diff --git a/genomix/genomix-pregelix/data/sequencefile/BridgePath b/genomix/genomix-pregelix/data/PathTestSet/BridgePath/BridgePath
similarity index 100%
rename from genomix/genomix-pregelix/data/sequencefile/BridgePath
rename to genomix/genomix-pregelix/data/PathTestSet/BridgePath/BridgePath
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/CyclePath/part-0 b/genomix/genomix-pregelix/data/PathTestSet/CyclePath/part-0
new file mode 100755
index 0000000..b986370
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/CyclePath/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/CyclePath/part-1 b/genomix/genomix-pregelix/data/PathTestSet/CyclePath/part-1
new file mode 100755
index 0000000..729417d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/CyclePath/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/sequencefile/LongPath b/genomix/genomix-pregelix/data/PathTestSet/LongPath/LongPath
similarity index 100%
rename from genomix/genomix-pregelix/data/sequencefile/LongPath
rename to genomix/genomix-pregelix/data/PathTestSet/LongPath/LongPath
Binary files differ
diff --git a/genomix/genomix-pregelix/data/sequencefile/Path b/genomix/genomix-pregelix/data/PathTestSet/Path/Path
similarity index 100%
rename from genomix/genomix-pregelix/data/sequencefile/Path
rename to genomix/genomix-pregelix/data/PathTestSet/Path/Path
Binary files differ
diff --git a/genomix/genomix-pregelix/data/sequencefile/CyclePath b/genomix/genomix-pregelix/data/PathTestSet/RingPath/CyclePath
similarity index 100%
rename from genomix/genomix-pregelix/data/sequencefile/CyclePath
rename to genomix/genomix-pregelix/data/PathTestSet/RingPath/CyclePath
Binary files differ
diff --git a/genomix/genomix-pregelix/data/sequencefile/SimplePath b/genomix/genomix-pregelix/data/PathTestSet/SimplePath/SimplePath
similarity index 100%
rename from genomix/genomix-pregelix/data/sequencefile/SimplePath
rename to genomix/genomix-pregelix/data/PathTestSet/SimplePath/SimplePath
Binary files differ
diff --git a/genomix/genomix-pregelix/data/sequencefile/SinglePath b/genomix/genomix-pregelix/data/PathTestSet/SinglePath/SinglePath
similarity index 100%
rename from genomix/genomix-pregelix/data/sequencefile/SinglePath
rename to genomix/genomix-pregelix/data/PathTestSet/SinglePath/SinglePath
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/ThreeKmer/part-0 b/genomix/genomix-pregelix/data/PathTestSet/ThreeKmer/part-0
new file mode 100755
index 0000000..b02d917
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/ThreeKmer/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/ThreeKmer/part-1 b/genomix/genomix-pregelix/data/PathTestSet/ThreeKmer/part-1
new file mode 100755
index 0000000..37e9986
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/ThreeKmer/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/sequencefile/TreePath b/genomix/genomix-pregelix/data/PathTestSet/TreePath/TreePath
similarity index 100%
rename from genomix/genomix-pregelix/data/sequencefile/TreePath
rename to genomix/genomix-pregelix/data/PathTestSet/TreePath/TreePath
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/TwoKmer/part-0 b/genomix/genomix-pregelix/data/PathTestSet/TwoKmer/part-0
new file mode 100755
index 0000000..7973858
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/TwoKmer/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathTestSet/TwoKmer/part-1 b/genomix/genomix-pregelix/data/PathTestSet/TwoKmer/part-1
new file mode 100755
index 0000000..02d893d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/PathTestSet/TwoKmer/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/graph/mergeTest/TwoKmer b/genomix/genomix-pregelix/graph/mergeTest/TwoKmer
index 86790c6..8c2a74b 100644
--- a/genomix/genomix-pregelix/graph/mergeTest/TwoKmer
+++ b/genomix/genomix-pregelix/graph/mergeTest/TwoKmer
@@ -1,2 +1 @@
-ACACT	|G	1
-CACTG	A|	1
+ACACTG
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java
index 285976a..47db449 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/NaiveAlgorithmForPathMergeOutputFormat.java
@@ -36,7 +36,7 @@
             @Override
             public void writeVertex(Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, ?> vertex) throws IOException,
                     InterruptedException {
-            	if(vertex.getVertexValue().getLengthOfMergeChain() != NaiveAlgorithmForPathMergeVertex.kmerSize)
+            	//if(vertex.getVertexValue().getLengthOfMergeChain() != NaiveAlgorithmForPathMergeVertex.kmerSize)
             		getRecordWriter().write(vertex.getVertexId(),vertex.getVertexValue());
             }
         }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/Graph.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/Graph.java
index df09a64..298864e 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/Graph.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/Graph.java
@@ -50,6 +50,6 @@
 	public static void main(String[] args) throws Exception
 	{
 		Graph g = new Graph();
-		g.start("Path");
+		g.start("result.txt.txt");
 	}
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
index 057ab08..e4317f0 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
@@ -19,7 +19,7 @@
 
 	public ValueStateWritable() {
 		state = State.NON_VERTEX;
-		mergeChain = new VKmerBytesWritable(NaiveAlgorithmForPathMergeVertex.kmerSize);
+		mergeChain = new VKmerBytesWritable(-1);
 	}
 
 	public ValueStateWritable(byte adjMap, byte state, VKmerBytesWritable mergeChain) {
@@ -87,7 +87,7 @@
 	
 	@Override
 	public String toString() {
-		if(mergeChain.getKmerLength() == -1)
+		if(mergeChain.getKmerLength() == -1 || mergeChain.getKmerLength() == 0)
 			return GeneCode.getSymbolFromBitMap(adjMap);
 		return 	GeneCode.getSymbolFromBitMap(adjMap) + "\t" +
 				getLengthOfMergeChain() + "\t" +
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
index d75ea48..6db02c7 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
@@ -71,7 +71,7 @@
 		if(kmerSize == -1)
 			kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
         if (maxIteration < 0) 
-            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 100);
+            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
 	}
 	public void findDestination(){
 		destVertexId.set(msg.getSourceVertexId());
@@ -171,12 +171,12 @@
 		//head node sends message to path node
 		else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
 			while (msgIterator.hasNext()){
-				if(getSuperstep() == 3 && GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap()))
-					voteToHalt();
-				else{
-					msg = msgIterator.next();
-					sendMsgToPathVertex();
-				}
+				//if(getSuperstep() == 3 && GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap()))
+				//	voteToHalt();
+				//else{
+				msg = msgIterator.next();
+				sendMsgToPathVertex();
+				//}
 			}
 		}
 		//path node sends message back to head node
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
index b613ec1..0ac4345 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
@@ -67,7 +67,7 @@
 		if(kmerSize == -1)
 			kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
         if (maxIteration < 0) 
-            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 20);
+            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
 	}
 	/**
 	 * get destination vertex
@@ -206,7 +206,7 @@
 	/**
 	 *  set vertexValue's state chainVertexId, value
 	 */
-	public void setVertexValueAttributes(){
+	public boolean setVertexValueAttributes(){
 		if(msg.getMessage() == Message.END){
 			if(getVertexValue().getState() != State.START_VERTEX)
 				getVertexValue().setState(State.END_VERTEX);
@@ -220,10 +220,19 @@
 			chainVertexId.set(getVertexValue().getMergeChain());
 		lastKmer.set(kmerFactory.getLastKmerFromChain(msg.getLengthOfChain() - kmerSize + 1, msg.getChainVertexId()));
 		chainVertexId.set(kmerFactory.mergeTwoKmer(chainVertexId, lastKmer));
-		getVertexValue().setMergeChain(chainVertexId);
+		if(GraphVertexOperation.isCycle(getVertexId(), chainVertexId)){
+			getVertexValue().setMergeChain(null);
+			getVertexValue().setAdjMap(GraphVertexOperation.reverseAdjMap(getVertexValue().getAdjMap(),
+					chainVertexId.getGeneCodeAtPosition(kmerSize)));
+			getVertexValue().setState(State.CYCLE);
+			return false;
+		}
+		else
+			getVertexValue().setMergeChain(chainVertexId);
 		
 		byte tmpVertexValue = GraphVertexOperation.updateRightNeighber(getVertexValue().getAdjMap(), msg.getAdjMap());
 		getVertexValue().setAdjMap(tmpVertexValue);
+		return true;
 	}
 	/**
 	 *  send message to self
@@ -280,8 +289,10 @@
 		else{
 			if(msgIterator.hasNext()){
 				msg = msgIterator.next();
-				mergeChainVertex(msgIterator);
-				sendMsgToPathVertex(getVertexValue().getMergeChain(), getVertexValue().getAdjMap());
+				if(mergeChainVertex(msgIterator))
+					sendMsgToPathVertex(getVertexValue().getMergeChain(), getVertexValue().getAdjMap());
+				else
+					voteToHalt();
 			}
 			if(getVertexValue().getState() == State.END_VERTEX || getVertexValue().getState() == State.FINAL_DELETE){
 				voteToHalt();
@@ -296,7 +307,7 @@
 	 * path response message to head
 	 */
 	public void responseMsgToHeadVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		if(msgIterator.hasNext()){
+		if(msgIterator.hasNext()){		
 			msg = msgIterator.next();
 			responseMsgToHeadVertex();
 		}
@@ -310,8 +321,8 @@
 	/**
 	 * merge chainVertex and store in vertexVal.chainVertexId
 	 */
-	public void mergeChainVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		setVertexValueAttributes();
+	public boolean mergeChainVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
+		return setVertexValueAttributes();
 	}
 	@Override
 	public void compute(Iterator<LogAlgorithmMessageWritable> msgIterator) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/CombineSequenceFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/CombineSequenceFile.java
index 55ddcff..84d846e 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/CombineSequenceFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/CombineSequenceFile.java
@@ -23,9 +23,9 @@
 		Configuration conf = new Configuration();
 		FileSystem fileSys = FileSystem.get(conf);
 		
-		Path p = new Path("output");
+		Path p = new Path("graphbuildresult/CyclePath2_result");
 		//Path p2 = new Path("data/result");
-		Path outFile = new Path("output2"); 
+		Path outFile = new Path("here"); 
 		SequenceFile.Reader reader;
 	    SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf,
 	         outFile, KmerBytesWritable.class, KmerCountValue.class, 
@@ -33,7 +33,7 @@
 	    KmerBytesWritable key = new KmerBytesWritable(kmerSize);
 	    KmerCountValue value = new KmerCountValue();
 	    
-	    File dir = new File("output");
+	    File dir = new File("graphbuildresult/CyclePath2_result");
 		for(File child : dir.listFiles()){
 			String name = child.getAbsolutePath();
 			Path inFile = new Path(p, name);
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 249c293..026bba2 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
@@ -1,9 +1,12 @@
 package edu.uci.ics.genomix.pregelix.sequencefile;
 
 import java.io.BufferedWriter;
+import java.io.File;
 import java.io.FileWriter;
+import java.io.FilenameFilter;
 import java.io.IOException;
 
+import org.apache.commons.io.filefilter.WildcardFileFilter;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
@@ -16,14 +19,16 @@
 
 public class GenerateTextFile {
 
-	public static void generateFromPathmergeResult() throws IOException{
-		BufferedWriter bw = new BufferedWriter(new FileWriter("output2"));
+	public static void generateFromPathmergeResult(int kmerSize, String strSrcDir, String outPutDir) throws IOException{
 		Configuration conf = new Configuration();
-		FileSystem fileSys = FileSystem.get(conf);
-		for(int i = 0; i < 2; i++){
-			Path path = new Path("output/part-" + i);
-			SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
-			KmerBytesWritable key = new KmerBytesWritable(55);
+		FileSystem fileSys = FileSystem.getLocal(conf);
+		
+		fileSys.create(new Path(outPutDir));
+		BufferedWriter bw = new BufferedWriter(new FileWriter(outPutDir));
+		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);
+			KmerBytesWritable key = new KmerBytesWritable(kmerSize);
 		    ValueStateWritable value = new ValueStateWritable();
 		    
 		    while(reader.next(key, value)){
@@ -111,7 +116,7 @@
 	 * @throws IOException 
 	 */
 	public static void main(String[] args) throws IOException {
-		generateFromPathmergeResult();
+		//generateFromPathmergeResult();
 		//generateFromGraphbuildResult();
 		//generateSpecificLengthChainFromPathmergeResult(68);
 		//generateSpecificLengthChainFromLogPathmergeResult(68);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
index fc26f66..50f1679 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
@@ -56,7 +56,7 @@
 		OutputStreamWriter writer;
 		try {
 			writer = new OutputStreamWriter(new FileOutputStream("graph/55/SinglePath_55"));
-			writer.write(simplePath(55,500,1));
+			writer.write(simplePath(55,320,1));
 			writer.close();
 			/*writer = new OutputStreamWriter(new FileOutputStream("graph/55/SimplePath_55"));
 			writer.write(simplePath(55,60,3));
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/State.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/State.java
index 4bb40c9..4257f89 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/State.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/State.java
@@ -9,7 +9,7 @@
 	public static final byte TODELETE = 4;
 	public static final byte FINAL_VERTEX = 5;
 	public static final byte FINAL_DELETE = 6;
-	public static final byte KILL_SELF = 7;
+	public static final byte CYCLE = 7;
 	
 	public final static class STATE_CONTENT{
 
@@ -37,8 +37,8 @@
 			case FINAL_DELETE:
 				r = "FINAL_DELETE";
 				break;
-			case KILL_SELF:
-				r = "KILL_SELF";
+			case CYCLE:
+				r = "CYCLE";
 				break;
 			}
 			return r;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/GraphVertexOperation.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/GraphVertexOperation.java
index 47f2c63..f086df4 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/GraphVertexOperation.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/GraphVertexOperation.java
@@ -47,5 +47,19 @@
 	public static byte updateRightNeighber(byte oldVertexValue, byte newVertexValue){
 		return (byte) ((byte)(oldVertexValue & 0xF0) | (byte) (newVertexValue & 0x0F));
 	}
-
+	/**
+	 * check if mergeChain is cycle
+	 */
+	public static boolean isCycle(KmerBytesWritable vertexId, VKmerBytesWritable mergeChain){
+		String chain = mergeChain.toString().substring(1);
+		if(chain.contains(vertexId.toString()))
+			return true;
+		return false;
+	}
+	/**
+	 * reverse neighber
+	 */
+	public static byte reverseAdjMap(byte oldAdjMap, byte geneCode){
+		return (byte) ((oldAdjMap & 0xF0) | (GeneCode.getBitMapFromGeneCode(geneCode) & 0x0F));
+	}
 }
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 cda48f7..ca033e6 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
@@ -23,28 +23,9 @@
 
 public class JobGenerator {
 
-    private static String outputBase = "src/test/resources/jobs/";
-    private static String HDFS_INPUTPATH = "/webmap";
-    private static String HDFS_OUTPUTPAH = "/result";
+    public static String outputBase = "src/test/resources/jobs/";
     
-    private static void generateLoadGraphJob(String jobName, String outputPath) throws IOException {
-    	PregelixJob job = new PregelixJob(jobName);
-    	job.setVertexClass(LoadGraphVertex.class);
-    	job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
-        FileInputFormat.setInputPaths(job, HDFS_INPUTPATH);
-        FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH));
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-    
-    private static void genLoadGraph() throws IOException {
-    	generateLoadGraphJob("LoadGraph", outputBase + "LoadGraph.xml");
-    }
-    
-    private static void generateMergeGraphJob(String jobName, String outputPath) throws IOException {
+    private static void generateNaiveAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
     	PregelixJob job = new PregelixJob(jobName);
     	job.setVertexClass(NaiveAlgorithmForPathMergeVertex.class);
     	job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
@@ -52,34 +33,12 @@
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(KmerBytesWritable.class);
         job.setOutputValueClass(ValueStateWritable.class);
-        FileInputFormat.setInputPaths(job, HDFS_INPUTPATH);
-        FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH));
         job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, 5);
-        //job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.ITERATIONS, 10);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
     
-    private static void genMergeGraph() throws IOException {
-    	generateMergeGraphJob("MergeGraph", outputBase + "MergeGraph.xml");
-    }
-    
-    private static void generateThreeStepLogAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
-    	PregelixJob job = new PregelixJob(jobName);
-    	job.setVertexClass(ThreeStepLogAlgorithmForPathMergeVertex.class);
-        job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class); 
-        job.setVertexOutputFormatClass(LogAlgorithmForPathMergeOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
-        FileInputFormat.setInputPaths(job, HDFS_INPUTPATH);
-        FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH));
-        job.getConfiguration().setInt(ThreeStepLogAlgorithmForPathMergeVertex.KMER_SIZE, 5);
-        job.getConfiguration().setInt(ThreeStepLogAlgorithmForPathMergeVertex.ITERATIONS, 5);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-    
-    private static void genThreeStepLogAlgorithmForMergeGraph() throws IOException {
-    	generateThreeStepLogAlgorithmForMergeGraphJob("ThreeStepLogAlgorithmForMergeGraph", outputBase + "ThreeStepLogAlgorithmForMergeGraph.xml");
+    private static void genNaiveAlgorithmForMergeGraph() throws IOException {
+    	generateNaiveAlgorithmForMergeGraphJob("NaiveAlgorithmForMergeGraph", outputBase + "NaiveAlgorithmForMergeGraph.xml");
     }
     
     private static void generateTwoStepLogAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
@@ -90,9 +49,7 @@
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(KmerBytesWritable.class);
         job.setOutputValueClass(ValueStateWritable.class);
-        FileInputFormat.setInputPaths(job, HDFS_INPUTPATH);
-        FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH));
-        job.getConfiguration().setInt(TwoStepLogAlgorithmForPathMergeVertex.KMER_SIZE, 55);
+        job.getConfiguration().setInt(TwoStepLogAlgorithmForPathMergeVertex.KMER_SIZE, 5);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
     
@@ -105,11 +62,8 @@
 	 * @throws IOException 
 	 */
 	public static void main(String[] args) throws IOException {
-		// TODO Auto-generated method stub
-		//genLoadGraph();
-		genMergeGraph();
-		//genThreeStepLogAlgorithmForMergeGraph();
-		//genTwoStepLogAlgorithmForMergeGraph();
+		genNaiveAlgorithmForMergeGraph();
+		genTwoStepLogAlgorithmForMergeGraph();
 	}
 
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
index 45d8185..1af0d6e 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
@@ -40,7 +40,7 @@
 	private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
 	private static final String FILE_EXTENSION_OF_RESULTS = "result";
 
-	private static final String DATA_PATH = "data/sequencefile/TreePath";
+	private static final String DATA_PATH = "data/sequencefile/Path";
 	private static final String HDFS_PATH = "/webmap/";
 
 	private static final String HYRACKS_APP_NAME = "pregelix";
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java
index 7ecf31f..16fe317 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java
@@ -33,156 +33,168 @@
 
 public class GraphBuildTest {
 	private static final String ACTUAL_RESULT_DIR = "graphbuildresult";
-    private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
+	private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
 
-    private static final String DATA_PATH = "data/sequencefile/BridgePath";
-    private static final String HDFS_INPUT_PATH = "/BridgePath";
-    private static final String HDFS_OUTPUT_PATH = "/BridgePath_result";
+	private static final String DATA_PATH = "data/TwoKmer";
+	private static final String HDFS_INPUT_PATH = "/CyclePath2";
+	private static final String HDFS_OUTPUT_PATH = "/CyclePath2_result";
 
-    private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + "/result.txt";
-    private static final String CONVERT_RESULT = DUMPED_RESULT + ".txt";
-    private static final String EXPECTED_PATH = "src/test/resources/expected/result2";
-    private static final String EXPECTED_REVERSE_PATH = "src/test/resources/expected/result_reverse";
+	private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR
+			+ HDFS_OUTPUT_PATH + "/result.txt";
+	private static final String CONVERT_RESULT = DUMPED_RESULT + ".txt";
+	private static final String EXPECTED_PATH = "src/test/resources/expected/result2";
+	private static final String EXPECTED_REVERSE_PATH = "src/test/resources/expected/result_reverse";
 
-    private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
-    private MiniDFSCluster dfsCluster;
+	private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR
+			+ File.separator + "conf.xml";
+	private MiniDFSCluster dfsCluster;
 
-    private JobConf conf = new JobConf();
-    private int numberOfNC = 2;
-    private int numPartitionPerMachine = 1;
+	private JobConf conf = new JobConf();
+	private int numberOfNC = 2;
+	private int numPartitionPerMachine = 1;
 
-    private Driver driver;
+	private Driver driver;
 
-    @Before
-    public void setUp() throws Exception {
-        cleanupStores();
-        edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.init();
-        FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
-        FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
-        startHDFS();
+	@Before
+	public void setUp() throws Exception {
+		cleanupStores();
+		edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.init();
+		FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
+		FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
+		startHDFS();
 
-        FileInputFormat.setInputPaths(conf, HDFS_INPUT_PATH);
-        FileOutputFormat.setOutputPath(conf, new Path(HDFS_OUTPUT_PATH));
+		FileInputFormat.setInputPaths(conf, HDFS_INPUT_PATH);
+		FileOutputFormat.setOutputPath(conf, new Path(HDFS_OUTPUT_PATH));
 
-        conf.setInt(GenomixJob.KMER_LENGTH, 5);
-        driver = new Driver(edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.CC_HOST,
-                edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.TEST_HYRACKS_CC_CLIENT_PORT, numPartitionPerMachine);
-    }
+		conf.setInt(GenomixJob.KMER_LENGTH, 5);
+		driver = new Driver(
+				edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.CC_HOST,
+				edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.TEST_HYRACKS_CC_CLIENT_PORT,
+				numPartitionPerMachine);
+	}
 
-    private void cleanupStores() throws IOException {
-        FileUtils.forceMkdir(new File("teststore"));
-        FileUtils.forceMkdir(new File("build"));
-        FileUtils.cleanDirectory(new File("teststore"));
-        FileUtils.cleanDirectory(new File("build"));
-    }
+	private void cleanupStores() throws IOException {
+		FileUtils.forceMkdir(new File("teststore"));
+		FileUtils.forceMkdir(new File("build"));
+		FileUtils.cleanDirectory(new File("teststore"));
+		FileUtils.cleanDirectory(new File("build"));
+	}
 
-    private void startHDFS() throws IOException {
-        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
-        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
-        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
+	private void startHDFS() throws IOException {
+		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
+		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
+		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
 
-        FileSystem lfs = FileSystem.getLocal(new Configuration());
-        lfs.delete(new Path("build"), true);
-        System.setProperty("hadoop.log.dir", "logs");
-        dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
-        FileSystem dfs = FileSystem.get(conf);
-        Path src = new Path(DATA_PATH);
-        Path dest = new Path(HDFS_INPUT_PATH);
-        dfs.mkdirs(dest);
-        dfs.copyFromLocalFile(src, dest);
+		FileSystem lfs = FileSystem.getLocal(new Configuration());
+		lfs.delete(new Path("build"), true);
+		System.setProperty("hadoop.log.dir", "logs");
+		dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
+		FileSystem dfs = FileSystem.get(conf);
+		Path src = new Path(DATA_PATH);
+		Path dest = new Path(HDFS_INPUT_PATH);
+		dfs.mkdirs(dest);
+		dfs.copyFromLocalFile(src, dest);
 
-        DataOutputStream confOutput = new DataOutputStream(new FileOutputStream(new File(HADOOP_CONF_PATH)));
-        conf.writeXml(confOutput);
-        confOutput.flush();
-        confOutput.close();
-    }
+		DataOutputStream confOutput = new DataOutputStream(
+				new FileOutputStream(new File(HADOOP_CONF_PATH)));
+		conf.writeXml(confOutput);
+		confOutput.flush();
+		confOutput.close();
+	}
 
-    private void cleanUpReEntry() throws IOException {
-        FileSystem lfs = FileSystem.getLocal(new Configuration());
-        if (lfs.exists(new Path(DUMPED_RESULT))) {
-            lfs.delete(new Path(DUMPED_RESULT), true);
-        }
-        FileSystem dfs = FileSystem.get(conf);
-        if (dfs.exists(new Path(HDFS_OUTPUT_PATH))) {
-            dfs.delete(new Path(HDFS_OUTPUT_PATH), true);
-        }
-    }
+	private void cleanUpReEntry() throws IOException {
+		FileSystem lfs = FileSystem.getLocal(new Configuration());
+		if (lfs.exists(new Path(DUMPED_RESULT))) {
+			lfs.delete(new Path(DUMPED_RESULT), true);
+		}
+		FileSystem dfs = FileSystem.get(conf);
+		if (dfs.exists(new Path(HDFS_OUTPUT_PATH))) {
+			dfs.delete(new Path(HDFS_OUTPUT_PATH), true);
+		}
+	}
 
-    @Test
-    public void TestAll() throws Exception {
-        cleanUpReEntry();
-        TestHybridGroupby();
-        cleanUpReEntry();
-        TestPreClusterGroupby();
-    }
+	@Test
+	public void TestAll() throws Exception {
+		cleanUpReEntry();
+		TestHybridGroupby();
+		cleanUpReEntry();
+		TestPreClusterGroupby();
+	}
 
-    public void TestPreClusterGroupby() throws Exception {
-        conf.set(GenomixJob.GROUPBY_TYPE, "precluster");
-        System.err.println("Testing PreClusterGroupBy");
-        driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
-        Assert.assertEquals(true, checkResults(EXPECTED_PATH));
-    }
-    
-    public void TestHybridGroupby() throws Exception {
-        conf.set(GenomixJob.GROUPBY_TYPE, "hybrid");
-        System.err.println("Testing HybridGroupBy");
-        driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
-        Assert.assertEquals(true, checkResults(EXPECTED_PATH));
-    }
+	public void TestPreClusterGroupby() throws Exception {
+		conf.set(GenomixJob.GROUPBY_TYPE, "precluster");
+		System.err.println("Testing PreClusterGroupBy");
+		driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+		Assert.assertEquals(true, checkResults(EXPECTED_PATH));
+	}
 
-    private boolean checkResults(String expectedPath) throws Exception {
-        File dumped = null;
-        String format = conf.get(GenomixJob.OUTPUT_FORMAT);
-        if ("text".equalsIgnoreCase(format)) {
-            FileUtil.copyMerge(FileSystem.get(conf), new Path(HDFS_OUTPUT_PATH),
-                    FileSystem.getLocal(new Configuration()), new Path(DUMPED_RESULT), false, conf, null);
-            dumped = new File(DUMPED_RESULT);
-        } else {
+	public void TestHybridGroupby() throws Exception {
+		conf.set(GenomixJob.GROUPBY_TYPE, "hybrid");
+		System.err.println("Testing HybridGroupBy");
+		driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+		Assert.assertEquals(true, checkResults(EXPECTED_PATH));
+	}
 
-            FileSystem.getLocal(new Configuration()).mkdirs(new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH));
-            File filePathTo = new File(CONVERT_RESULT);
-            BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
-            for (int i = 0; i < numPartitionPerMachine * numberOfNC; i++) {
-                String partname = "/part-" + i;
-                				FileUtil.copy(FileSystem.get(conf), new Path(HDFS_OUTPUT_PATH
-                						+ partname), FileSystem.getLocal(new Configuration()),
-                						new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + partname), false, conf);
+	private boolean checkResults(String expectedPath) throws Exception {
+		File dumped = null;
+		String format = conf.get(GenomixJob.OUTPUT_FORMAT);
+		if ("text".equalsIgnoreCase(format)) {
+			FileUtil.copyMerge(FileSystem.get(conf),
+					new Path(HDFS_OUTPUT_PATH), FileSystem
+							.getLocal(new Configuration()), new Path(
+							DUMPED_RESULT), false, conf, null);
+			dumped = new File(DUMPED_RESULT);
+		} else {
 
-                Path path = new Path(HDFS_OUTPUT_PATH + partname);
-                FileSystem dfs = FileSystem.get(conf);
-                if (dfs.getFileStatus(path).getLen() == 0) {
-                    continue;
-                }
-                SequenceFile.Reader reader = new SequenceFile.Reader(dfs, path, conf);
-                KmerBytesWritable key = new KmerBytesWritable(conf.getInt(GenomixJob.KMER_LENGTH,
-                        GenomixJob.DEFAULT_KMER));
-                KmerCountValue value = (KmerCountValue) ReflectionUtils.newInstance(reader.getValueClass(), conf);
+			FileSystem.getLocal(new Configuration()).mkdirs(
+					new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH));
+			File filePathTo = new File(CONVERT_RESULT);
+			BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
+			for (int i = 0; i < numPartitionPerMachine * numberOfNC; i++) {
+				String partname = "/part-" + i;
+				FileUtil.copy(FileSystem.get(conf), new Path(HDFS_OUTPUT_PATH
+						+ partname), FileSystem.getLocal(new Configuration()),
+						new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH
+								+ partname), false, conf);
 
-                while (reader.next(key, value)) {
-                    if (key == null || value == null) {
-                        break;
-                    }
-                    bw.write(key.toString() + "\t" + value.toString());
-                    System.out.println(key.toString() + "\t" + value.toString());
-                    bw.newLine();
-                }
-                reader.close();
-            }
-            bw.close();
-            dumped = new File(CONVERT_RESULT);
-        }
+				Path path = new Path(HDFS_OUTPUT_PATH + partname);
+				FileSystem dfs = FileSystem.get(conf);
+				if (dfs.getFileStatus(path).getLen() == 0) {
+					continue;
+				}
+				SequenceFile.Reader reader = new SequenceFile.Reader(dfs, path,
+						conf);
+				KmerBytesWritable key = new KmerBytesWritable(conf.getInt(
+						GenomixJob.KMER_LENGTH, GenomixJob.DEFAULT_KMER));
+				KmerCountValue value = (KmerCountValue) ReflectionUtils
+						.newInstance(reader.getValueClass(), conf);
 
-        //TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
-        return true;
-    }
+				while (reader.next(key, value)) {
+					if (key == null || value == null) {
+						break;
+					}
+					bw.write(key.toString() + "\t" + value.toString());
+					System.out
+							.println(key.toString() + "\t" + value.toString());
+					bw.newLine();
+				}
+				reader.close();
+			}
+			bw.close();
+			dumped = new File(CONVERT_RESULT);
+		}
 
-    @After
-    public void tearDown() throws Exception {
-        edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.deinit();
-        cleanupHDFS();
-    }
+		// TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
+		return true;
+	}
 
-    private void cleanupHDFS() throws Exception {
-        dfsCluster.shutdown();
-    }
+	@After
+	public void tearDown() throws Exception {
+		edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.deinit();
+		cleanupHDFS();
+	}
+
+	private void cleanupHDFS() throws Exception {
+		dfsCluster.shutdown();
+	}
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
index 8191496..67b6f21 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
@@ -15,8 +15,6 @@
 
 package edu.uci.ics.genomix.pregelix.pathmerge;
 
-import java.io.File;
-
 import junit.framework.TestCase;
 
 import org.apache.hadoop.fs.FileSystem;
@@ -25,101 +23,67 @@
 import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
 import org.junit.Test;
 
-import edu.uci.ics.genomix.pregelix.example.util.TestUtils;
+import edu.uci.ics.genomix.pregelix.sequencefile.GenerateTextFile;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 import edu.uci.ics.pregelix.core.base.IDriver.Plan;
 import edu.uci.ics.pregelix.core.driver.Driver;
 import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
 
 public class PathMergeSmallTestCase extends TestCase {
-    private static String HDFS_INPUTPATH = "/BridgePath";
-    private static String HDFS_OUTPUTPAH = "/resultBridgePath";
+	private final PregelixJob job;
+	private final String resultFileDir;
+	private final String textFileDir;
+	private final String jobFile;
+	private final Driver driver = new Driver(this.getClass());
+	private final FileSystem dfs;
 
-    /*private static String HDFS_INPUTPATH2 = "/CyclePath";
-    private static String HDFS_OUTPUTPAH2 = "/resultCyclePath";
+	public PathMergeSmallTestCase(String hadoopConfPath, String jobName,
+			String jobFile, FileSystem dfs, String hdfsInput, String resultFile, String textFile)
+			throws Exception {
+		super("test");
+		this.jobFile = jobFile;
+		this.job = new PregelixJob("test");
+		this.job.getConfiguration().addResource(new Path(jobFile));
+		this.job.getConfiguration().addResource(new Path(hadoopConfPath));
+		FileInputFormat.setInputPaths(job, hdfsInput);
+		FileOutputFormat.setOutputPath(job, new Path(hdfsInput + "_result"));
+		this.textFileDir = textFile;
+		job.setJobName(jobName);
+		this.resultFileDir = resultFile;
+		
+		this.dfs = dfs;
+	}
 
-    private static String HDFS_INPUTPATH3 = "/LongPath";
-    private static String HDFS_OUTPUTPAH3 = "/resultLongPath";
+	private void waitawhile() throws InterruptedException {
+		synchronized (this) {
+			this.wait(20);
+		}
+	}
 
-    private static String HDFS_INPUTPATH4 = "/Path";
-    private static String HDFS_OUTPUTPAH4 = "/resultPath";
+	@Test
+	public void test() throws Exception {
+		setUp();
+		Plan[] plans = new Plan[] { Plan.OUTER_JOIN };
+		for (Plan plan : plans) {
+			driver.runJob(job, plan, PregelixHyracksIntegrationUtil.CC_HOST,
+					PregelixHyracksIntegrationUtil.TEST_HYRACKS_CC_CLIENT_PORT,
+					false);
+		}
+		compareResults();
+		tearDown();
+		waitawhile();
+	}
 
-    private static String HDFS_INPUTPATH5 = "/SimplePath";
-    private static String HDFS_OUTPUTPAH5 = "/resultSimplePath";
-    
-    private static String HDFS_INPUTPATH6 = "/SinglePath";
-    private static String HDFS_OUTPUTPAH6 = "/resultSinglePath";
-    
-    private static String HDFS_INPUTPATH7 = "/TreePath";
-    private static String HDFS_OUTPUTPAH7 = "/resultTreePath";*/
+	private void compareResults() throws Exception {
+		dfs.copyToLocalFile(FileOutputFormat.getOutputPath(job), new Path(
+				resultFileDir));
+		GenerateTextFile.generateFromPathmergeResult(5, resultFileDir, textFileDir);
+		// TestUtils.compareWithResultDir(new File(expectedFileDir), new
+		// File(resultFileDir));
+	}
 
-    private final PregelixJob job;
-    private final String resultFileDir;
-    private final String jobFile;
-    private final Driver driver = new Driver(this.getClass());
-    private final FileSystem dfs;
+	public String toString() {
+		return jobFile;
+	}
 
-    public PathMergeSmallTestCase(String hadoopConfPath, String jobName, String jobFile, String resultFile,
-            FileSystem dfs) throws Exception {
-        super("test");
-        this.jobFile = jobFile;
-        this.job = new PregelixJob("test");
-        this.job.getConfiguration().addResource(new Path(jobFile));
-        this.job.getConfiguration().addResource(new Path(hadoopConfPath));
-        Path[] inputPaths = FileInputFormat.getInputPaths(job);
-        if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH)) {
-            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH);
-            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH));
-        } 
-        /*else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH2)) {
-            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH2);
-            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH2));
-        } else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH3)) {
-            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH3);
-            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH3));
-        } else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH4)) {
-            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH4);
-            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH4));
-        } else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH5)) {
-            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH5);
-            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH5));
-        } else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH6)) {
-            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH6);
-            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH6));
-        } else if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH7)) {
-            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH7);
-            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH7));
-        }*/
-        job.setJobName(jobName);
-        this.resultFileDir = resultFile;
-        this.dfs = dfs;
-    }
-
-    private void waitawhile() throws InterruptedException {
-        synchronized (this) {
-            this.wait(20);
-        }
-    }
-
-    @Test
-    public void test() throws Exception {
-        setUp();
-        Plan[] plans = new Plan[] { Plan.OUTER_JOIN };
-        for (Plan plan : plans) {
-            driver.runJob(job, plan, PregelixHyracksIntegrationUtil.CC_HOST,
-                    PregelixHyracksIntegrationUtil.TEST_HYRACKS_CC_CLIENT_PORT, false);
-        }
-        compareResults();
-        tearDown();
-        waitawhile();
-    }
-
-    private void compareResults() throws Exception {
-        dfs.copyToLocalFile(FileOutputFormat.getOutputPath(job), new Path(resultFileDir));
-        //TestUtils.compareWithResultDir(new File(expectedFileDir), new File(resultFileDir));
-    }
-
-    public String toString() {
-        return jobFile;
-    }
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
index 5329515..43555c5 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
@@ -20,6 +20,7 @@
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.FileReader;
+import java.io.FilenameFilter;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
@@ -30,6 +31,7 @@
 import junit.framework.TestSuite;
 
 import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.filefilter.WildcardFileFilter;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
@@ -41,195 +43,179 @@
 
 @SuppressWarnings("deprecation")
 public class PathMergeSmallTestSuite extends TestSuite {
-    private static final Logger LOGGER = Logger.getLogger(PathMergeSmallTestSuite.class.getName());
+	private static final Logger LOGGER = Logger
+			.getLogger(PathMergeSmallTestSuite.class.getName());
 
-    private static final String ACTUAL_RESULT_DIR = "actual";
-    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";
-    private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
-    private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
-    private static final String PATH_TO_IGNORE = "src/test/resources/ignore.txt";
-    private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
+	public static final String PreFix = "data/PathTestSet";
+	public static final String[] TestDir = { PreFix + File.separator
+		+ "TwoKmer", PreFix + File.separator
+		+ "ThreeKmer", PreFix + File.separator
+		+ "SinglePath", PreFix + File.separator
+		+ "SimplePath", PreFix + File.separator
+		+ "Path", PreFix + File.separator
+		+ "BridgePath", PreFix + File.separator
+		+ "CyclePath", PreFix + File.separator
+		+ "CyclePath2", PreFix + File.separator
+		+ "LongPath", PreFix + File.separator
+		+ "TreePath"};
+	private static final String ACTUAL_RESULT_DIR = "actual";
+	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";
+	private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
+	private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
+	private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
 
-    private static final String DATA_PATH = "data/input/BridgePath";
-    private static final String HDFS_PATH = "/BridgePath/";
+	public static final String HDFS_INPUTPATH = "/PathTestSet";
 
-    /*private static final String DATA_PATH2 = "data/sequencefile/CyclePath";
-    private static final String HDFS_PATH2 = "/CyclePath/";
+	private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR
+			+ File.separator + "conf.xml";
+	private MiniDFSCluster dfsCluster;
 
-    private static final String DATA_PATH3 = "data/sequencefile/LongPath";
-    private static final String HDFS_PATH3 = "/LongPath/";
+	private JobConf conf = new JobConf();
+	private int numberOfNC = 2;
 
-    private static final String DATA_PATH4 = "data/sequencefile/Path";
-    private static final String HDFS_PATH4 = "/Path/";
+	public void setUp() throws Exception {
+		ClusterConfig.setStorePath(PATH_TO_CLUSTER_STORE);
+		ClusterConfig.setClusterPropertiesPath(PATH_TO_CLUSTER_PROPERTIES);
+		cleanupStores();
+		PregelixHyracksIntegrationUtil.init("src/test/resources/topology.xml");
+		LOGGER.info("Hyracks mini-cluster started");
+		FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
+		FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
+		startHDFS();
+	}
 
-    private static final String DATA_PATH5 = "data/sequencefile/SimplePath";
-    private static final String HDFS_PATH5 = "/SimplePath/";
-    
-    private static final String DATA_PATH6 = "data/sequencefile/SinglePath";
-    private static final String HDFS_PATH6 = "/SinglePath/";
-    
-    private static final String DATA_PATH7 = "data/sequencefile/TreePath";
-    private static final String HDFS_PATH7 = "/TreePath/";*/
+	private void cleanupStores() throws IOException {
+		FileUtils.forceMkdir(new File("teststore"));
+		FileUtils.forceMkdir(new File("build"));
+		FileUtils.cleanDirectory(new File("teststore"));
+		FileUtils.cleanDirectory(new File("build"));
+	}
 
-    private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
-    private MiniDFSCluster dfsCluster;
+	private void startHDFS() throws IOException {
+		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
+		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
+		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
+		FileSystem lfs = FileSystem.getLocal(new Configuration());
+		lfs.delete(new Path("build"), true);
+		System.setProperty("hadoop.log.dir", "logs");
+		dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
+		FileSystem dfs = FileSystem.get(conf);
 
-    private JobConf conf = new JobConf();
-    private int numberOfNC = 1;
+		for (String testDir : TestDir) {
+			File src = new File(testDir);
+			Path dest = new Path(HDFS_INPUTPATH + File.separator + src.getName());
+			dfs.mkdirs(dest);
+			//src.listFiles((FilenameFilter)(new WildcardFileFilter("part*")))
+			for (File f : src.listFiles()){
+				dfs.copyFromLocalFile(new Path(f.getAbsolutePath()), dest);
+			}
+		}
 
-    public void setUp() throws Exception {
-        ClusterConfig.setStorePath(PATH_TO_CLUSTER_STORE);
-        ClusterConfig.setClusterPropertiesPath(PATH_TO_CLUSTER_PROPERTIES);
-        cleanupStores();
-        PregelixHyracksIntegrationUtil.init("src/test/resources/topology.xml");
-        LOGGER.info("Hyracks mini-cluster started");
-        FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
-        FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
-        startHDFS();
-    }
+		DataOutputStream confOutput = new DataOutputStream(
+				new FileOutputStream(new File(HADOOP_CONF_PATH)));
+		conf.writeXml(confOutput);
+		confOutput.flush();
+		confOutput.close();
+	}
 
-    private void cleanupStores() throws IOException {
-        FileUtils.forceMkdir(new File("teststore"));
-        FileUtils.forceMkdir(new File("build"));
-        FileUtils.cleanDirectory(new File("teststore"));
-        FileUtils.cleanDirectory(new File("build"));
-    }
+	/**
+	 * cleanup hdfs cluster
+	 */
+	private void cleanupHDFS() throws Exception {
+		dfsCluster.shutdown();
+	}
 
-    private void startHDFS() throws IOException {
-        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
-        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
-        conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
-        FileSystem lfs = FileSystem.getLocal(new Configuration());
-        lfs.delete(new Path("build"), true);
-        System.setProperty("hadoop.log.dir", "logs");
-        dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
-        FileSystem dfs = FileSystem.get(conf);
-        Path src = new Path(DATA_PATH);
-        Path dest = new Path(HDFS_PATH);
-        dfs.mkdirs(dest);
-        dfs.copyFromLocalFile(src, dest);
+	public void tearDown() throws Exception {
+		PregelixHyracksIntegrationUtil.deinit();
+		LOGGER.info("Hyracks mini-cluster shut down");
+		cleanupHDFS();
+	}
 
-        /*src = new Path(DATA_PATH2);
-        dest = new Path(HDFS_PATH2);
-        dfs.mkdirs(dest);
-        dfs.copyFromLocalFile(src, dest);
+	public static Test suite() throws Exception {
+		List<String> onlys = getFileList(PATH_TO_ONLY);
+		File testData = new File(PATH_TO_JOBS);
+		File[] queries = testData.listFiles();
+		PathMergeSmallTestSuite testSuite = new PathMergeSmallTestSuite();
+		testSuite.setUp();
+		boolean onlyEnabled = false;
+		FileSystem dfs = FileSystem.get(testSuite.conf);
 
-        src = new Path(DATA_PATH3);
-        dest = new Path(HDFS_PATH3);
-        dfs.mkdirs(dest);
-        dfs.copyFromLocalFile(src, dest);
+		if (onlys.size() > 0) {
+			onlyEnabled = true;
+		}
 
-        src = new Path(DATA_PATH4);
-        dest = new Path(HDFS_PATH4);
-        dfs.mkdirs(dest);
-        dfs.copyFromLocalFile(src, dest);
+		for (File qFile : queries) {
+			if (qFile.isFile()) {
+				if (onlyEnabled && !isInList(onlys, qFile.getName())) {
+					continue;
+				} else {
+					for (String testPathStr : TestDir) {
+						File testDir = new File(testPathStr);
+						String resultFileName = ACTUAL_RESULT_DIR
+								+ File.separator
+								+ jobExtToResExt(qFile.getName())
+								+ File.separator + "BinaryOutput"
+								+ File.separator + testDir.getName();
+						String textFileName = ACTUAL_RESULT_DIR
+								+ File.separator
+								+ jobExtToResExt(qFile.getName())
+								+ File.separator + "TextOutput"
+								+ File.separator + testDir.getName();
+						testSuite.addTest(new PathMergeSmallTestCase(
+								HADOOP_CONF_PATH, qFile.getName(), qFile
+										.getAbsolutePath().toString(),
+								 dfs, HDFS_INPUTPATH + File.separator + testDir.getName(),
+								 resultFileName, textFileName));
+					}
+				}
+			}
+		}
+		return testSuite;
+	}
 
-        src = new Path(DATA_PATH5);
-        dest = new Path(HDFS_PATH5);
-        dfs.mkdirs(dest);
-        dfs.copyFromLocalFile(src, dest);
-        
-        src = new Path(DATA_PATH6);
-        dest = new Path(HDFS_PATH6);
-        dfs.mkdirs(dest);
-        dfs.copyFromLocalFile(src, dest);
-        
-        src = new Path(DATA_PATH7);
-        dest = new Path(HDFS_PATH7);
-        dfs.mkdirs(dest);
-        dfs.copyFromLocalFile(src, dest);*/
+	/**
+	 * Runs the tests and collects their result in a TestResult.
+	 */
+	@Override
+	public void run(TestResult result) {
+		try {
+			int testCount = countTestCases();
+			for (int i = 0; i < testCount; i++) {
+				// cleanupStores();
+				Test each = this.testAt(i);
+				if (result.shouldStop())
+					break;
+				runTest(each, result);
+			}
+			tearDown();
+		} catch (Exception e) {
+			throw new IllegalStateException(e);
+		}
+	}
 
-        DataOutputStream confOutput = new DataOutputStream(new FileOutputStream(new File(HADOOP_CONF_PATH)));
-        conf.writeXml(confOutput);
-        confOutput.flush();
-        confOutput.close();
-    }
+	protected static List<String> getFileList(String ignorePath)
+			throws FileNotFoundException, IOException {
+		BufferedReader reader = new BufferedReader(new FileReader(ignorePath));
+		String s = null;
+		List<String> ignores = new ArrayList<String>();
+		while ((s = reader.readLine()) != null) {
+			ignores.add(s);
+		}
+		reader.close();
+		return ignores;
+	}
 
-    /**
-     * cleanup hdfs cluster
-     */
-    private void cleanupHDFS() throws Exception {
-        dfsCluster.shutdown();
-    }
+	private static String jobExtToResExt(String fname) {
+		int dot = fname.lastIndexOf('.');
+		return fname.substring(0, dot);
+	}
 
-    public void tearDown() throws Exception {
-        PregelixHyracksIntegrationUtil.deinit();
-        LOGGER.info("Hyracks mini-cluster shut down");
-        cleanupHDFS();
-    }
-
-    public static Test suite() throws Exception {
-        List<String> ignores = getFileList(PATH_TO_IGNORE);
-        List<String> onlys = getFileList(PATH_TO_ONLY);
-        File testData = new File(PATH_TO_JOBS);
-        File[] queries = testData.listFiles();
-        PathMergeSmallTestSuite testSuite = new PathMergeSmallTestSuite();
-        testSuite.setUp();
-        boolean onlyEnabled = false;
-        FileSystem dfs = FileSystem.get(testSuite.conf);
-
-        if (onlys.size() > 0) {
-            onlyEnabled = true;
-        }
-        for (File qFile : queries) {
-            if (isInList(ignores, qFile.getName()))
-                continue;
-
-            if (qFile.isFile()) {
-                if (onlyEnabled && !isInList(onlys, qFile.getName())) {
-                    continue;
-                } else {
-                    String resultFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName());
-                    testSuite.addTest(new PathMergeSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile.getAbsolutePath()
-                            .toString(), resultFileName, dfs));
-                }
-            }
-        }
-        return testSuite;
-    }
-
-    /**
-     * Runs the tests and collects their result in a TestResult.
-     */
-    @Override
-    public void run(TestResult result) {
-        try {
-            int testCount = countTestCases();
-            for (int i = 0; i < testCount; i++) {
-                // cleanupStores();
-                Test each = this.testAt(i);
-                if (result.shouldStop())
-                    break;
-                runTest(each, result);
-            }
-            tearDown();
-        } catch (Exception e) {
-            throw new IllegalStateException(e);
-        }
-    }
-
-    protected static List<String> getFileList(String ignorePath) throws FileNotFoundException, IOException {
-        BufferedReader reader = new BufferedReader(new FileReader(ignorePath));
-        String s = null;
-        List<String> ignores = new ArrayList<String>();
-        while ((s = reader.readLine()) != null) {
-            ignores.add(s);
-        }
-        reader.close();
-        return ignores;
-    }
-
-    private static String jobExtToResExt(String fname) {
-        int dot = fname.lastIndexOf('.');
-        return fname.substring(0, dot);
-    }
-
-    private static boolean isInList(List<String> onlys, String name) {
-        for (String only : onlys)
-            if (name.indexOf(only) >= 0)
-                return true;
-        return false;
-    }
+	private static boolean isInList(List<String> onlys, String name) {
+		for (String only : onlys)
+			if (name.indexOf(only) >= 0)
+				return true;
+		return false;
+	}
 
 }