList.reset();
+        this.forwardForwardList.reset(kmerSize);
+        this.forwardReverseList.reset(kmerSize);
+        this.reverseForwardList.reset(kmerSize);
+        this.reverseReverseList.reset(kmerSize);
+        this.kmer.reset(0);
     }
     
     
@@ -95,10 +90,17 @@
     }
 
     public void setKmer(KmerBytesWritable kmer) {
-//        kmerMark = KMER.EXIST;
         this.kmer.set(kmer);
     }
     
+    public int getKmerlength() {
+        return kmerlength;
+    }
+
+    public void setKmerlength(int kmerlength) {
+        this.kmerlength = kmerlength;
+    }
+
     public int getCount() {
         return kmer.getKmerLength();
     }
@@ -149,28 +151,28 @@
                 throw new RuntimeException("Unrecognized direction in getListFromDir: " + dir);
         }
     }
+	
     @Override
     public void write(DataOutput out) throws IOException {
-//        out.writeByte(kmerMark);
-//        this.nodeIdList.write(out);
+        out.writeInt(kmerlength);
+        this.nodeIdList.write(out);
         this.forwardForwardList.write(out);
         this.forwardReverseList.write(out);
-//        this.reverseForwardList.write(out);
-//        this.reverseReverseList.write(out);
-//        if(kmerMark == KMER.EXIST) 
-//        this.kmer.write(out);
+        this.reverseForwardList.write(out);
+        this.reverseReverseList.write(out);
+        this.kmer.write(out);
     }
 
     @Override
     public void readFields(DataInput in) throws IOException {
-//        kmerMark = in.readByte();
-//        this.nodeIdList.readFields(in);
+        this.kmerlength = in.readInt();
+        reset(kmerlength);
+        this.nodeIdList.readFields(in);
         this.forwardForwardList.readFields(in);
         this.forwardReverseList.readFields(in);
-//        this.reverseForwardList.readFields(in);
-//        this.reverseReverseList.readFields(in);
-//        if(kmerMark == KMER.EXIST)
-//        this.kmer.readFields(in);
+        this.reverseForwardList.readFields(in);
+        this.reverseReverseList.readFields(in);
+        this.kmer.readFields(in);
     }
 
     @Override
@@ -199,13 +201,13 @@
     @Override
     public String toString() {
         StringBuilder sbuilder = new StringBuilder();
-        sbuilder.append('(');
+        sbuilder.append('{');
         sbuilder.append(nodeIdList.toString()).append('\t');
         sbuilder.append(forwardForwardList.toString()).append('\t');
         sbuilder.append(forwardReverseList.toString()).append('\t');
         sbuilder.append(reverseForwardList.toString()).append('\t');
         sbuilder.append(reverseReverseList.toString()).append('\t');
-        sbuilder.append(kmer.toString()).append(')');
+        sbuilder.append(kmer.toString()).append('}');
         return sbuilder.toString();
     }
 
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
index 37c64aa..b4361ac 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
@@ -228,6 +228,15 @@
         merge.set(kmer1);
         merge.mergeWithRFKmer(i, kmer2);
         Assert.assertEquals("GGCACAACAACCC", merge.toString());
+        
+        String test1 = "CTA";
+        String test2 = "AGA";
+        KmerBytesWritable k1 = new KmerBytesWritable(3);
+        KmerBytesWritable k2 = new KmerBytesWritable(3);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k1.mergeWithRFKmer(3, k2);
+        Assert.assertEquals("CTAT", k1);
     }
     
     
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
index 71246a1..1bbb771 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
@@ -30,7 +30,7 @@
             Assert.assertEquals(1, kmerList.getCountOfPosition());
         }
         
-        kmerList.reset(kmer.getKmerLength());
+        kmerList.reset(0);
         //add one more kmer each time and fix kmerSize
         for (int i = 0; i < 200; i++) {
             kmer = new KmerBytesWritable(5);
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java
index 540c6eb..fc67245 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java
@@ -1,4 +1,5 @@
 package edu.uci.ics.genomix.data.test;
+
 import java.util.Random;
 
 import junit.framework.Assert;
diff --git a/genomix/genomix-hadoop/data/webmap/8 b/genomix/genomix-hadoop/data/webmap/8
new file mode 100644
index 0000000..3959d4d
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/8
@@ -0,0 +1 @@
+1	AATAGAACTT
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/2 b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/2
new file mode 100644
index 0000000..0f501fe
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/2
@@ -0,0 +1 @@
+1	AATA
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/2~ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/2~
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/2~
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/3 b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/3
new file mode 100644
index 0000000..b90246c
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/3
@@ -0,0 +1 @@
+1	AATAG
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/3~ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/3~
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/3~
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/4 b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/4
new file mode 100644
index 0000000..3f1cd5c
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/4
@@ -0,0 +1 @@
+1	AATAGA
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/4~ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/4~
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/4~
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/5 b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/5
new file mode 100644
index 0000000..a720dc4
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/5
@@ -0,0 +1 @@
+1	AATAGAA
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/5~ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/5~
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/5~
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/6 b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/6
new file mode 100644
index 0000000..7a95b7c
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/6
@@ -0,0 +1 @@
+1	AATAGAAC
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/6~ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/6~
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/6~
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/7 b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/7
new file mode 100644
index 0000000..ce4b8a8
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/7
@@ -0,0 +1 @@
+1	AATAGAACT
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/7~ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/7~
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/7~
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/8 b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/8
new file mode 100644
index 0000000..3959d4d
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/8
@@ -0,0 +1 @@
+1	AATAGAACTT
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/8~ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/8~
new file mode 100644
index 0000000..89ead1e
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/8~
@@ -0,0 +1 @@
+1	AATAGAACTTA
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/9 b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/9
new file mode 100644
index 0000000..89ead1e
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/9
@@ -0,0 +1 @@
+1	AATAGAACTTA
diff --git a/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/9~ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/9~
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/pathmerge_TestSet/9~
diff --git a/genomix/genomix-hadoop/data/webmap/test.txt b/genomix/genomix-hadoop/data/webmap/test.txt
index 17770fa..990dbd1 100644
--- a/genomix/genomix-hadoop/data/webmap/test.txt
+++ b/genomix/genomix-hadoop/data/webmap/test.txt
@@ -1 +1,3 @@
 1	AATAGAAG
+2	TATAGACC
+3	CATAGATT
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
index 3b615cb..98f561f 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
@@ -226,7 +226,7 @@
     public void setCurKmerByOldNextKmer(){
     	curKmerDir = nextKmerDir;
     	curForwardKmer.set(nextForwardKmer);
-    	preReverseKmer.set(nextReverseKmer);
+    	curReverseKmer.set(nextReverseKmer);
     }
     
     public void setMapperOutput(OutputCollector<KmerBytesWritable, NodeWritable> output) throws IOException{
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
index 6472f05..1633c26 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
@@ -3,6 +3,7 @@
 import java.io.IOException;
 import java.util.Iterator;
 
+import org.apache.hadoop.mapred.JobConf;
 import org.apache.hadoop.mapred.MapReduceBase;
 import org.apache.hadoop.mapred.OutputCollector;
 import org.apache.hadoop.mapred.Reducer;
@@ -15,19 +16,23 @@
 public class GenomixReducer extends MapReduceBase implements
 	Reducer<KmerBytesWritable, NodeWritable, KmerBytesWritable, NodeWritable>{
     
-    private NodeWritable outputNode = new NodeWritable();
-    private NodeWritable tmpNode = new NodeWritable();
+    public static int KMER_SIZE;
+    private NodeWritable outputNode;
+    private NodeWritable tmpNode;
+    
+    @Override
+    public void configure(JobConf job) {
+        KMER_SIZE = GenomixMapper.KMER_SIZE;
+        outputNode = new NodeWritable(KMER_SIZE);
+        tmpNode = new NodeWritable(KMER_SIZE);
+    }
+    
 	@Override
 	public void reduce(KmerBytesWritable key, Iterator<NodeWritable> values,
 			OutputCollector<KmerBytesWritable, NodeWritable> output,
 			Reporter reporter) throws IOException {
-		outputNode.reset(0);
+		outputNode.reset(KMER_SIZE);
 		
-//		//copy first item to outputNode
-//		if(values.hasNext()){
-//		    NodeWritable tmpNode = values.next();
-//		    outputNode.set(tmpNode);
-//		}
 		while (values.hasNext()) {
 		    tmpNode.set(values.next());
 		    outputNode.getNodeIdList().appendList(tmpNode.getNodeIdList());
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
index 4716072..217e882 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
@@ -22,13 +22,13 @@
     private JobConf conf = new JobConf();
     private static final String ACTUAL_RESULT_DIR = "actual";
     private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
-    private static final String DATA_PATH = "data/webmap/test.txt";
+    private static final String DATA_PATH = "data/webmap/pathmerge_TestSet/9";
     private static final String HDFS_PATH = "/webmap";
     private static final String RESULT_PATH = "/result";
     
 //    private static final int COUNT_REDUCER = 2;
-    private static final int SIZE_KMER = 5;
-    private static final int READ_LENGTH = 8;
+    private static final int SIZE_KMER = 3;
+    private static final int READ_LENGTH = 11;
     
     private MiniDFSCluster dfsCluster;
     private MiniMRCluster mrCluster;
@@ -45,7 +45,7 @@
     
     public void TestMapKmerToNode() throws Exception {
         GenomixDriver driver = new GenomixDriver();
-        driver.run(HDFS_PATH, RESULT_PATH, 0, SIZE_KMER, READ_LENGTH, true, HADOOP_CONF_PATH);
+        driver.run(HDFS_PATH, RESULT_PATH, 1, SIZE_KMER, READ_LENGTH, true, HADOOP_CONF_PATH);
         dumpResult();
     }
     
@@ -77,6 +77,6 @@
         Path src = new Path(RESULT_PATH);
         Path dest = new Path(ACTUAL_RESULT_DIR);
         dfs.copyToLocalFile(src, dest);
-        HadoopMiniClusterTest.copyResultsToLocal(RESULT_PATH, "test.txt", false, conf, true, dfs);
+        HadoopMiniClusterTest.copyResultsToLocal(RESULT_PATH, "actual/test.txt", false, conf, true, dfs);
     }
 }
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/2/part-00000 b/genomix/genomix-pregelix/data/PathMergeTestSet/2/part-00000
new file mode 100755
index 0000000..6be54c5
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathMergeTestSet/2/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/3/part-00000 b/genomix/genomix-pregelix/data/PathMergeTestSet/3/part-00000
new file mode 100755
index 0000000..6f2b1d8
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathMergeTestSet/3/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/4/part-00000 b/genomix/genomix-pregelix/data/PathMergeTestSet/4/part-00000
new file mode 100755
index 0000000..7fbe1a4
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathMergeTestSet/4/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/5/part-00000 b/genomix/genomix-pregelix/data/PathMergeTestSet/5/part-00000
new file mode 100755
index 0000000..1887e36
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathMergeTestSet/5/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/6/part-00000 b/genomix/genomix-pregelix/data/PathMergeTestSet/6/part-00000
new file mode 100755
index 0000000..72b4009
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathMergeTestSet/6/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/7/part-00000 b/genomix/genomix-pregelix/data/PathMergeTestSet/7/part-00000
new file mode 100755
index 0000000..394c8c9
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathMergeTestSet/7/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/8/part-00000 b/genomix/genomix-pregelix/data/PathMergeTestSet/8/part-00000
new file mode 100755
index 0000000..db653a7
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathMergeTestSet/8/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/9/part-00000 b/genomix/genomix-pregelix/data/PathMergeTestSet/9/part-00000
new file mode 100755
index 0000000..b7760c2
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathMergeTestSet/9/part-00000
Binary files differ
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/DataCleanOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java
deleted file mode 100644
index 11606db..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanOutputFormat.java
+++ /dev/null
@@ -1,42 +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.PositionWritable;
-import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexOutputFormat;
-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 DataCleanOutputFormat extends
-    BinaryDataCleanVertexOutputFormat<PositionWritable, VertexValueWritable, NullWritable> {
-
-    @Override
-    public VertexWriter<PositionWritable, VertexValueWritable, NullWritable> createVertexWriter(
-            TaskAttemptContext context) throws IOException, InterruptedException {
-        @SuppressWarnings("unchecked")
-        RecordWriter<PositionWritable, VertexValueWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
-        return new BinaryLoadGraphVertexWriter(recordWriter);
-    }
-
-    /**
-     * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
-     */
-    public static class BinaryLoadGraphVertexWriter extends
-            BinaryVertexWriter<PositionWritable, VertexValueWritable, NullWritable> {
-        public BinaryLoadGraphVertexWriter(RecordWriter<PositionWritable, VertexValueWritable> lineRecordWriter) {
-            super(lineRecordWriter);
-        }
-
-        @Override
-        public void writeVertex(Vertex<PositionWritable, 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/DataCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
similarity index 75%
rename from genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/DataCleanInputFormat.java
rename to genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
index 23a53f9..e36e344 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/GraphCleanInputFormat.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> {
+public class GraphCleanInputFormat extends
+    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/GraphCleanOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanOutputFormat.java
new file mode 100644
index 0000000..32f71be
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanOutputFormat.java
@@ -0,0 +1,41 @@
+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.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 GraphCleanOutputFormat extends
+    BinaryDataCleanVertexOutputFormat<KmerBytesWritable, VertexValueWritable, NullWritable> {
+
+    @Override
+    public VertexWriter<KmerBytesWritable, VertexValueWritable, NullWritable> createVertexWriter(
+            TaskAttemptContext context) throws IOException, InterruptedException {
+        @SuppressWarnings("unchecked")
+        RecordWriter<KmerBytesWritable, VertexValueWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
+        return new BinaryLoadGraphVertexWriter(recordWriter);
+    }
+
+    /**
+     * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
+     */
+    public static class BinaryLoadGraphVertexWriter extends
+            BinaryVertexWriter<KmerBytesWritable, VertexValueWritable, NullWritable> {
+        public BinaryLoadGraphVertexWriter(RecordWriter<KmerBytesWritable, VertexValueWritable> lineRecordWriter) {
+            super(lineRecordWriter);
+        }
+
+        @Override
+        public void writeVertex(Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, ?> vertex)
+                throws IOException, InterruptedException {
+            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 62%
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..0d685de 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 +51,36 @@
 
     @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.setKmerlength(node.getKmerlength());
+            vertexValue.setNodeIdList(node.getNodeIdList());
             vertexValue.setFFList(node.getFFList());
             vertexValue.setFRList(node.getFRList());
             vertexValue.setRFList(node.getRFList());
             vertexValue.setRRList(node.getRRList());
-            vertexValue.setKmer(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..c35ad7f 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 +7,20 @@
 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 AdjacencyListWritable(int kmerSize){
+        forwardList = new KmerListWritable(kmerSize);
+        reverseList = new KmerListWritable(kmerSize);
     }
 
     public void set(AdjacencyListWritable adjacencyList){
@@ -27,23 +33,28 @@
         reverseList.reset();
     }
     
+    public void reset(int kmerSize){
+        forwardList.reset(kmerSize);
+        reverseList.reset(kmerSize);
+    }
+    
     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..1c5f325 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;
@@ -17,16 +16,17 @@
      * 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;
     private boolean isFlip;
+    private int kmerlength = 0;
 
     private byte checkMessage;
 
     public MessageWritable() {
-        sourceVertexId = new PositionWritable();
+        sourceVertexId = new KmerBytesWritable();
         kmer = new KmerBytesWritable(0);
         neighberNode = new AdjacencyListWritable();
         flag = Message.NON;
@@ -34,7 +34,18 @@
         checkMessage = (byte) 0;
     }
     
+    public MessageWritable(int kmerSize) {
+        kmerlength = kmerSize;
+        sourceVertexId = new KmerBytesWritable();
+        kmer = new KmerBytesWritable(0);
+        neighberNode = new AdjacencyListWritable(kmerSize);
+        flag = Message.NON;
+        isFlip = false;
+        checkMessage = (byte) 0;
+    }
+    
     public void set(MessageWritable msg) {
+        this.kmerlength = msg.kmerlength;
         checkMessage = 0;
         if (sourceVertexId != null) {
             checkMessage |= CheckMessage.SOURCE;
@@ -52,11 +63,12 @@
         this.flag = msg.getFlag();
     }
 
-    public void set(PositionWritable sourceVertexId, KmerBytesWritable chainVertexId, AdjacencyListWritable neighberNode, byte message) {
+    public void set(int kmerlength, KmerBytesWritable sourceVertexId, KmerBytesWritable chainVertexId, AdjacencyListWritable neighberNode, byte message) {
+        this.kmerlength = kmerlength;
         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;
@@ -75,15 +87,22 @@
         neighberNode.reset();
         flag = Message.NON;
     }
+    
+    public void reset(int kmerSize) {
+        checkMessage = 0;
+        kmer.reset(1);
+        neighberNode.reset(kmerSize);
+        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);
         }
     }
     
@@ -131,6 +150,7 @@
 
     @Override
     public void write(DataOutput out) throws IOException {
+        out.writeInt(kmerlength);
         out.writeByte(checkMessage);
         if ((checkMessage & CheckMessage.SOURCE) != 0)
             sourceVertexId.write(out);
@@ -139,12 +159,13 @@
         if ((checkMessage & CheckMessage.NEIGHBER) != 0)
             neighberNode.write(out);
         out.writeBoolean(isFlip);
-        out.write(flag);
+        out.writeByte(flag); 
     }
 
     @Override
     public void readFields(DataInput in) throws IOException {
-        this.reset();
+        kmerlength = in.readInt();
+        this.reset(kmerlength);
         checkMessage = in.readByte();
         if ((checkMessage & CheckMessage.SOURCE) != 0)
             sourceVertexId.readFields(in);
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..5d06234 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> {
 
@@ -35,31 +35,40 @@
         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;
+    private int kmerlength = 0;
 
     public VertexValueWritable() {
+        this(0);
+    }
+    
+    public VertexValueWritable(int kmerSize){
+        kmerlength = kmerSize;
+        nodeIdList = new PositionListWritable();
         incomingList = new AdjacencyListWritable();
         outgoingList = new AdjacencyListWritable();
         state = State.IS_NON;
-        kmer = new KmerBytesWritable(0);
-        mergeDest = new PositionWritable();
+        kmer = new KmerBytesWritable(kmerSize);
+        mergeDest = new KmerBytesWritable(kmerSize);
     }
 
-    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.kmerlength = kmer.kmerByteSize;
         this.incomingList.setForwardList(reverseForwardList);
         this.incomingList.setReverseList(reverseReverseList);
         this.outgoingList.setForwardList(forwardForwardList);
@@ -69,39 +78,49 @@
     }
     
     public void set(VertexValueWritable value) {
-        set(value.getFFList(),value.getFRList(),value.getRFList(),value.getRRList(),value.getState(),
+        this.kmerlength = value.kmerlength;
+        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);
     }
     
@@ -141,30 +160,54 @@
         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;
     }
+    
+    
+    public int getKmerlength() {
+        return kmerlength;
+    }
 
+    public void setKmerlength(int kmerlength) {
+        this.kmerlength = kmerlength;
+    }
+
+    public void reset(int kmerSize) {
+        this.kmerlength = kmerSize;
+        this.nodeIdList.reset();
+        this.incomingList.getForwardList().reset(kmerSize);
+        this.incomingList.getReverseList().reset(kmerSize);
+        this.outgoingList.getForwardList().reset(kmerSize);
+        this.outgoingList.getReverseList().reset(kmerSize);
+        this.kmer.reset(0);
+    }
+    
     @Override
     public void readFields(DataInput in) throws IOException {
-        incomingList.readFields(in);
-        outgoingList.readFields(in);
-        state = in.readByte();
-        kmer.readFields(in);
-        mergeDest.readFields(in);
+        this.kmerlength = in.readInt();
+        this.reset(kmerlength);
+        this.nodeIdList.readFields(in);
+        this.incomingList.readFields(in);
+        this.outgoingList.readFields(in);
+        this.state = in.readByte();
+        this.kmer.readFields(in);
+        this.mergeDest.readFields(in);
     }
 
     @Override
     public void write(DataOutput out) throws IOException {
-        incomingList.write(out);
-        outgoingList.write(out);
-        out.writeByte(state);
-        kmer.write(out);
-        mergeDest.write(out);
+        out.writeInt(this.kmerlength);
+        this.nodeIdList.write(out);
+        this.incomingList.write(out);
+        this.outgoingList.write(out);
+        out.writeByte(this.state);
+        this.kmer.write(out);
+        this.mergeDest.write(out);
     }
 
     @Override
@@ -175,12 +218,13 @@
     @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 +239,8 @@
     /*
      * 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);
@@ -234,21 +278,25 @@
     /*
      * 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:
                 this.getFFList().remove(nodeToDelete); //set(null);
+                this.getKmer().mergeWithFFKmer(kmerSize, kmer);
                 break;
             case MessageFlag.DIR_FR:
                 this.getFRList().remove(nodeToDelete);
+                this.getKmer().mergeWithFRKmer(kmerSize, kmer);
                 break;
             case MessageFlag.DIR_RF:
                 this.getRFList().remove(nodeToDelete);
+                this.getKmer().mergeWithRFKmer(kmerSize, kmer);
                 break;
             case MessageFlag.DIR_RR:
                 this.getRRList().remove(nodeToDelete);
+                this.getKmer().mergeWithRRKmer(kmerSize, kmer);
                 break;
         }
         // TODO: remove switch below and replace with general direction merge
@@ -256,19 +304,15 @@
         
         switch (neighborToMergeDir & MessageFlag.DIR_MASK) {
             case MessageFlag.DIR_FF:
-                this.getKmer().mergeWithFFKmer(kmerSize, kmer);
                 this.getFFList().append(nodeToAdd);
                 break;
             case MessageFlag.DIR_FR:
-                this.getKmer().mergeWithFRKmer(kmerSize, kmer);
                 this.getFRList().append(nodeToAdd);
                 break;
             case MessageFlag.DIR_RF:
-                this.getKmer().mergeWithRFKmer(kmerSize, kmer);
                 this.getRFList().append(nodeToAdd);
                 break;
             case MessageFlag.DIR_RR:
-                this.getKmer().mergeWithRRKmer(kmerSize, kmer);
                 this.getRRList().append(nodeToAdd);
                 break;
         }
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 15b77bd..fa353d0 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
@@ -10,8 +10,8 @@
 import edu.uci.ics.genomix.oldtype.PositionListWritable;
 import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.client.Client;
-import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
-import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 
@@ -112,8 +112,8 @@
         /**
          * BinaryInput and BinaryOutput
          */
-        job.setVertexInputFormatClass(DataCleanInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
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 7bef7cf..9db9418 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
@@ -6,8 +6,8 @@
 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.DataCleanInputFormat;
-import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicPathMergeVertex;
@@ -167,8 +167,8 @@
         /**
          * BinaryInput and BinaryOutput
          */
-        job.setVertexInputFormatClass(DataCleanInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
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 5f30d23..ebb4f74 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
@@ -10,8 +10,8 @@
 import edu.uci.ics.genomix.oldtype.PositionListWritable;
 import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.client.Client;
-import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
-import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 
@@ -108,8 +108,8 @@
         /**
          * BinaryInput and BinaryOutput
          */
-        job.setVertexInputFormatClass(DataCleanInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
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 6ca08eb..40e3191 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
@@ -12,8 +12,8 @@
 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.DataCleanInputFormat;
-import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MergeBubbleMessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.type.AdjMessage;
@@ -356,8 +356,8 @@
         /**
          * BinaryInput and BinaryOutput
          */
-        job.setVertexInputFormatClass(DataCleanInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
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..937fa42 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
@@ -7,29 +7,29 @@
 
 
 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;
     protected int maxIteration = -1;
     
-    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 MessageWritable incomingMsg = null; // = new MessageWritable();
+    protected MessageWritable outgoingMsg = null; // = new MessageWritable();
+    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;
@@ -315,10 +315,10 @@
      * @throws IOException 
      */
     public void broadcastUpdateMsg(){
-        if((getVertexValue().getState() & MessageFlag.IS_HEAD) > 0)
+        if((getVertexValue().getState() & State.IS_HEAD) > 0)
             outFlag |= MessageFlag.IS_HEAD;
-        switch(getVertexValue().getState() & MessageFlag.SHOULD_MERGE_MASK){
-            case MessageFlag.SHOULD_MERGEWITHPREV:
+        switch(getVertexValue().getState() & State.SHOULD_MERGE_MASK){
+            case State.SHOULD_MERGEWITHPREV:
                 setSuccessorAdjMsg();
                 if(ifFlipWithPredecessor())
                     outgoingMsg.setFlip(true);
@@ -328,7 +328,7 @@
                 if(getNextDestVertexId(getVertexValue()) != null)
                     sendMsg(getNextDestVertexId(getVertexValue()), outgoingMsg);
                 break;
-            case MessageFlag.SHOULD_MERGEWITHNEXT:
+            case State.SHOULD_MERGEWITHNEXT:
                 setPredecessorAdjMsg();
                 if(ifFilpWithSuccessor())
                     outgoingMsg.setFlip(true);
@@ -365,6 +365,8 @@
                 setSuccessorAdjMsg();
                 if(ifFlipWithPredecessor())
                     outgoingMsg.setFlip(true);
+                else
+                    outgoingMsg.setFlip(false);
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
@@ -376,6 +378,8 @@
                 setPredecessorAdjMsg();
                 if(ifFilpWithSuccessor())
                     outgoingMsg.setFlip(true);
+                else
+                    outgoingMsg.setFlip(false);
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
@@ -397,6 +401,8 @@
                 setSuccessorAdjMsg();
                 if(ifFlipWithPredecessor())
                     outgoingMsg.setFlip(true);
+                else
+                    outgoingMsg.setFlip(false);
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
@@ -408,6 +414,8 @@
                 setPredecessorAdjMsg();
                 if(ifFilpWithSuccessor())
                     outgoingMsg.setFlip(true);
+                else
+                    outgoingMsg.setFlip(false);
                 outgoingMsg.setFlag(outFlag);
                 outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
                 outgoingMsg.setSourceVertexId(getVertexId());
@@ -424,20 +432,13 @@
         getVertexValue().setState(state);
     }
     
-//    public byte isHeadShouldMergeWithPrev(){
-//    	return (byte) (getVertexValue().getState() & State.HEAD_SHOULD_MERGEWITHPREV);
-//    }
     /**
      * This vertex tries to merge with next vertex and send update msg to neighber
      * @throws IOException 
      */
     public void sendUpdateMsgToPredecessor(){
-    	setStateAsMergeWithNext();
     	if(hasNextDest(getVertexValue())){
-//		    if(getVertexValue().getFFList().getLength() > 0)
-//		        getVertexValue().setMergeDest(getVertexValue().getFFList().getPosition(0));
-//		    else
-//		        getVertexValue().setMergeDest(getVertexValue().getFRList().getPosition(0));
+    	    setStateAsMergeWithNext();
 		    broadcastUpdateMsg();
     	}
     }
@@ -448,20 +449,13 @@
         getVertexValue().setState(state);
     }
     
-//    public byte isHeadShouldMergeWithNext(){
-//    	return (byte) (getVertexValue().getState() & State.HEAD_SHOULD_MERGEWITHNEXT);
-//    }
     /**
      * This vertex tries to merge with next vertex and send update msg to neighber
      * @throws IOException 
      */
     public void sendUpdateMsgToSuccessor(){
-    	setStateAsMergeWithPrev();
-    	if(hasNextDest(getVertexValue())){
-//		    if(getVertexValue().getRFList().getLength() > 0)
-//		        getVertexValue().setMergeDest(getVertexValue().getRFList().getPosition(0));
-//		    else
-//		        getVertexValue().setMergeDest(getVertexValue().getRRList().getPosition(0));
+    	if(hasPrevDest(getVertexValue())){
+    	    setStateAsMergeWithPrev();
 		    broadcastUpdateMsg();
     	}
     }
@@ -618,8 +612,8 @@
                 //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 +622,8 @@
                 //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 +632,8 @@
                 //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 +642,8 @@
                 //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..94428ca 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
@@ -7,13 +7,14 @@
 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.format.GraphCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat;
 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.MessageFlag;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 
 /*
  * vertexId: BytesWritable
@@ -55,9 +56,9 @@
     private float probBeingRandomHead = -1;
     private Random randGenerator;
     
-    private PositionWritable curID = new PositionWritable();
-    private PositionWritable nextID = new PositionWritable();
-    private PositionWritable prevID = new PositionWritable();
+    private KmerBytesWritable curKmer = new KmerBytesWritable();
+    private KmerBytesWritable nextKmer = new KmerBytesWritable();
+    private KmerBytesWritable prevKmer = new KmerBytesWritable();
     private boolean hasNext;
     private boolean hasPrev;
     private boolean curHead;
@@ -73,6 +74,10 @@
             kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
         if (maxIteration < 0)
             maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
+        if(incomingMsg == null)
+            incomingMsg = new MessageWritable(kmerSize);
+        if(outgoingMsg == null)
+            outgoingMsg = new MessageWritable(kmerSize);
         //if (randSeed < 0)
         //    randSeed = getContext().getConfiguration().getLong("randomSeed", 0);
         randSeed = getSuperstep();
@@ -91,43 +96,45 @@
         outgoingMsg.reset();
     }
 
-    protected boolean isNodeRandomHead(PositionWritable nodeID) {
+    protected boolean isNodeRandomHead(KmerBytesWritable nodeKmer) {
         // "deterministically random", based on node id
         //randGenerator.setSeed(randSeed);
         //randSeed = randGenerator.nextInt();
-        randGenerator.setSeed((randSeed ^ nodeID.hashCode()) * 100000 * getSuperstep());//randSeed + nodeID.hashCode()
+        randGenerator.setSeed((randSeed ^ nodeKmer.hashCode()) * 100000 * getSuperstep());//randSeed + nodeID.hashCode()
+        for(int i = 0; i < 500; i++)
+            randGenerator.nextFloat();
         return randGenerator.nextFloat() < probBeingRandomHead;
     }
     
     /**
-     * set nextID to the element that's next (in the node's FF or FR list), returning true when there is a next neighbor
+     * set nextKmer 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(VertexValueWritable value) {
         if (value.getFFList().getCountOfPosition() > 0) {
-            nextID.set(value.getFFList().getPosition(0));
-            nextHead = isNodeRandomHead(nextID);
+            nextKmer.set(value.getFFList().getPosition(0));
+            nextHead = isNodeRandomHead(nextKmer);
             return true;
         }
         if (value.getFRList().getCountOfPosition() > 0) {
-            nextID.set(value.getFRList().getPosition(0));
-            nextHead = isNodeRandomHead(nextID);
+            nextKmer.set(value.getFRList().getPosition(0));
+            nextHead = isNodeRandomHead(nextKmer);
             return true;
         }
         return false;
     }
 
     /**
-     * set prevID to the element that's previous (in the node's RR or RF list), returning true when there is a previous neighbor
+     * set prevKmer 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(VertexValueWritable value) {
         if (value.getRRList().getCountOfPosition() > 0) {
-            prevID.set(value.getRRList().getPosition(0));
-            prevHead = isNodeRandomHead(prevID);
+            prevKmer.set(value.getRRList().getPosition(0));
+            prevHead = isNodeRandomHead(prevKmer);
             return true;
         }
         if (value.getRFList().getCountOfPosition() > 0) {
-            prevID.set(value.getRFList().getPosition(0));
-            prevHead = isNodeRandomHead(prevID);
+            prevKmer.set(value.getRFList().getPosition(0));
+            prevHead = isNodeRandomHead(prevKmer);
             return true;
         }
         return false;
@@ -149,9 +156,9 @@
             setStateAsNoMerge();
             
             // only PATH vertices are present. Find the ID's for my neighbors
-            curID.set(getVertexId());
+            curKmer.set(getVertexId());
             
-            curHead = isNodeRandomHead(curID);
+            curHead = isNodeRandomHead(curKmer);
             
             
             // the headFlag and tailFlag's indicate if the node is at the beginning or end of a simple path. 
@@ -162,34 +169,35 @@
                 if (curHead) {
                     if (hasNext && !nextHead) {
                         // compress this head to the forward tail
-                		sendUpdateMsgToPredecessor(); //TODO up -> update  From -> to
+                		sendUpdateMsgToPredecessor(); 
                     } else if (hasPrev && !prevHead) {
                         // compress this head to the reverse tail
                         sendUpdateMsgToSuccessor();
                     } 
                 }
-            }else {
+                else {
                     // I'm a tail
                     if (hasNext && hasPrev) {
-                         if ((!nextHead && !prevHead) && (curID.compareTo(nextID) < 0 && curID.compareTo(prevID) < 0)) {
+                         if ((!nextHead && !prevHead) && (curKmer.compareTo(nextKmer) < 0 && curKmer.compareTo(prevKmer) < 0)) {
                             // tails on both sides, and I'm the "local minimum"
                             // compress me towards the tail in forward dir
                             sendUpdateMsgToPredecessor();
                         }
                     } else if (!hasPrev) {
                         // no previous node
-                        if (!nextHead && curID.compareTo(nextID) < 0) {
+                        if (!nextHead && curKmer.compareTo(nextKmer) < 0) {
                             // merge towards tail in forward dir
                             sendUpdateMsgToPredecessor();
                         }
                     } else if (!hasNext) {
                         // no next node
-                        if (!prevHead && curID.compareTo(prevID) < 0) {
+                        if (!prevHead && curKmer.compareTo(prevKmer) < 0) {
                             // merge towards tail in reverse dir
                             sendUpdateMsgToSuccessor();
                         }
                     }
                 }
+            }
         }
         else if (getSuperstep() % 4 == 0){
             //update neighber
@@ -222,8 +230,8 @@
         /**
          * BinaryInput and BinaryOutput
          */
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
+        job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
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 b8d4098..519ffb9 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
@@ -10,8 +10,8 @@
 import edu.uci.ics.genomix.oldtype.PositionListWritable;
 import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.client.Client;
-import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
-import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 
@@ -103,8 +103,8 @@
         /**
          * BinaryInput and BinaryOutput
          */
-        job.setVertexInputFormatClass(DataCleanInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
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 cecaa48..7141ae7 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
@@ -5,8 +5,8 @@
 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.DataCleanInputFormat;
-import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicPathMergeVertex;
@@ -105,8 +105,8 @@
         /**
          * BinaryInput and BinaryOutput
          */
-        job.setVertexInputFormatClass(DataCleanInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
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 e151123..bc08600 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 +12,6 @@
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.SequenceFile;
 
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
@@ -28,16 +27,14 @@
         File srcPath = new File(strSrcDir);
         for (File f : srcPath.listFiles((FilenameFilter) (new WildcardFileFilter("part*")))) {
             SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, new Path(f.getAbsolutePath()), conf);
-            //NodeWritable key = new NodeWritable(kmerSize);
-            //NullWritable value = NullWritable.get();
-            PositionWritable key = new PositionWritable();
+            KmerBytesWritable key = new KmerBytesWritable();
             VertexValueWritable value = new VertexValueWritable();
 
             while (reader.next(key, value)) {
                 if (key == null) {
                     break;
                 }
-                bw.write(key.toString() + value.toString());
+                bw.write(key.toString() + "\t" + value.toString());
                 System.out.println(key.toString());
                 bw.newLine();
             }
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)
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 488e23d..0e798fe 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
@@ -4,13 +4,9 @@
 import java.io.FileOutputStream;
 import java.io.IOException;
 
-import edu.uci.ics.genomix.oldtype.PositionWritable;
-import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
-import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
-import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeInputFormat;
-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.format.GraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat;
 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;
@@ -22,73 +18,74 @@
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.P4ForPathMergeVertex;
 import edu.uci.ics.genomix.pregelix.operator.tipremove.TipAddVertex;
 import edu.uci.ics.genomix.pregelix.operator.tipremove.TipRemoveVertex;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 
 public class JobGenerator {
 
     public static String outputBase = "src/test/resources/jobs/";
 
-    private static void generateNaiveAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
-        PregelixJob job = new PregelixJob(jobName);
-        job.setVertexClass(NaiveAlgorithmForPathMergeVertex.class);
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class); //DataCleanInputFormat
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, 3);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
+//    private static void generateNaiveAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
+//        PregelixJob job = new PregelixJob(jobName);
+//        job.setVertexClass(NaiveAlgorithmForPathMergeVertex.class);
+//        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class); //GraphCleanInputFormat
+//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+//        job.setDynamicVertexValueSize(true);
+//        job.setOutputKeyClass(PositionWritable.class);
+//        job.setOutputValueClass(VertexValueWritable.class);
+//        job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, 3);
+//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+//    }
+//
+//    private static void genNaiveAlgorithmForMergeGraph() throws IOException {
+//        generateNaiveAlgorithmForMergeGraphJob("NaiveAlgorithmForMergeGraph", outputBase
+//                + "NaiveAlgorithmForMergeGraph.xml");
+//    }
 
-    private static void genNaiveAlgorithmForMergeGraph() throws IOException {
-        generateNaiveAlgorithmForMergeGraphJob("NaiveAlgorithmForMergeGraph", outputBase
-                + "NaiveAlgorithmForMergeGraph.xml");
-    }
-
-    private static void generateLogAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
-        PregelixJob job = new PregelixJob(jobName);
-        job.setVertexClass(LogAlgorithmForPathMergeVertex.class);
-        job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class); //LogAlgorithmForPathMergeOutputFormat
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.KMER_SIZE, 3);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-
-    private static void genLogAlgorithmForMergeGraph() throws IOException {
-        generateLogAlgorithmForMergeGraphJob("LogAlgorithmForMergeGraph", outputBase + "LogAlgorithmForMergeGraph.xml");
-    }
-    
-    private static void generateP3ForMergeGraphJob(String jobName, String outputPath) throws IOException {
-        PregelixJob job = new PregelixJob(jobName);
-        job.setVertexClass(P3ForPathMergeVertex.class);
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.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);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-
-    private static void genP3ForMergeGraph() throws IOException {
-        generateP3ForMergeGraphJob("P3ForMergeGraph", outputBase
-                + "P3ForMergeGraph.xml");
-    }
+//    private static void generateLogAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
+//        PregelixJob job = new PregelixJob(jobName);
+//        job.setVertexClass(LogAlgorithmForPathMergeVertex.class);
+//        job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class);
+//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class); //LogAlgorithmForPathMergeOutputFormat
+//        job.setDynamicVertexValueSize(true);
+//        job.setOutputKeyClass(PositionWritable.class);
+//        job.setOutputValueClass(VertexValueWritable.class);
+//        job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.KMER_SIZE, 3);
+//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+//    }
+//
+//    private static void genLogAlgorithmForMergeGraph() throws IOException {
+//        generateLogAlgorithmForMergeGraphJob("LogAlgorithmForMergeGraph", outputBase + "LogAlgorithmForMergeGraph.xml");
+//    }
+//    
+//    private static void generateP3ForMergeGraphJob(String jobName, String outputPath) throws IOException {
+//        PregelixJob job = new PregelixJob(jobName);
+//        job.setVertexClass(P3ForPathMergeVertex.class);
+//        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+//        job.setDynamicVertexValueSize(true);
+//        job.setOutputKeyClass(PositionWritable.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);
+//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+//    }
+//
+//    private static void genP3ForMergeGraph() throws IOException {
+//        generateP3ForMergeGraphJob("P3ForMergeGraph", outputBase
+//                + "P3ForMergeGraph.xml");
+//    }
     
     private static void generateP4ForMergeGraphJob(String jobName, String outputPath) throws IOException {
         PregelixJob job = new PregelixJob(jobName);
         job.setVertexClass(P4ForPathMergeVertex.class);
-        job.setVertexInputFormatClass(DataCleanInputFormat.class); //NaiveAlgorithmForPathMergeInputFormat //
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputKeyClass(KmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(P4ForPathMergeVertex.KMER_SIZE, 5);
+        job.getConfiguration().setInt(P4ForPathMergeVertex.KMER_SIZE, 3);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
 
@@ -97,118 +94,118 @@
                 + "P4ForMergeGraph.xml");
     }
     
-    private static void generateTipAddGraphJob(String jobName, String outputPath) throws IOException {
-        PregelixJob job = new PregelixJob(jobName);
-        job.setVertexClass(TipAddVertex.class);
-        job.setVertexInputFormatClass(DataCleanOutputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(TipAddVertex.KMER_SIZE, 3);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-
-    private static void genTipAddGraph() throws IOException {
-        generateTipAddGraphJob("TipAddGraph", outputBase
-                + "TipAddGraph.xml");
-    }
-    
-    private static void generateTipRemoveGraphJob(String jobName, String outputPath) throws IOException {
-        PregelixJob job = new PregelixJob(jobName);
-        job.setVertexClass(TipRemoveVertex.class);
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 5);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-
-    private static void genTipRemoveGraph() throws IOException {
-        generateTipRemoveGraphJob("TipRemoveGraph", outputBase
-                + "TipRemoveGraph.xml");
-    }
-    
-    private static void generateBridgeAddGraphJob(String jobName, String outputPath) throws IOException {
-        PregelixJob job = new PregelixJob(jobName);
-        job.setVertexClass(BridgeAddVertex.class);
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(BridgeAddVertex.KMER_SIZE, 3);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-
-    private static void genBridgeAddGraph() throws IOException {
-        generateBridgeAddGraphJob("BridgeAddGraph", outputBase
-                + "BridgeAddGraph.xml");
-    }
-
-    private static void generateBridgeRemoveGraphJob(String jobName, String outputPath) throws IOException {
-        PregelixJob job = new PregelixJob(jobName);
-        job.setVertexClass(BridgeRemoveVertex.class);
-        job.setVertexInputFormatClass(DataCleanInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 5);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-
-    private static void genBridgeRemoveGraph() throws IOException {
-        generateBridgeRemoveGraphJob("BridgeRemoveGraph", outputBase
-                + "BridgeRemoveGraph.xml");
-    }
-    
-    private static void generateBubbleAddGraphJob(String jobName, String outputPath) throws IOException {
-        PregelixJob job = new PregelixJob(jobName);
-        job.setVertexClass(BubbleAddVertex.class);
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(BubbleAddVertex.KMER_SIZE, 3);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-
-    private static void genBubbleAddGraph() throws IOException {
-        generateBubbleAddGraphJob("BubbleAddGraph", outputBase
-                + "BubbleAddGraph.xml");
-    }
-    
-    private static void generateBubbleMergeGraphJob(String jobName, String outputPath) throws IOException {
-        PregelixJob job = new PregelixJob(jobName);
-        job.setVertexClass(BubbleMergeVertex.class);
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 5);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-
-    private static void genBubbleMergeGraph() throws IOException {
-        generateBubbleMergeGraphJob("BubbleMergeGraph", outputBase
-                + "BubbleMergeGraph.xml");
-    }
+//    private static void generateTipAddGraphJob(String jobName, String outputPath) throws IOException {
+//        PregelixJob job = new PregelixJob(jobName);
+//        job.setVertexClass(TipAddVertex.class);
+//        job.setVertexInputFormatClass(GraphCleanOutputFormat.class);
+//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+//        job.setDynamicVertexValueSize(true);
+//        job.setOutputKeyClass(PositionWritable.class);
+//        job.setOutputValueClass(VertexValueWritable.class);
+//        job.getConfiguration().setInt(TipAddVertex.KMER_SIZE, 3);
+//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+//    }
+//
+//    private static void genTipAddGraph() throws IOException {
+//        generateTipAddGraphJob("TipAddGraph", outputBase
+//                + "TipAddGraph.xml");
+//    }
+//    
+//    private static void generateTipRemoveGraphJob(String jobName, String outputPath) throws IOException {
+//        PregelixJob job = new PregelixJob(jobName);
+//        job.setVertexClass(TipRemoveVertex.class);
+//        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+//        job.setDynamicVertexValueSize(true);
+//        job.setOutputKeyClass(PositionWritable.class);
+//        job.setOutputValueClass(VertexValueWritable.class);
+//        job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 5);
+//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+//    }
+//
+//    private static void genTipRemoveGraph() throws IOException {
+//        generateTipRemoveGraphJob("TipRemoveGraph", outputBase
+//                + "TipRemoveGraph.xml");
+//    }
+//    
+//    private static void generateBridgeAddGraphJob(String jobName, String outputPath) throws IOException {
+//        PregelixJob job = new PregelixJob(jobName);
+//        job.setVertexClass(BridgeAddVertex.class);
+//        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+//        job.setDynamicVertexValueSize(true);
+//        job.setOutputKeyClass(PositionWritable.class);
+//        job.setOutputValueClass(VertexValueWritable.class);
+//        job.getConfiguration().setInt(BridgeAddVertex.KMER_SIZE, 3);
+//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+//    }
+//
+//    private static void genBridgeAddGraph() throws IOException {
+//        generateBridgeAddGraphJob("BridgeAddGraph", outputBase
+//                + "BridgeAddGraph.xml");
+//    }
+//
+//    private static void generateBridgeRemoveGraphJob(String jobName, String outputPath) throws IOException {
+//        PregelixJob job = new PregelixJob(jobName);
+//        job.setVertexClass(BridgeRemoveVertex.class);
+//        job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+//        job.setDynamicVertexValueSize(true);
+//        job.setOutputKeyClass(PositionWritable.class);
+//        job.setOutputValueClass(VertexValueWritable.class);
+//        job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 5);
+//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+//    }
+//
+//    private static void genBridgeRemoveGraph() throws IOException {
+//        generateBridgeRemoveGraphJob("BridgeRemoveGraph", outputBase
+//                + "BridgeRemoveGraph.xml");
+//    }
+//    
+//    private static void generateBubbleAddGraphJob(String jobName, String outputPath) throws IOException {
+//        PregelixJob job = new PregelixJob(jobName);
+//        job.setVertexClass(BubbleAddVertex.class);
+//        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+//        job.setDynamicVertexValueSize(true);
+//        job.setOutputKeyClass(PositionWritable.class);
+//        job.setOutputValueClass(VertexValueWritable.class);
+//        job.getConfiguration().setInt(BubbleAddVertex.KMER_SIZE, 3);
+//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+//    }
+//
+//    private static void genBubbleAddGraph() throws IOException {
+//        generateBubbleAddGraphJob("BubbleAddGraph", outputBase
+//                + "BubbleAddGraph.xml");
+//    }
+//    
+//    private static void generateBubbleMergeGraphJob(String jobName, String outputPath) throws IOException {
+//        PregelixJob job = new PregelixJob(jobName);
+//        job.setVertexClass(BubbleMergeVertex.class);
+//        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+//        job.setDynamicVertexValueSize(true);
+//        job.setOutputKeyClass(PositionWritable.class);
+//        job.setOutputValueClass(VertexValueWritable.class);
+//        job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 5);
+//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+//    }
+//
+//    private static void genBubbleMergeGraph() throws IOException {
+//        generateBubbleMergeGraphJob("BubbleMergeGraph", outputBase
+//                + "BubbleMergeGraph.xml");
+//    }
     
     public static void main(String[] args) throws IOException {
         //genNaiveAlgorithmForMergeGraph();
         //genLogAlgorithmForMergeGraph();
         //genP3ForMergeGraph();
         //genTipAddGraph();
-        genTipRemoveGraph();
-        genBridgeAddGraph();
-        genBridgeRemoveGraph();
-        genBubbleAddGraph();
-        genBubbleMergeGraph();
+//        genTipRemoveGraph();
+//        genBridgeAddGraph();
+//        genBridgeRemoveGraph();
+//        genBubbleAddGraph();
+//        genBubbleMergeGraph();
         genP4ForMergeGraph();
     }
 
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
index 79a13b3..5aedeb7 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
@@ -43,22 +43,16 @@
 public class PathMergeSmallTestSuite extends TestSuite {
     private static final Logger LOGGER = Logger.getLogger(PathMergeSmallTestSuite.class.getName());
 
-    public static final String PreFix = "data/actual"; //"graphbuildresult";
+    public static final String PreFix = "data/PathMergeTestSet"; //"graphbuildresult";
     public static final String[] TestDir = { PreFix + File.separator
-    + "bubblemerge/BubbleMergeGraph/bin/small_bubble"};
-    //+ "tipremove/TipRemoveGraph/bin/fr_with_tip"};
-    //+ "graphs/pathmerge/singleread"};
-    //+ "bridgeadd/BridgeAddGraph/bin/tworeads"};
-    /*+ "2", PreFix + File.separator
-    + "3", PreFix + File.separator
-    + "4", PreFix + File.separator
-    + "5", PreFix + File.separator
-    + "6", PreFix + File.separator
-    + "7", PreFix + File.separator
-    + "8", PreFix + File.separator
-    + "9", PreFix + File.separator
-    + "tworeads3", PreFix + File.separator
-    + "tworeads_6"};*/
+//    + "2", PreFix + File.separator
+//    + "3", PreFix + File.separator
+//    + "4", PreFix + File.separator
+//    + "5", PreFix + File.separator
+//    + "6", PreFix + File.separator
+//    + "7", PreFix + File.separator
+//    + "8", PreFix + File.separator
+    + "4"};
     private static final String ACTUAL_RESULT_DIR = "data/actual/pathmerge";
     private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
     private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/BridgeAddGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/BridgeAddGraph.xml
deleted file mode 100644
index 4739d59..0000000
--- a/genomix/genomix-pregelix/src/test/resources/jobs/BridgeAddGraph.xml
+++ /dev/null
@@ -1,142 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><configuration>
-<property><name>mapred.tasktracker.dns.nameserver</name><value>default</value></property>
-<property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
-<property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
-<property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
-<property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
-<property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
-<property><name>mapred.submit.replication</name><value>10</value></property>
-<property><name>ipc.server.tcpnodelay</name><value>false</value></property>
-<property><name>fs.checkpoint.dir</name><value>${hadoop.tmp.dir}/dfs/namesecondary</value></property>
-<property><name>mapred.output.compression.type</name><value>RECORD</value></property>
-<property><name>mapred.job.shuffle.merge.percent</name><value>0.66</value></property>
-<property><name>mapred.child.java.opts</name><value>-Xmx200m</value></property>
-<property><name>mapred.queue.default.acl-submit-job</name><value>*</value></property>
-<property><name>keep.failed.task.files</name><value>false</value></property>
-<property><name>mapred.jobtracker.job.history.block.size</name><value>3145728</value></property>
-<property><name>mapred.output.value.class</name><value>edu.uci.ics.genomix.pregelix.io.VertexValueWritable</value></property>
-<property><name>io.bytes.per.checksum</name><value>512</value></property>
-<property><name>mapred.task.tracker.report.address</name><value>127.0.0.1:0</value></property>
-<property><name>hadoop.util.hash.type</name><value>murmur</value></property>
-<property><name>fs.hdfs.impl</name><value>org.apache.hadoop.hdfs.DistributedFileSystem</value></property>
-<property><name>fs.ramfs.impl</name><value>org.apache.hadoop.fs.InMemoryFileSystem</value></property>
-<property><name>mapred.jobtracker.restart.recover</name><value>false</value></property>
-<property><name>fs.hftp.impl</name><value>org.apache.hadoop.hdfs.HftpFileSystem</value></property>
-<property><name>BridgeRemoveVertex.kmerSize</name><value>3</value></property>
-<property><name>fs.checkpoint.period</name><value>3600</value></property>
-<property><name>mapred.child.tmp</name><value>./tmp</value></property>
-<property><name>mapred.local.dir.minspacekill</name><value>0</value></property>
-<property><name>map.sort.class</name><value>org.apache.hadoop.util.QuickSort</value></property>
-<property><name>hadoop.logfile.count</name><value>10</value></property>
-<property><name>ipc.client.connection.maxidletime</name><value>10000</value></property>
-<property><name>io.map.index.skip</name><value>0</value></property>
-<property><name>mapred.tasktracker.expiry.interval</name><value>600000</value></property>
-<property><name>mapred.output.compress</name><value>false</value></property>
-<property><name>io.seqfile.lazydecompress</name><value>true</value></property>
-<property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
-<property><name>fs.checkpoint.size</name><value>67108864</value></property>
-<property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
-<property><name>mapred.job.name</name><value>BridgeAddGraph</value></property>
-<property><name>local.cache.size</name><value>10737418240</value></property>
-<property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
-<property><name>mapred.userlog.limit.kb</name><value>0</value></property>
-<property><name>fs.file.impl</name><value>org.apache.hadoop.fs.LocalFileSystem</value></property>
-<property><name>mapred.task.tracker.http.address</name><value>0.0.0.0:50060</value></property>
-<property><name>mapred.task.timeout</name><value>600000</value></property>
-<property><name>fs.kfs.impl</name><value>org.apache.hadoop.fs.kfs.KosmosFileSystem</value></property>
-<property><name>mapred.max.tracker.blacklists</name><value>4</value></property>
-<property><name>fs.s3.buffer.dir</name><value>${hadoop.tmp.dir}/s3</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.dir</name><value>/jobtracker/jobsInfo</value></property>
-<property><name>ipc.client.kill.max</name><value>10</value></property>
-<property><name>mapred.tasktracker.instrumentation</name><value>org.apache.hadoop.mapred.TaskTrackerMetricsInst</value></property>
-<property><name>mapred.reduce.tasks.speculative.execution</name><value>true</value></property>
-<property><name>io.sort.record.percent</name><value>0.05</value></property>
-<property><name>hadoop.security.authorization</name><value>false</value></property>
-<property><name>mapred.max.tracker.failures</name><value>4</value></property>
-<property><name>mapred.jobtracker.taskScheduler</name><value>org.apache.hadoop.mapred.JobQueueTaskScheduler</value></property>
-<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
-<property><name>mapred.map.tasks</name><value>2</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
-<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
-<property><name>fs.default.name</name><value>file:///</value></property>
-<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.PositionWritable</value></property>
-<property><name>tasktracker.http.threads</name><value>40</value></property>
-<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
-<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
-<property><name>mapred.reduce.tasks</name><value>1</value></property>
-<property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.ScriptBasedMapping</value></property>
-<property><name>pregelix.vertexClass</name><value>edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeAddVertex</value></property>
-<property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
-<property><name>io.file.buffer.size</name><value>4096</value></property>
-<property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
-<property><name>mapred.tasktracker.indexcache.mb</name><value>10</value></property>
-<property><name>mapred.tasktracker.map.tasks.maximum</name><value>2</value></property>
-<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
-<property><name>mapred.task.profile.maps</name><value>0-2</value></property>
-<property><name>hadoop.native.lib</name><value>true</value></property>
-<property><name>fs.s3.block.size</name><value>67108864</value></property>
-<property><name>mapred.job.reuse.jvm.num.tasks</name><value>1</value></property>
-<property><name>mapred.job.tracker.http.address</name><value>0.0.0.0:50030</value></property>
-<property><name>mapred.tasktracker.reduce.tasks.maximum</name><value>2</value></property>
-<property><name>io.compression.codecs</name><value>org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec</value></property>
-<property><name>mapred.job.shuffle.input.buffer.percent</name><value>0.70</value></property>
-<property><name>io.seqfile.compress.blocksize</name><value>1000000</value></property>
-<property><name>mapred.queue.names</name><value>default</value></property>
-<property><name>fs.har.impl</name><value>org.apache.hadoop.fs.HarFileSystem</value></property>
-<property><name>io.mapfile.bloom.error.rate</name><value>0.005</value></property>
-<property><name>mapred.job.tracker</name><value>local</value></property>
-<property><name>io.skip.checksum.errors</name><value>false</value></property>
-<property><name>mapred.reduce.max.attempts</name><value>4</value></property>
-<property><name>fs.s3.maxRetries</name><value>4</value></property>
-<property><name>ipc.server.listen.queue.size</name><value>128</value></property>
-<property><name>fs.trash.interval</name><value>0</value></property>
-<property><name>mapred.local.dir.minspacestart</name><value>0</value></property>
-<property><name>fs.s3.impl</name><value>org.apache.hadoop.fs.s3.S3FileSystem</value></property>
-<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
-<property><name>io.mapfile.bloom.size</name><value>1048576</value></property>
-<property><name>io.sort.mb</name><value>100</value></property>
-<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
-<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>mapred.task.profile</name><value>false</value></property>
-<property><name>job.end.retry.interval</name><value>30000</value></property>
-<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
-<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
-<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
-<property><name>webinterface.private.actions</name><value>false</value></property>
-<property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${user.name}</value></property>
-<property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
-<property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
-<property><name>mapred.merge.recordsBeforeProgress</name><value>10000</value></property>
-<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.compress.map.output</name><value>false</value></property>
-<property><name>io.sort.spill.percent</name><value>0.80</value></property>
-<property><name>fs.checkpoint.edits.dir</name><value>${fs.checkpoint.dir}</value></property>
-<property><name>mapred.userlog.retain.hours</name><value>24</value></property>
-<property><name>mapred.system.dir</name><value>${hadoop.tmp.dir}/mapred/system</value></property>
-<property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
-<property><name>job.end.retry.attempts</name><value>0</value></property>
-<property><name>ipc.client.idlethreshold</name><value>4000</value></property>
-<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat</value></property>
-<property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
-<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
-<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
-<property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat</value></property>
-<property><name>mapred.job.queue.name</name><value>default</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
-<property><name>pregelix.incStateLength</name><value>true</value></property>
-<property><name>mapred.reduce.slowstart.completed.maps</name><value>0.05</value></property>
-<property><name>topology.script.number.args</name><value>100</value></property>
-<property><name>mapred.skip.map.max.skip.records</name><value>0</value></property>
-<property><name>fs.ftp.impl</name><value>org.apache.hadoop.fs.ftp.FTPFileSystem</value></property>
-<property><name>mapred.task.cache.levels</name><value>2</value></property>
-<property><name>mapred.job.tracker.handler.count</name><value>10</value></property>
-<property><name>io.serializations</name><value>org.apache.hadoop.io.serializer.WritableSerialization</value></property>
-<property><name>ipc.client.connect.max.retries</name><value>10</value></property>
-<property><name>mapred.min.split.size</name><value>0</value></property>
-<property><name>mapred.map.max.attempts</name><value>4</value></property>
-<property><name>jobclient.output.filter</name><value>FAILED</value></property>
-<property><name>ipc.client.tcpnodelay</name><value>false</value></property>
-<property><name>mapred.acls.enabled</name><value>false</value></property>
-</configuration>
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/BridgeRemoveGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/BridgeRemoveGraph.xml
deleted file mode 100644
index f9b801a..0000000
--- a/genomix/genomix-pregelix/src/test/resources/jobs/BridgeRemoveGraph.xml
+++ /dev/null
@@ -1,142 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><configuration>
-<property><name>mapred.tasktracker.dns.nameserver</name><value>default</value></property>
-<property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
-<property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
-<property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
-<property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
-<property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
-<property><name>mapred.submit.replication</name><value>10</value></property>
-<property><name>ipc.server.tcpnodelay</name><value>false</value></property>
-<property><name>fs.checkpoint.dir</name><value>${hadoop.tmp.dir}/dfs/namesecondary</value></property>
-<property><name>mapred.output.compression.type</name><value>RECORD</value></property>
-<property><name>mapred.job.shuffle.merge.percent</name><value>0.66</value></property>
-<property><name>mapred.child.java.opts</name><value>-Xmx200m</value></property>
-<property><name>mapred.queue.default.acl-submit-job</name><value>*</value></property>
-<property><name>keep.failed.task.files</name><value>false</value></property>
-<property><name>mapred.jobtracker.job.history.block.size</name><value>3145728</value></property>
-<property><name>mapred.output.value.class</name><value>edu.uci.ics.genomix.pregelix.io.VertexValueWritable</value></property>
-<property><name>io.bytes.per.checksum</name><value>512</value></property>
-<property><name>mapred.task.tracker.report.address</name><value>127.0.0.1:0</value></property>
-<property><name>hadoop.util.hash.type</name><value>murmur</value></property>
-<property><name>fs.hdfs.impl</name><value>org.apache.hadoop.hdfs.DistributedFileSystem</value></property>
-<property><name>fs.ramfs.impl</name><value>org.apache.hadoop.fs.InMemoryFileSystem</value></property>
-<property><name>mapred.jobtracker.restart.recover</name><value>false</value></property>
-<property><name>fs.hftp.impl</name><value>org.apache.hadoop.hdfs.HftpFileSystem</value></property>
-<property><name>fs.checkpoint.period</name><value>3600</value></property>
-<property><name>mapred.child.tmp</name><value>./tmp</value></property>
-<property><name>mapred.local.dir.minspacekill</name><value>0</value></property>
-<property><name>map.sort.class</name><value>org.apache.hadoop.util.QuickSort</value></property>
-<property><name>hadoop.logfile.count</name><value>10</value></property>
-<property><name>ipc.client.connection.maxidletime</name><value>10000</value></property>
-<property><name>io.map.index.skip</name><value>0</value></property>
-<property><name>mapred.tasktracker.expiry.interval</name><value>600000</value></property>
-<property><name>mapred.output.compress</name><value>false</value></property>
-<property><name>io.seqfile.lazydecompress</name><value>true</value></property>
-<property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
-<property><name>fs.checkpoint.size</name><value>67108864</value></property>
-<property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
-<property><name>mapred.job.name</name><value>BridgeRemoveGraph</value></property>
-<property><name>local.cache.size</name><value>10737418240</value></property>
-<property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
-<property><name>mapred.userlog.limit.kb</name><value>0</value></property>
-<property><name>fs.file.impl</name><value>org.apache.hadoop.fs.LocalFileSystem</value></property>
-<property><name>mapred.task.tracker.http.address</name><value>0.0.0.0:50060</value></property>
-<property><name>mapred.task.timeout</name><value>600000</value></property>
-<property><name>fs.kfs.impl</name><value>org.apache.hadoop.fs.kfs.KosmosFileSystem</value></property>
-<property><name>mapred.max.tracker.blacklists</name><value>4</value></property>
-<property><name>fs.s3.buffer.dir</name><value>${hadoop.tmp.dir}/s3</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.dir</name><value>/jobtracker/jobsInfo</value></property>
-<property><name>ipc.client.kill.max</name><value>10</value></property>
-<property><name>mapred.tasktracker.instrumentation</name><value>org.apache.hadoop.mapred.TaskTrackerMetricsInst</value></property>
-<property><name>mapred.reduce.tasks.speculative.execution</name><value>true</value></property>
-<property><name>io.sort.record.percent</name><value>0.05</value></property>
-<property><name>hadoop.security.authorization</name><value>false</value></property>
-<property><name>mapred.max.tracker.failures</name><value>4</value></property>
-<property><name>mapred.jobtracker.taskScheduler</name><value>org.apache.hadoop.mapred.JobQueueTaskScheduler</value></property>
-<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
-<property><name>mapred.map.tasks</name><value>2</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
-<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
-<property><name>fs.default.name</name><value>file:///</value></property>
-<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.PositionWritable</value></property>
-<property><name>tasktracker.http.threads</name><value>40</value></property>
-<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
-<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
-<property><name>mapred.reduce.tasks</name><value>1</value></property>
-<property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.ScriptBasedMapping</value></property>
-<property><name>pregelix.vertexClass</name><value>edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeRemoveVertex</value></property>
-<property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
-<property><name>io.file.buffer.size</name><value>4096</value></property>
-<property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
-<property><name>mapred.tasktracker.indexcache.mb</name><value>10</value></property>
-<property><name>mapred.tasktracker.map.tasks.maximum</name><value>2</value></property>
-<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
-<property><name>mapred.task.profile.maps</name><value>0-2</value></property>
-<property><name>hadoop.native.lib</name><value>true</value></property>
-<property><name>fs.s3.block.size</name><value>67108864</value></property>
-<property><name>mapred.job.reuse.jvm.num.tasks</name><value>1</value></property>
-<property><name>mapred.job.tracker.http.address</name><value>0.0.0.0:50030</value></property>
-<property><name>mapred.tasktracker.reduce.tasks.maximum</name><value>2</value></property>
-<property><name>io.compression.codecs</name><value>org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec</value></property>
-<property><name>mapred.job.shuffle.input.buffer.percent</name><value>0.70</value></property>
-<property><name>io.seqfile.compress.blocksize</name><value>1000000</value></property>
-<property><name>mapred.queue.names</name><value>default</value></property>
-<property><name>fs.har.impl</name><value>org.apache.hadoop.fs.HarFileSystem</value></property>
-<property><name>io.mapfile.bloom.error.rate</name><value>0.005</value></property>
-<property><name>mapred.job.tracker</name><value>local</value></property>
-<property><name>io.skip.checksum.errors</name><value>false</value></property>
-<property><name>mapred.reduce.max.attempts</name><value>4</value></property>
-<property><name>fs.s3.maxRetries</name><value>4</value></property>
-<property><name>ipc.server.listen.queue.size</name><value>128</value></property>
-<property><name>fs.trash.interval</name><value>0</value></property>
-<property><name>mapred.local.dir.minspacestart</name><value>0</value></property>
-<property><name>fs.s3.impl</name><value>org.apache.hadoop.fs.s3.S3FileSystem</value></property>
-<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
-<property><name>io.mapfile.bloom.size</name><value>1048576</value></property>
-<property><name>io.sort.mb</name><value>100</value></property>
-<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
-<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>BasicPathMergeVertex.kmerSize</name><value>5</value></property>
-<property><name>mapred.task.profile</name><value>false</value></property>
-<property><name>job.end.retry.interval</name><value>30000</value></property>
-<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
-<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
-<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
-<property><name>webinterface.private.actions</name><value>false</value></property>
-<property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${user.name}</value></property>
-<property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
-<property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
-<property><name>mapred.merge.recordsBeforeProgress</name><value>10000</value></property>
-<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.compress.map.output</name><value>false</value></property>
-<property><name>io.sort.spill.percent</name><value>0.80</value></property>
-<property><name>fs.checkpoint.edits.dir</name><value>${fs.checkpoint.dir}</value></property>
-<property><name>mapred.userlog.retain.hours</name><value>24</value></property>
-<property><name>mapred.system.dir</name><value>${hadoop.tmp.dir}/mapred/system</value></property>
-<property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
-<property><name>job.end.retry.attempts</name><value>0</value></property>
-<property><name>ipc.client.idlethreshold</name><value>4000</value></property>
-<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat</value></property>
-<property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
-<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
-<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
-<property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat</value></property>
-<property><name>mapred.job.queue.name</name><value>default</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
-<property><name>pregelix.incStateLength</name><value>true</value></property>
-<property><name>mapred.reduce.slowstart.completed.maps</name><value>0.05</value></property>
-<property><name>topology.script.number.args</name><value>100</value></property>
-<property><name>mapred.skip.map.max.skip.records</name><value>0</value></property>
-<property><name>fs.ftp.impl</name><value>org.apache.hadoop.fs.ftp.FTPFileSystem</value></property>
-<property><name>mapred.task.cache.levels</name><value>2</value></property>
-<property><name>mapred.job.tracker.handler.count</name><value>10</value></property>
-<property><name>io.serializations</name><value>org.apache.hadoop.io.serializer.WritableSerialization</value></property>
-<property><name>ipc.client.connect.max.retries</name><value>10</value></property>
-<property><name>mapred.min.split.size</name><value>0</value></property>
-<property><name>mapred.map.max.attempts</name><value>4</value></property>
-<property><name>jobclient.output.filter</name><value>FAILED</value></property>
-<property><name>ipc.client.tcpnodelay</name><value>false</value></property>
-<property><name>mapred.acls.enabled</name><value>false</value></property>
-</configuration>
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/BubbleAddGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/BubbleAddGraph.xml
deleted file mode 100644
index 452834a..0000000
--- a/genomix/genomix-pregelix/src/test/resources/jobs/BubbleAddGraph.xml
+++ /dev/null
@@ -1,142 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><configuration>
-<property><name>mapred.tasktracker.dns.nameserver</name><value>default</value></property>
-<property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
-<property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
-<property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
-<property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
-<property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
-<property><name>mapred.submit.replication</name><value>10</value></property>
-<property><name>ipc.server.tcpnodelay</name><value>false</value></property>
-<property><name>fs.checkpoint.dir</name><value>${hadoop.tmp.dir}/dfs/namesecondary</value></property>
-<property><name>mapred.output.compression.type</name><value>RECORD</value></property>
-<property><name>mapred.job.shuffle.merge.percent</name><value>0.66</value></property>
-<property><name>mapred.child.java.opts</name><value>-Xmx200m</value></property>
-<property><name>mapred.queue.default.acl-submit-job</name><value>*</value></property>
-<property><name>keep.failed.task.files</name><value>false</value></property>
-<property><name>mapred.jobtracker.job.history.block.size</name><value>3145728</value></property>
-<property><name>mapred.output.value.class</name><value>edu.uci.ics.genomix.pregelix.io.VertexValueWritable</value></property>
-<property><name>io.bytes.per.checksum</name><value>512</value></property>
-<property><name>mapred.task.tracker.report.address</name><value>127.0.0.1:0</value></property>
-<property><name>hadoop.util.hash.type</name><value>murmur</value></property>
-<property><name>fs.hdfs.impl</name><value>org.apache.hadoop.hdfs.DistributedFileSystem</value></property>
-<property><name>fs.ramfs.impl</name><value>org.apache.hadoop.fs.InMemoryFileSystem</value></property>
-<property><name>mapred.jobtracker.restart.recover</name><value>false</value></property>
-<property><name>fs.hftp.impl</name><value>org.apache.hadoop.hdfs.HftpFileSystem</value></property>
-<property><name>fs.checkpoint.period</name><value>3600</value></property>
-<property><name>mapred.child.tmp</name><value>./tmp</value></property>
-<property><name>mapred.local.dir.minspacekill</name><value>0</value></property>
-<property><name>map.sort.class</name><value>org.apache.hadoop.util.QuickSort</value></property>
-<property><name>hadoop.logfile.count</name><value>10</value></property>
-<property><name>ipc.client.connection.maxidletime</name><value>10000</value></property>
-<property><name>io.map.index.skip</name><value>0</value></property>
-<property><name>mapred.tasktracker.expiry.interval</name><value>600000</value></property>
-<property><name>mapred.output.compress</name><value>false</value></property>
-<property><name>io.seqfile.lazydecompress</name><value>true</value></property>
-<property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
-<property><name>fs.checkpoint.size</name><value>67108864</value></property>
-<property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
-<property><name>mapred.job.name</name><value>BubbleAddGraph</value></property>
-<property><name>local.cache.size</name><value>10737418240</value></property>
-<property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
-<property><name>mapred.userlog.limit.kb</name><value>0</value></property>
-<property><name>fs.file.impl</name><value>org.apache.hadoop.fs.LocalFileSystem</value></property>
-<property><name>mapred.task.tracker.http.address</name><value>0.0.0.0:50060</value></property>
-<property><name>mapred.task.timeout</name><value>600000</value></property>
-<property><name>fs.kfs.impl</name><value>org.apache.hadoop.fs.kfs.KosmosFileSystem</value></property>
-<property><name>mapred.max.tracker.blacklists</name><value>4</value></property>
-<property><name>fs.s3.buffer.dir</name><value>${hadoop.tmp.dir}/s3</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.dir</name><value>/jobtracker/jobsInfo</value></property>
-<property><name>ipc.client.kill.max</name><value>10</value></property>
-<property><name>mapred.tasktracker.instrumentation</name><value>org.apache.hadoop.mapred.TaskTrackerMetricsInst</value></property>
-<property><name>mapred.reduce.tasks.speculative.execution</name><value>true</value></property>
-<property><name>io.sort.record.percent</name><value>0.05</value></property>
-<property><name>hadoop.security.authorization</name><value>false</value></property>
-<property><name>mapred.max.tracker.failures</name><value>4</value></property>
-<property><name>mapred.jobtracker.taskScheduler</name><value>org.apache.hadoop.mapred.JobQueueTaskScheduler</value></property>
-<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
-<property><name>mapred.map.tasks</name><value>2</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
-<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
-<property><name>fs.default.name</name><value>file:///</value></property>
-<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.PositionWritable</value></property>
-<property><name>tasktracker.http.threads</name><value>40</value></property>
-<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
-<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
-<property><name>mapred.reduce.tasks</name><value>1</value></property>
-<property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.ScriptBasedMapping</value></property>
-<property><name>pregelix.vertexClass</name><value>edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleAddVertex</value></property>
-<property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
-<property><name>io.file.buffer.size</name><value>4096</value></property>
-<property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
-<property><name>mapred.tasktracker.indexcache.mb</name><value>10</value></property>
-<property><name>mapred.tasktracker.map.tasks.maximum</name><value>2</value></property>
-<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
-<property><name>mapred.task.profile.maps</name><value>0-2</value></property>
-<property><name>hadoop.native.lib</name><value>true</value></property>
-<property><name>fs.s3.block.size</name><value>67108864</value></property>
-<property><name>mapred.job.reuse.jvm.num.tasks</name><value>1</value></property>
-<property><name>mapred.job.tracker.http.address</name><value>0.0.0.0:50030</value></property>
-<property><name>mapred.tasktracker.reduce.tasks.maximum</name><value>2</value></property>
-<property><name>io.compression.codecs</name><value>org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec</value></property>
-<property><name>mapred.job.shuffle.input.buffer.percent</name><value>0.70</value></property>
-<property><name>io.seqfile.compress.blocksize</name><value>1000000</value></property>
-<property><name>mapred.queue.names</name><value>default</value></property>
-<property><name>fs.har.impl</name><value>org.apache.hadoop.fs.HarFileSystem</value></property>
-<property><name>io.mapfile.bloom.error.rate</name><value>0.005</value></property>
-<property><name>mapred.job.tracker</name><value>local</value></property>
-<property><name>BubbleAddVertex.kmerSize</name><value>3</value></property>
-<property><name>io.skip.checksum.errors</name><value>false</value></property>
-<property><name>mapred.reduce.max.attempts</name><value>4</value></property>
-<property><name>fs.s3.maxRetries</name><value>4</value></property>
-<property><name>ipc.server.listen.queue.size</name><value>128</value></property>
-<property><name>fs.trash.interval</name><value>0</value></property>
-<property><name>mapred.local.dir.minspacestart</name><value>0</value></property>
-<property><name>fs.s3.impl</name><value>org.apache.hadoop.fs.s3.S3FileSystem</value></property>
-<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
-<property><name>io.mapfile.bloom.size</name><value>1048576</value></property>
-<property><name>io.sort.mb</name><value>100</value></property>
-<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
-<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>mapred.task.profile</name><value>false</value></property>
-<property><name>job.end.retry.interval</name><value>30000</value></property>
-<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
-<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
-<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
-<property><name>webinterface.private.actions</name><value>false</value></property>
-<property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${user.name}</value></property>
-<property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
-<property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
-<property><name>mapred.merge.recordsBeforeProgress</name><value>10000</value></property>
-<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.compress.map.output</name><value>false</value></property>
-<property><name>io.sort.spill.percent</name><value>0.80</value></property>
-<property><name>fs.checkpoint.edits.dir</name><value>${fs.checkpoint.dir}</value></property>
-<property><name>mapred.userlog.retain.hours</name><value>24</value></property>
-<property><name>mapred.system.dir</name><value>${hadoop.tmp.dir}/mapred/system</value></property>
-<property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
-<property><name>job.end.retry.attempts</name><value>0</value></property>
-<property><name>ipc.client.idlethreshold</name><value>4000</value></property>
-<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat</value></property>
-<property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
-<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
-<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
-<property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat</value></property>
-<property><name>mapred.job.queue.name</name><value>default</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
-<property><name>pregelix.incStateLength</name><value>true</value></property>
-<property><name>mapred.reduce.slowstart.completed.maps</name><value>0.05</value></property>
-<property><name>topology.script.number.args</name><value>100</value></property>
-<property><name>mapred.skip.map.max.skip.records</name><value>0</value></property>
-<property><name>fs.ftp.impl</name><value>org.apache.hadoop.fs.ftp.FTPFileSystem</value></property>
-<property><name>mapred.task.cache.levels</name><value>2</value></property>
-<property><name>mapred.job.tracker.handler.count</name><value>10</value></property>
-<property><name>io.serializations</name><value>org.apache.hadoop.io.serializer.WritableSerialization</value></property>
-<property><name>ipc.client.connect.max.retries</name><value>10</value></property>
-<property><name>mapred.min.split.size</name><value>0</value></property>
-<property><name>mapred.map.max.attempts</name><value>4</value></property>
-<property><name>jobclient.output.filter</name><value>FAILED</value></property>
-<property><name>ipc.client.tcpnodelay</name><value>false</value></property>
-<property><name>mapred.acls.enabled</name><value>false</value></property>
-</configuration>
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/BubbleMergeGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/BubbleMergeGraph.xml
deleted file mode 100644
index 605a004..0000000
--- a/genomix/genomix-pregelix/src/test/resources/jobs/BubbleMergeGraph.xml
+++ /dev/null
@@ -1,142 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><configuration>
-<property><name>mapred.tasktracker.dns.nameserver</name><value>default</value></property>
-<property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
-<property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
-<property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
-<property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
-<property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
-<property><name>mapred.submit.replication</name><value>10</value></property>
-<property><name>ipc.server.tcpnodelay</name><value>false</value></property>
-<property><name>fs.checkpoint.dir</name><value>${hadoop.tmp.dir}/dfs/namesecondary</value></property>
-<property><name>mapred.output.compression.type</name><value>RECORD</value></property>
-<property><name>mapred.job.shuffle.merge.percent</name><value>0.66</value></property>
-<property><name>mapred.child.java.opts</name><value>-Xmx200m</value></property>
-<property><name>mapred.queue.default.acl-submit-job</name><value>*</value></property>
-<property><name>keep.failed.task.files</name><value>false</value></property>
-<property><name>mapred.jobtracker.job.history.block.size</name><value>3145728</value></property>
-<property><name>mapred.output.value.class</name><value>edu.uci.ics.genomix.pregelix.io.VertexValueWritable</value></property>
-<property><name>io.bytes.per.checksum</name><value>512</value></property>
-<property><name>mapred.task.tracker.report.address</name><value>127.0.0.1:0</value></property>
-<property><name>hadoop.util.hash.type</name><value>murmur</value></property>
-<property><name>fs.hdfs.impl</name><value>org.apache.hadoop.hdfs.DistributedFileSystem</value></property>
-<property><name>fs.ramfs.impl</name><value>org.apache.hadoop.fs.InMemoryFileSystem</value></property>
-<property><name>mapred.jobtracker.restart.recover</name><value>false</value></property>
-<property><name>fs.hftp.impl</name><value>org.apache.hadoop.hdfs.HftpFileSystem</value></property>
-<property><name>fs.checkpoint.period</name><value>3600</value></property>
-<property><name>mapred.child.tmp</name><value>./tmp</value></property>
-<property><name>mapred.local.dir.minspacekill</name><value>0</value></property>
-<property><name>map.sort.class</name><value>org.apache.hadoop.util.QuickSort</value></property>
-<property><name>hadoop.logfile.count</name><value>10</value></property>
-<property><name>ipc.client.connection.maxidletime</name><value>10000</value></property>
-<property><name>io.map.index.skip</name><value>0</value></property>
-<property><name>mapred.tasktracker.expiry.interval</name><value>600000</value></property>
-<property><name>mapred.output.compress</name><value>false</value></property>
-<property><name>io.seqfile.lazydecompress</name><value>true</value></property>
-<property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
-<property><name>fs.checkpoint.size</name><value>67108864</value></property>
-<property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
-<property><name>mapred.job.name</name><value>BubbleMergeGraph</value></property>
-<property><name>local.cache.size</name><value>10737418240</value></property>
-<property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
-<property><name>mapred.userlog.limit.kb</name><value>0</value></property>
-<property><name>fs.file.impl</name><value>org.apache.hadoop.fs.LocalFileSystem</value></property>
-<property><name>mapred.task.tracker.http.address</name><value>0.0.0.0:50060</value></property>
-<property><name>mapred.task.timeout</name><value>600000</value></property>
-<property><name>fs.kfs.impl</name><value>org.apache.hadoop.fs.kfs.KosmosFileSystem</value></property>
-<property><name>mapred.max.tracker.blacklists</name><value>4</value></property>
-<property><name>fs.s3.buffer.dir</name><value>${hadoop.tmp.dir}/s3</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.dir</name><value>/jobtracker/jobsInfo</value></property>
-<property><name>ipc.client.kill.max</name><value>10</value></property>
-<property><name>mapred.tasktracker.instrumentation</name><value>org.apache.hadoop.mapred.TaskTrackerMetricsInst</value></property>
-<property><name>mapred.reduce.tasks.speculative.execution</name><value>true</value></property>
-<property><name>io.sort.record.percent</name><value>0.05</value></property>
-<property><name>hadoop.security.authorization</name><value>false</value></property>
-<property><name>mapred.max.tracker.failures</name><value>4</value></property>
-<property><name>mapred.jobtracker.taskScheduler</name><value>org.apache.hadoop.mapred.JobQueueTaskScheduler</value></property>
-<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
-<property><name>mapred.map.tasks</name><value>2</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
-<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
-<property><name>fs.default.name</name><value>file:///</value></property>
-<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.PositionWritable</value></property>
-<property><name>tasktracker.http.threads</name><value>40</value></property>
-<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
-<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
-<property><name>mapred.reduce.tasks</name><value>1</value></property>
-<property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.ScriptBasedMapping</value></property>
-<property><name>pregelix.vertexClass</name><value>edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleMergeVertex</value></property>
-<property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
-<property><name>io.file.buffer.size</name><value>4096</value></property>
-<property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
-<property><name>mapred.tasktracker.indexcache.mb</name><value>10</value></property>
-<property><name>mapred.tasktracker.map.tasks.maximum</name><value>2</value></property>
-<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
-<property><name>mapred.task.profile.maps</name><value>0-2</value></property>
-<property><name>hadoop.native.lib</name><value>true</value></property>
-<property><name>fs.s3.block.size</name><value>67108864</value></property>
-<property><name>mapred.job.reuse.jvm.num.tasks</name><value>1</value></property>
-<property><name>mapred.job.tracker.http.address</name><value>0.0.0.0:50030</value></property>
-<property><name>mapred.tasktracker.reduce.tasks.maximum</name><value>2</value></property>
-<property><name>io.compression.codecs</name><value>org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec</value></property>
-<property><name>mapred.job.shuffle.input.buffer.percent</name><value>0.70</value></property>
-<property><name>io.seqfile.compress.blocksize</name><value>1000000</value></property>
-<property><name>mapred.queue.names</name><value>default</value></property>
-<property><name>fs.har.impl</name><value>org.apache.hadoop.fs.HarFileSystem</value></property>
-<property><name>io.mapfile.bloom.error.rate</name><value>0.005</value></property>
-<property><name>mapred.job.tracker</name><value>local</value></property>
-<property><name>io.skip.checksum.errors</name><value>false</value></property>
-<property><name>mapred.reduce.max.attempts</name><value>4</value></property>
-<property><name>fs.s3.maxRetries</name><value>4</value></property>
-<property><name>ipc.server.listen.queue.size</name><value>128</value></property>
-<property><name>fs.trash.interval</name><value>0</value></property>
-<property><name>mapred.local.dir.minspacestart</name><value>0</value></property>
-<property><name>fs.s3.impl</name><value>org.apache.hadoop.fs.s3.S3FileSystem</value></property>
-<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
-<property><name>io.mapfile.bloom.size</name><value>1048576</value></property>
-<property><name>io.sort.mb</name><value>100</value></property>
-<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
-<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>mapred.task.profile</name><value>false</value></property>
-<property><name>job.end.retry.interval</name><value>30000</value></property>
-<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
-<property><name>BubbleMergeVertex.kmerSize</name><value>5</value></property>
-<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
-<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
-<property><name>webinterface.private.actions</name><value>false</value></property>
-<property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${user.name}</value></property>
-<property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
-<property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
-<property><name>mapred.merge.recordsBeforeProgress</name><value>10000</value></property>
-<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.compress.map.output</name><value>false</value></property>
-<property><name>io.sort.spill.percent</name><value>0.80</value></property>
-<property><name>fs.checkpoint.edits.dir</name><value>${fs.checkpoint.dir}</value></property>
-<property><name>mapred.userlog.retain.hours</name><value>24</value></property>
-<property><name>mapred.system.dir</name><value>${hadoop.tmp.dir}/mapred/system</value></property>
-<property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
-<property><name>job.end.retry.attempts</name><value>0</value></property>
-<property><name>ipc.client.idlethreshold</name><value>4000</value></property>
-<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat</value></property>
-<property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
-<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
-<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
-<property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat</value></property>
-<property><name>mapred.job.queue.name</name><value>default</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
-<property><name>pregelix.incStateLength</name><value>true</value></property>
-<property><name>mapred.reduce.slowstart.completed.maps</name><value>0.05</value></property>
-<property><name>topology.script.number.args</name><value>100</value></property>
-<property><name>mapred.skip.map.max.skip.records</name><value>0</value></property>
-<property><name>fs.ftp.impl</name><value>org.apache.hadoop.fs.ftp.FTPFileSystem</value></property>
-<property><name>mapred.task.cache.levels</name><value>2</value></property>
-<property><name>mapred.job.tracker.handler.count</name><value>10</value></property>
-<property><name>io.serializations</name><value>org.apache.hadoop.io.serializer.WritableSerialization</value></property>
-<property><name>ipc.client.connect.max.retries</name><value>10</value></property>
-<property><name>mapred.min.split.size</name><value>0</value></property>
-<property><name>mapred.map.max.attempts</name><value>4</value></property>
-<property><name>jobclient.output.filter</name><value>FAILED</value></property>
-<property><name>ipc.client.tcpnodelay</name><value>false</value></property>
-<property><name>mapred.acls.enabled</name><value>false</value></property>
-</configuration>
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
index 5ef1509..597e5c3 100644
--- a/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
@@ -58,7 +58,7 @@
 <property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
 <property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
 <property><name>fs.default.name</name><value>file:///</value></property>
-<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.PositionWritable</value></property>
+<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.KmerBytesWritable</value></property>
 <property><name>tasktracker.http.threads</name><value>40</value></property>
 <property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
 <property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
@@ -96,7 +96,7 @@
 <property><name>io.sort.mb</name><value>100</value></property>
 <property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
 <property><name>io.sort.factor</name><value>10</value></property>
-<property><name>BasicPathMergeVertex.kmerSize</name><value>5</value></property>
+<property><name>BasicPathMergeVertex.kmerSize</name><value>3</value></property>
 <property><name>mapred.task.profile</name><value>false</value></property>
 <property><name>job.end.retry.interval</name><value>30000</value></property>
 <property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
@@ -117,12 +117,12 @@
 <property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
 <property><name>job.end.retry.attempts</name><value>0</value></property>
 <property><name>ipc.client.idlethreshold</name><value>4000</value></property>
-<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat</value></property>
+<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat</value></property>
 <property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
 <property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
 <property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
 <property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat</value></property>
+<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat</value></property>
 <property><name>mapred.job.queue.name</name><value>default</value></property>
 <property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
 <property><name>pregelix.incStateLength</name><value>true</value></property>
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/TipAddGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/TipAddGraph.xml
deleted file mode 100644
index 00c857e..0000000
--- a/genomix/genomix-pregelix/src/test/resources/jobs/TipAddGraph.xml
+++ /dev/null
@@ -1,142 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><configuration>
-<property><name>mapred.tasktracker.dns.nameserver</name><value>default</value></property>
-<property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
-<property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
-<property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
-<property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
-<property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
-<property><name>mapred.submit.replication</name><value>10</value></property>
-<property><name>ipc.server.tcpnodelay</name><value>false</value></property>
-<property><name>fs.checkpoint.dir</name><value>${hadoop.tmp.dir}/dfs/namesecondary</value></property>
-<property><name>mapred.output.compression.type</name><value>RECORD</value></property>
-<property><name>mapred.job.shuffle.merge.percent</name><value>0.66</value></property>
-<property><name>mapred.child.java.opts</name><value>-Xmx200m</value></property>
-<property><name>mapred.queue.default.acl-submit-job</name><value>*</value></property>
-<property><name>keep.failed.task.files</name><value>false</value></property>
-<property><name>mapred.jobtracker.job.history.block.size</name><value>3145728</value></property>
-<property><name>mapred.output.value.class</name><value>edu.uci.ics.genomix.pregelix.io.VertexValueWritable</value></property>
-<property><name>io.bytes.per.checksum</name><value>512</value></property>
-<property><name>mapred.task.tracker.report.address</name><value>127.0.0.1:0</value></property>
-<property><name>hadoop.util.hash.type</name><value>murmur</value></property>
-<property><name>fs.hdfs.impl</name><value>org.apache.hadoop.hdfs.DistributedFileSystem</value></property>
-<property><name>fs.ramfs.impl</name><value>org.apache.hadoop.fs.InMemoryFileSystem</value></property>
-<property><name>mapred.jobtracker.restart.recover</name><value>false</value></property>
-<property><name>fs.hftp.impl</name><value>org.apache.hadoop.hdfs.HftpFileSystem</value></property>
-<property><name>fs.checkpoint.period</name><value>3600</value></property>
-<property><name>TipAddVertex.kmerSize</name><value>3</value></property>
-<property><name>mapred.child.tmp</name><value>./tmp</value></property>
-<property><name>mapred.local.dir.minspacekill</name><value>0</value></property>
-<property><name>map.sort.class</name><value>org.apache.hadoop.util.QuickSort</value></property>
-<property><name>hadoop.logfile.count</name><value>10</value></property>
-<property><name>ipc.client.connection.maxidletime</name><value>10000</value></property>
-<property><name>io.map.index.skip</name><value>0</value></property>
-<property><name>mapred.tasktracker.expiry.interval</name><value>600000</value></property>
-<property><name>mapred.output.compress</name><value>false</value></property>
-<property><name>io.seqfile.lazydecompress</name><value>true</value></property>
-<property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
-<property><name>fs.checkpoint.size</name><value>67108864</value></property>
-<property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
-<property><name>mapred.job.name</name><value>TipAddGraph</value></property>
-<property><name>local.cache.size</name><value>10737418240</value></property>
-<property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
-<property><name>mapred.userlog.limit.kb</name><value>0</value></property>
-<property><name>fs.file.impl</name><value>org.apache.hadoop.fs.LocalFileSystem</value></property>
-<property><name>mapred.task.tracker.http.address</name><value>0.0.0.0:50060</value></property>
-<property><name>mapred.task.timeout</name><value>600000</value></property>
-<property><name>fs.kfs.impl</name><value>org.apache.hadoop.fs.kfs.KosmosFileSystem</value></property>
-<property><name>mapred.max.tracker.blacklists</name><value>4</value></property>
-<property><name>fs.s3.buffer.dir</name><value>${hadoop.tmp.dir}/s3</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.dir</name><value>/jobtracker/jobsInfo</value></property>
-<property><name>ipc.client.kill.max</name><value>10</value></property>
-<property><name>mapred.tasktracker.instrumentation</name><value>org.apache.hadoop.mapred.TaskTrackerMetricsInst</value></property>
-<property><name>mapred.reduce.tasks.speculative.execution</name><value>true</value></property>
-<property><name>io.sort.record.percent</name><value>0.05</value></property>
-<property><name>hadoop.security.authorization</name><value>false</value></property>
-<property><name>mapred.max.tracker.failures</name><value>4</value></property>
-<property><name>mapred.jobtracker.taskScheduler</name><value>org.apache.hadoop.mapred.JobQueueTaskScheduler</value></property>
-<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
-<property><name>mapred.map.tasks</name><value>2</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
-<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
-<property><name>fs.default.name</name><value>file:///</value></property>
-<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.PositionWritable</value></property>
-<property><name>tasktracker.http.threads</name><value>40</value></property>
-<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
-<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
-<property><name>mapred.reduce.tasks</name><value>1</value></property>
-<property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.ScriptBasedMapping</value></property>
-<property><name>pregelix.vertexClass</name><value>edu.uci.ics.genomix.pregelix.operator.tipremove.TipAddVertex</value></property>
-<property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
-<property><name>io.file.buffer.size</name><value>4096</value></property>
-<property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
-<property><name>mapred.tasktracker.indexcache.mb</name><value>10</value></property>
-<property><name>mapred.tasktracker.map.tasks.maximum</name><value>2</value></property>
-<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
-<property><name>mapred.task.profile.maps</name><value>0-2</value></property>
-<property><name>hadoop.native.lib</name><value>true</value></property>
-<property><name>fs.s3.block.size</name><value>67108864</value></property>
-<property><name>mapred.job.reuse.jvm.num.tasks</name><value>1</value></property>
-<property><name>mapred.job.tracker.http.address</name><value>0.0.0.0:50030</value></property>
-<property><name>mapred.tasktracker.reduce.tasks.maximum</name><value>2</value></property>
-<property><name>io.compression.codecs</name><value>org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec</value></property>
-<property><name>mapred.job.shuffle.input.buffer.percent</name><value>0.70</value></property>
-<property><name>io.seqfile.compress.blocksize</name><value>1000000</value></property>
-<property><name>mapred.queue.names</name><value>default</value></property>
-<property><name>fs.har.impl</name><value>org.apache.hadoop.fs.HarFileSystem</value></property>
-<property><name>io.mapfile.bloom.error.rate</name><value>0.005</value></property>
-<property><name>mapred.job.tracker</name><value>local</value></property>
-<property><name>io.skip.checksum.errors</name><value>false</value></property>
-<property><name>mapred.reduce.max.attempts</name><value>4</value></property>
-<property><name>fs.s3.maxRetries</name><value>4</value></property>
-<property><name>ipc.server.listen.queue.size</name><value>128</value></property>
-<property><name>fs.trash.interval</name><value>0</value></property>
-<property><name>mapred.local.dir.minspacestart</name><value>0</value></property>
-<property><name>fs.s3.impl</name><value>org.apache.hadoop.fs.s3.S3FileSystem</value></property>
-<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
-<property><name>io.mapfile.bloom.size</name><value>1048576</value></property>
-<property><name>io.sort.mb</name><value>100</value></property>
-<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
-<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>mapred.task.profile</name><value>false</value></property>
-<property><name>job.end.retry.interval</name><value>30000</value></property>
-<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
-<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
-<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
-<property><name>webinterface.private.actions</name><value>false</value></property>
-<property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${user.name}</value></property>
-<property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
-<property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
-<property><name>mapred.merge.recordsBeforeProgress</name><value>10000</value></property>
-<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.compress.map.output</name><value>false</value></property>
-<property><name>io.sort.spill.percent</name><value>0.80</value></property>
-<property><name>fs.checkpoint.edits.dir</name><value>${fs.checkpoint.dir}</value></property>
-<property><name>mapred.userlog.retain.hours</name><value>24</value></property>
-<property><name>mapred.system.dir</name><value>${hadoop.tmp.dir}/mapred/system</value></property>
-<property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
-<property><name>job.end.retry.attempts</name><value>0</value></property>
-<property><name>ipc.client.idlethreshold</name><value>4000</value></property>
-<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat</value></property>
-<property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
-<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
-<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
-<property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat</value></property>
-<property><name>mapred.job.queue.name</name><value>default</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
-<property><name>pregelix.incStateLength</name><value>true</value></property>
-<property><name>mapred.reduce.slowstart.completed.maps</name><value>0.05</value></property>
-<property><name>topology.script.number.args</name><value>100</value></property>
-<property><name>mapred.skip.map.max.skip.records</name><value>0</value></property>
-<property><name>fs.ftp.impl</name><value>org.apache.hadoop.fs.ftp.FTPFileSystem</value></property>
-<property><name>mapred.task.cache.levels</name><value>2</value></property>
-<property><name>mapred.job.tracker.handler.count</name><value>10</value></property>
-<property><name>io.serializations</name><value>org.apache.hadoop.io.serializer.WritableSerialization</value></property>
-<property><name>ipc.client.connect.max.retries</name><value>10</value></property>
-<property><name>mapred.min.split.size</name><value>0</value></property>
-<property><name>mapred.map.max.attempts</name><value>4</value></property>
-<property><name>jobclient.output.filter</name><value>FAILED</value></property>
-<property><name>ipc.client.tcpnodelay</name><value>false</value></property>
-<property><name>mapred.acls.enabled</name><value>false</value></property>
-</configuration>
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/TipRemoveGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/TipRemoveGraph.xml
deleted file mode 100644
index 588cc9f..0000000
--- a/genomix/genomix-pregelix/src/test/resources/jobs/TipRemoveGraph.xml
+++ /dev/null
@@ -1,142 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><configuration>
-<property><name>mapred.tasktracker.dns.nameserver</name><value>default</value></property>
-<property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
-<property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
-<property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
-<property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
-<property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
-<property><name>mapred.submit.replication</name><value>10</value></property>
-<property><name>ipc.server.tcpnodelay</name><value>false</value></property>
-<property><name>fs.checkpoint.dir</name><value>${hadoop.tmp.dir}/dfs/namesecondary</value></property>
-<property><name>mapred.output.compression.type</name><value>RECORD</value></property>
-<property><name>mapred.job.shuffle.merge.percent</name><value>0.66</value></property>
-<property><name>mapred.child.java.opts</name><value>-Xmx200m</value></property>
-<property><name>mapred.queue.default.acl-submit-job</name><value>*</value></property>
-<property><name>keep.failed.task.files</name><value>false</value></property>
-<property><name>mapred.jobtracker.job.history.block.size</name><value>3145728</value></property>
-<property><name>mapred.output.value.class</name><value>edu.uci.ics.genomix.pregelix.io.VertexValueWritable</value></property>
-<property><name>io.bytes.per.checksum</name><value>512</value></property>
-<property><name>mapred.task.tracker.report.address</name><value>127.0.0.1:0</value></property>
-<property><name>hadoop.util.hash.type</name><value>murmur</value></property>
-<property><name>fs.hdfs.impl</name><value>org.apache.hadoop.hdfs.DistributedFileSystem</value></property>
-<property><name>fs.ramfs.impl</name><value>org.apache.hadoop.fs.InMemoryFileSystem</value></property>
-<property><name>mapred.jobtracker.restart.recover</name><value>false</value></property>
-<property><name>fs.hftp.impl</name><value>org.apache.hadoop.hdfs.HftpFileSystem</value></property>
-<property><name>fs.checkpoint.period</name><value>3600</value></property>
-<property><name>mapred.child.tmp</name><value>./tmp</value></property>
-<property><name>mapred.local.dir.minspacekill</name><value>0</value></property>
-<property><name>map.sort.class</name><value>org.apache.hadoop.util.QuickSort</value></property>
-<property><name>hadoop.logfile.count</name><value>10</value></property>
-<property><name>ipc.client.connection.maxidletime</name><value>10000</value></property>
-<property><name>io.map.index.skip</name><value>0</value></property>
-<property><name>mapred.tasktracker.expiry.interval</name><value>600000</value></property>
-<property><name>mapred.output.compress</name><value>false</value></property>
-<property><name>io.seqfile.lazydecompress</name><value>true</value></property>
-<property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
-<property><name>fs.checkpoint.size</name><value>67108864</value></property>
-<property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
-<property><name>mapred.job.name</name><value>TipRemoveGraph</value></property>
-<property><name>local.cache.size</name><value>10737418240</value></property>
-<property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
-<property><name>mapred.userlog.limit.kb</name><value>0</value></property>
-<property><name>fs.file.impl</name><value>org.apache.hadoop.fs.LocalFileSystem</value></property>
-<property><name>mapred.task.tracker.http.address</name><value>0.0.0.0:50060</value></property>
-<property><name>mapred.task.timeout</name><value>600000</value></property>
-<property><name>fs.kfs.impl</name><value>org.apache.hadoop.fs.kfs.KosmosFileSystem</value></property>
-<property><name>mapred.max.tracker.blacklists</name><value>4</value></property>
-<property><name>fs.s3.buffer.dir</name><value>${hadoop.tmp.dir}/s3</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.dir</name><value>/jobtracker/jobsInfo</value></property>
-<property><name>ipc.client.kill.max</name><value>10</value></property>
-<property><name>mapred.tasktracker.instrumentation</name><value>org.apache.hadoop.mapred.TaskTrackerMetricsInst</value></property>
-<property><name>mapred.reduce.tasks.speculative.execution</name><value>true</value></property>
-<property><name>io.sort.record.percent</name><value>0.05</value></property>
-<property><name>hadoop.security.authorization</name><value>false</value></property>
-<property><name>mapred.max.tracker.failures</name><value>4</value></property>
-<property><name>mapred.jobtracker.taskScheduler</name><value>org.apache.hadoop.mapred.JobQueueTaskScheduler</value></property>
-<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
-<property><name>mapred.map.tasks</name><value>2</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
-<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
-<property><name>fs.default.name</name><value>file:///</value></property>
-<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.PositionWritable</value></property>
-<property><name>tasktracker.http.threads</name><value>40</value></property>
-<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
-<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
-<property><name>mapred.reduce.tasks</name><value>1</value></property>
-<property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.ScriptBasedMapping</value></property>
-<property><name>pregelix.vertexClass</name><value>edu.uci.ics.genomix.pregelix.operator.tipremove.TipRemoveVertex</value></property>
-<property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
-<property><name>io.file.buffer.size</name><value>4096</value></property>
-<property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
-<property><name>mapred.tasktracker.indexcache.mb</name><value>10</value></property>
-<property><name>mapred.tasktracker.map.tasks.maximum</name><value>2</value></property>
-<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
-<property><name>mapred.task.profile.maps</name><value>0-2</value></property>
-<property><name>hadoop.native.lib</name><value>true</value></property>
-<property><name>fs.s3.block.size</name><value>67108864</value></property>
-<property><name>mapred.job.reuse.jvm.num.tasks</name><value>1</value></property>
-<property><name>mapred.job.tracker.http.address</name><value>0.0.0.0:50030</value></property>
-<property><name>mapred.tasktracker.reduce.tasks.maximum</name><value>2</value></property>
-<property><name>io.compression.codecs</name><value>org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec</value></property>
-<property><name>mapred.job.shuffle.input.buffer.percent</name><value>0.70</value></property>
-<property><name>io.seqfile.compress.blocksize</name><value>1000000</value></property>
-<property><name>mapred.queue.names</name><value>default</value></property>
-<property><name>fs.har.impl</name><value>org.apache.hadoop.fs.HarFileSystem</value></property>
-<property><name>io.mapfile.bloom.error.rate</name><value>0.005</value></property>
-<property><name>mapred.job.tracker</name><value>local</value></property>
-<property><name>io.skip.checksum.errors</name><value>false</value></property>
-<property><name>mapred.reduce.max.attempts</name><value>4</value></property>
-<property><name>fs.s3.maxRetries</name><value>4</value></property>
-<property><name>ipc.server.listen.queue.size</name><value>128</value></property>
-<property><name>fs.trash.interval</name><value>0</value></property>
-<property><name>mapred.local.dir.minspacestart</name><value>0</value></property>
-<property><name>fs.s3.impl</name><value>org.apache.hadoop.fs.s3.S3FileSystem</value></property>
-<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
-<property><name>io.mapfile.bloom.size</name><value>1048576</value></property>
-<property><name>io.sort.mb</name><value>100</value></property>
-<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
-<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>BasicPathMergeVertex.kmerSize</name><value>5</value></property>
-<property><name>mapred.task.profile</name><value>false</value></property>
-<property><name>job.end.retry.interval</name><value>30000</value></property>
-<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
-<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
-<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
-<property><name>webinterface.private.actions</name><value>false</value></property>
-<property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${user.name}</value></property>
-<property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
-<property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
-<property><name>mapred.merge.recordsBeforeProgress</name><value>10000</value></property>
-<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
-<property><name>mapred.compress.map.output</name><value>false</value></property>
-<property><name>io.sort.spill.percent</name><value>0.80</value></property>
-<property><name>fs.checkpoint.edits.dir</name><value>${fs.checkpoint.dir}</value></property>
-<property><name>mapred.userlog.retain.hours</name><value>24</value></property>
-<property><name>mapred.system.dir</name><value>${hadoop.tmp.dir}/mapred/system</value></property>
-<property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
-<property><name>job.end.retry.attempts</name><value>0</value></property>
-<property><name>ipc.client.idlethreshold</name><value>4000</value></property>
-<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat</value></property>
-<property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
-<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
-<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
-<property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat</value></property>
-<property><name>mapred.job.queue.name</name><value>default</value></property>
-<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
-<property><name>pregelix.incStateLength</name><value>true</value></property>
-<property><name>mapred.reduce.slowstart.completed.maps</name><value>0.05</value></property>
-<property><name>topology.script.number.args</name><value>100</value></property>
-<property><name>mapred.skip.map.max.skip.records</name><value>0</value></property>
-<property><name>fs.ftp.impl</name><value>org.apache.hadoop.fs.ftp.FTPFileSystem</value></property>
-<property><name>mapred.task.cache.levels</name><value>2</value></property>
-<property><name>mapred.job.tracker.handler.count</name><value>10</value></property>
-<property><name>io.serializations</name><value>org.apache.hadoop.io.serializer.WritableSerialization</value></property>
-<property><name>ipc.client.connect.max.retries</name><value>10</value></property>
-<property><name>mapred.min.split.size</name><value>0</value></property>
-<property><name>mapred.map.max.attempts</name><value>4</value></property>
-<property><name>jobclient.output.filter</name><value>FAILED</value></property>
-<property><name>ipc.client.tcpnodelay</name><value>false</value></property>
-<property><name>mapred.acls.enabled</name><value>false</value></property>
-</configuration>
\ No newline at end of file