diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Kmer.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Kmer.java
index e4ff126..133e7f8 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Kmer.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Kmer.java
@@ -197,7 +197,6 @@
 			byte in = (byte) (kmer[i - 1] & 0x03);
 			kmer[i] = (byte) (((kmer[i] >>> 2) & 0x3f) | (in << 6));
 		}
-
 		int pos = ((k - 1) % 4) << 1;
 		byte code = (byte) (GENE_CODE.getCodeFromSymbol(c) << pos);
 		kmer[0] = (byte) (((kmer[0] >>> 2) & 0x3f) | code);
@@ -295,4 +294,5 @@
 				.getCodeFromSymbol(c));
 		return (byte) (1 << output);
 	}
+
 }
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerTest.java
index 8dacea1..d9c1846 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerTest.java
@@ -24,7 +24,7 @@
 	@Test
 	public void TestMoveKmer(){
 		byte[] kmer = Kmer.compressKmer(k, array, 0);
-		String result = Kmer.recoverKmerFrom(k, kmer, 0, kmer.length);
+		String result = Kmer.recoverKmerFrom(k, kmer, 0, kmer.length); 
 		Assert.assertEquals(result, "AATAGAA");
 		
 		for (int i = k; i < array.length-1; i++) {
@@ -36,8 +36,8 @@
 		Assert.assertEquals(out, Kmer.GENE_CODE.getAdjBit((byte) 'A'));
 		result = Kmer.recoverKmerFrom(k, kmer, 0, kmer.length);
 		Assert.assertEquals(result, "ATAGAAG");
-		
 	}
+
 	
 	@Test
 	public void TestReverseKmer(){
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
index f9bf5b0..5a64f78 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
@@ -37,7 +37,7 @@
 	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 DATA_PATH = "src/test/resources/data/webmap/text.txt";
+	private static final String DATA_PATH = "src/test/resources/data/mergeTest/ThreeKmer";
 	private static final String HDFS_INPUT_PATH = "/webmap";
 	private static final String HDFS_OUTPUT_PATH = "/webmap_result";
 
@@ -195,11 +195,10 @@
 			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);
-				
-				
+				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);
+					
 				Path path = new Path(HDFS_OUTPUT_PATH
 						+ partname);
 				FileSystem dfs = FileSystem.get(conf);
diff --git a/genomix/genomix-pregelix/graph/BridgePath b/genomix/genomix-pregelix/graph/BridgePath
new file mode 100644
index 0000000..c10ea60
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+++ b/genomix/genomix-pregelix/graph/BridgePath
@@ -0,0 +1,14 @@
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+CACCC	C|C	1
+TTTCC	|A	2
+CCCGT	C|G	1
+TCCGT	C|G	1
+CACTC	C|C	1
diff --git a/genomix/genomix-pregelix/graph/BridgePath_out.ps b/genomix/genomix-pregelix/graph/BridgePath_out.ps
new file mode 100644
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diff --git a/genomix/genomix-pregelix/graph/CyclePath b/genomix/genomix-pregelix/graph/CyclePath
new file mode 100644
index 0000000..db30e3a
--- /dev/null
+++ b/genomix/genomix-pregelix/graph/CyclePath
@@ -0,0 +1,10 @@
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diff --git a/genomix/genomix-pregelix/graph/CyclePath_out.ps b/genomix/genomix-pregelix/graph/CyclePath_out.ps
new file mode 100644
index 0000000..1b13ecb
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@@ -0,0 +1 @@
+GGCCTCAGTACGCCCGG
diff --git a/genomix/genomix-pregelix/graph/mergeTest/Path b/genomix/genomix-pregelix/graph/mergeTest/Path
new file mode 100644
index 0000000..f63bbcf
--- /dev/null
+++ b/genomix/genomix-pregelix/graph/mergeTest/Path
@@ -0,0 +1 @@
+GGCCTCAGTACG
diff --git a/genomix/genomix-pregelix/graph/mergeTest/SimplePath b/genomix/genomix-pregelix/graph/mergeTest/SimplePath
new file mode 100644
index 0000000..80c03af
--- /dev/null
+++ b/genomix/genomix-pregelix/graph/mergeTest/SimplePath
@@ -0,0 +1,3 @@
+ATATCGCATC
+AAGACAGCAC
+GCGGCAAGAA
diff --git a/genomix/genomix-pregelix/graph/mergeTest/SinglePath b/genomix/genomix-pregelix/graph/mergeTest/SinglePath
new file mode 100644
index 0000000..56ef5f8
--- /dev/null
+++ b/genomix/genomix-pregelix/graph/mergeTest/SinglePath
@@ -0,0 +1 @@
+AGACAACAGT
diff --git a/genomix/genomix-pregelix/graph/mergeTest/ThreeKmer b/genomix/genomix-pregelix/graph/mergeTest/ThreeKmer
new file mode 100644
index 0000000..ec004fa
--- /dev/null
+++ b/genomix/genomix-pregelix/graph/mergeTest/ThreeKmer
@@ -0,0 +1 @@
+ACTCGGT
diff --git a/genomix/genomix-pregelix/graph/mergeTest/TreePath b/genomix/genomix-pregelix/graph/mergeTest/TreePath
new file mode 100644
index 0000000..f3c13ce
--- /dev/null
+++ b/genomix/genomix-pregelix/graph/mergeTest/TreePath
@@ -0,0 +1,3 @@
+GGCCTGGCTATCCC
+GGCCTCAGTAACTAAAC
+GGCCTCAGTACGCCCGG
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/graph/mergeTest/TwoKmer b/genomix/genomix-pregelix/graph/mergeTest/TwoKmer
new file mode 100644
index 0000000..86790c6
--- /dev/null
+++ b/genomix/genomix-pregelix/graph/mergeTest/TwoKmer
@@ -0,0 +1,2 @@
+ACACT	|G	1
+CACTG	A|	1
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
new file mode 100644
index 0000000..128b0dc
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
@@ -0,0 +1,58 @@
+
+package edu.uci.ics.genomix.pregelix.client;
+
+import java.io.IOException;
+
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
+import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.Option;
+
+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;
+
+public class Client {
+
+    private static class Options {
+        @Option(name = "-inputpaths", usage = "comma seprated input paths", required = true)
+        public String inputPaths;
+
+        @Option(name = "-outputpath", usage = "output path", required = true)
+        public String outputPath;
+
+        @Option(name = "-ip", usage = "ip address of cluster controller", required = true)
+        public String ipAddress;
+
+        @Option(name = "-port", usage = "port of cluster controller", required = false)
+        public int port;
+
+        @Option(name = "-plan", usage = "query plan choice", required = false)
+        public Plan planChoice = Plan.OUTER_JOIN;
+
+        @Option(name = "-runtime-profiling", usage = "whether to do runtime profifling", required = false)
+        public String profiling = "false";
+    }
+
+    public static void run(String[] args, PregelixJob job) throws Exception {
+        Options options = prepareJob(args, job);
+        Driver driver = new Driver(Client.class);
+        driver.runJob(job, options.planChoice, options.ipAddress, options.port, Boolean.parseBoolean(options.profiling));
+    }
+
+    private static Options prepareJob(String[] args, PregelixJob job) throws CmdLineException, IOException {
+        Options options = new Options();
+        CmdLineParser parser = new CmdLineParser(options);
+        parser.parseArgument(args);
+
+        String[] inputs = options.inputPaths.split(";");
+        FileInputFormat.setInputPaths(job, inputs[0]);
+        for (int i = 1; i < inputs.length; i++)
+            FileInputFormat.addInputPaths(job, inputs[0]);
+        FileOutputFormat.setOutputPath(job, new Path(options.outputPath));
+        return options;
+    }
+
+}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestCase.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestCase.java
index 84b342e..c00e996 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestCase.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestCase.java
@@ -1,11 +1,16 @@
 package edu.uci.ics.genomix.pregelix.JobRun;
 
+import java.io.BufferedWriter;
 import java.io.File;
+import java.io.FileWriter;
 
 import junit.framework.TestCase;
 
+import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.FileUtil;
 import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.mapred.JobConf;
 import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
 import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
 import org.junit.Test;
@@ -33,6 +38,8 @@
     private final String resultFileName;
     private final String expectedFileName;
     private final String jobFile;
+    
+
 
     public RunJobTestCase(String hadoopConfPath, String jobName, String jobFile, String resultFile, String expectedFile)
             throws Exception {
@@ -151,6 +158,16 @@
     }
 
     private void compareResults() throws Exception {
+		FileSystem.getLocal(new Configuration()).mkdirs(new Path("actual"));
+		//File filePathTo = new File(CONVERT_RESULT);
+		//BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
+		for (int i = 0; i < 1 * 2; i++) {
+			String partname = "/part-" + i;
+			FileUtil.copy(FileSystem.get(job.getConfiguration()), new Path(HDFS_OUTPUTPAH						
+					+ partname), FileSystem.getLocal(new Configuration()),						
+					new Path("actual/test" + partname), false, job.getConfiguration());
+		}
+		
         TestUtils.compareWithResult(new File(resultFileName), new File(expectedFileName));
     }
 
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 fb698e5..e7589e3 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
@@ -187,4 +187,12 @@
 		return false;
 	}
 
+	public JobConf getConf() {
+		return conf;
+	}
+
+	public void setConf(JobConf conf) {
+		this.conf = conf;
+	}
+
 }