diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathH1Driver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathH1Driver.java
index 2ddeb6b..a8e5f7c 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathH1Driver.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathH1Driver.java
@@ -131,7 +131,7 @@
             dfs.rename(new Path(outputPath + "/" + complete), new Path(mergeResultPath + "/" + complete));
         }
         /*----------------------------------------*/
-        conf = new JobConf(MergePathH1Driver.class);
+/*        conf = new JobConf(MergePathH1Driver.class);
         conf.setInt("sizeKmer", sizeKmer);
         conf.setInt("iMerge", iMerge);
         
@@ -169,7 +169,7 @@
         JobClient.runJob(conf);
         dfs.delete(new Path(inputPath + "-step1"), true);
         dfs.rename(new Path(outputPath + "/" + uncomplete), new Path(inputPath + "-step1"));
-        dfs.rename(new Path(outputPath + "/" + complete), new Path(mergeResultPath + "/" + complete));
+        dfs.rename(new Path(outputPath + "/" + complete), new Path(mergeResultPath + "/" + complete));*/
     }
 
     public static void main(String[] args) throws Exception {
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathMultiSeqOutputFormat.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathMultiSeqOutputFormat.java
index 5ef8b4a..5e8f1d8 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathMultiSeqOutputFormat.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathMultiSeqOutputFormat.java
@@ -15,7 +15,6 @@
 package edu.uci.ics.genomix.pathmergingh1;
 
 import java.io.File;
-import org.apache.hadoop.io.BytesWritable;
 import org.apache.hadoop.mapred.lib.MultipleSequenceFileOutputFormat;
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathValueWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathValueWritable.java
index 0d94227..f14e5f2 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathValueWritable.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh1/MergePathValueWritable.java
@@ -17,12 +17,9 @@
 import java.io.DataInput;
 import java.io.DataOutput;
 import java.io.IOException;
-
 import org.apache.hadoop.io.BinaryComparable;
 import org.apache.hadoop.io.WritableComparable;
-
 import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 public class MergePathValueWritable extends BinaryComparable implements WritableComparable<BinaryComparable> {
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/gbresultschecking/ResultsCheckingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/gbresultschecking/ResultsCheckingTest.java
index d29c160..acca4e7 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/gbresultschecking/ResultsCheckingTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/gbresultschecking/ResultsCheckingTest.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.gbresultschecking;
 
 import java.io.DataOutputStream;
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/graphbuilding/GraphBuildingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/graphbuilding/GraphBuildingTest.java
index d329c6a..efd3619 100755
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/graphbuilding/GraphBuildingTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/graphbuilding/GraphBuildingTest.java
@@ -1,5 +1,3 @@
-package edu.uci.ics.genomix.graphbuilding;
-
 /*
  * Copyright 2009-2012 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
@@ -14,13 +12,14 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+package edu.uci.ics.genomix.graphbuilding;
+
 import java.io.BufferedWriter;
 import java.io.DataOutputStream;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.FileWriter;
 import java.io.IOException;
-
 import org.apache.commons.io.FileUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
@@ -31,7 +30,6 @@
 import org.apache.hadoop.mapred.MiniMRCluster;
 import org.apache.hadoop.util.ReflectionUtils;
 import org.junit.Test;
-
 import edu.uci.ics.genomix.graphbuilding.GenomixDriver;
 import edu.uci.ics.genomix.type.GeneCode;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
@@ -47,14 +45,14 @@
     private static final String COMPARE_DIR = "compare";
     private JobConf conf = new JobConf();
     private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
-    private static final String DATA_PATH = "data/webmap/TreePath";
+    private static final String DATA_PATH = "data/webmap/Test.txt";
     private static final String HDFS_PATH = "/webmap";
     private static final String RESULT_PATH = "/result1";
     private static final String EXPECTED_PATH = "expected/result1";
-    private static final String TEST_SOURCE_DIR = COMPARE_DIR + RESULT_PATH + "/comparesource.txt";
+    private static final String TEST_SOURCE_DIR = COMPARE_DIR + RESULT_PATH;
     private static final int COUNT_REDUCER = 4;
-    private static final int SIZE_KMER = 5;
-    private static final String GRAPHVIZ = "Graphviz/GenomixSource.txt";
+    private static final int SIZE_KMER = 3;
+    private static final String GRAPHVIZ = "Graphviz";
     
     private MiniDFSCluster dfsCluster;
     private MiniMRCluster mrCluster;
@@ -74,13 +72,16 @@
         SequenceFile.Reader reader = null;
         Path path = new Path(RESULT_PATH + "/part-00000");
         reader = new SequenceFile.Reader(dfs, path, conf); 
-//        KmerBytesWritable key = (KmerBytesWritable) ReflectionUtils.newInstance(reader.getKeyClass(), conf);
         KmerBytesWritable key = new KmerBytesWritable(SIZE_KMER);
         KmerCountValue value = (KmerCountValue) ReflectionUtils.newInstance(reader.getValueClass(), conf);
         File filePathTo = new File(TEST_SOURCE_DIR);
-        BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
+        FileUtils.forceMkdir(filePathTo);
+        FileUtils.cleanDirectory(filePathTo);
+        BufferedWriter bw = new BufferedWriter(new FileWriter(new File(TEST_SOURCE_DIR + "/comparesource.txt")));
         File GraphViz = new File(GRAPHVIZ);
-        BufferedWriter bw2 = new BufferedWriter(new FileWriter(GraphViz));
+        FileUtils.forceMkdir(GraphViz);
+        FileUtils.cleanDirectory(GraphViz);
+        BufferedWriter bw2 = new BufferedWriter(new FileWriter(new File(GRAPHVIZ + "/GenomixSource.txt")));
         
         while (reader.next(key, value)) {
             byte succeed = (byte) 0x0F;
@@ -108,7 +109,7 @@
        bw.close();
 
         dumpResult();
-//        TestUtils.compareWithResult(new File(TEST_SOURCE_DIR), new File(EXPECTED_PATH));
+        TestUtils.compareWithResult(new File(TEST_SOURCE_DIR + "/comparesource.txt"), new File(EXPECTED_PATH));
 
         cleanupHadoop();
 
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/graphcountfilter/CountFilterTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/graphcountfilter/CountFilterTest.java
index 6eaced2..bff0179 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/graphcountfilter/CountFilterTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/graphcountfilter/CountFilterTest.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.graphcountfilter;
 
 import java.io.BufferedWriter;
@@ -6,7 +20,6 @@
 import java.io.FileOutputStream;
 import java.io.FileWriter;
 import java.io.IOException;
-
 import org.apache.commons.io.FileUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
@@ -18,7 +31,6 @@
 import org.apache.hadoop.mapred.MiniMRCluster;
 import org.apache.hadoop.util.ReflectionUtils;
 import org.junit.Test;
-
 import edu.uci.ics.genomix.graphcountfilter.CountFilterDriver;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.utils.TestUtils;
@@ -34,9 +46,8 @@
     private static final String HDFS_PATH = "/webmap";
     private static final String RESULT_PATH = "/result2";
     private static final String EXPECTED_PATH = "expected/result2";
-    private static final String TEST_SOURCE_DIR = COMPARE_DIR + RESULT_PATH + "/comparesource.txt";
+    private static final String TEST_SOURCE_DIR = COMPARE_DIR + RESULT_PATH;
     private static final int COUNT_REDUCER = 4;
-    private static final int SIZE_KMER = 5;
     private MiniDFSCluster dfsCluster;
     private MiniMRCluster mrCluster;
     private FileSystem dfs;
@@ -58,7 +69,9 @@
         KmerBytesWritable key = (KmerBytesWritable) ReflectionUtils.newInstance(reader.getKeyClass(), conf);
         ByteWritable value = (ByteWritable) ReflectionUtils.newInstance(reader.getValueClass(), conf);
         File filePathTo = new File(TEST_SOURCE_DIR);
-        BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
+        FileUtils.forceMkdir(filePathTo);
+        FileUtils.cleanDirectory(filePathTo);
+        BufferedWriter bw = new BufferedWriter(new FileWriter(new File(TEST_SOURCE_DIR + "/comparesource.txt")));
         while (reader.next(key, value)) {
             bw.write(key.toString() + "\t" + value.toString());
             bw.newLine();
@@ -66,7 +79,7 @@
         bw.close();
 
         dumpResult();
-        TestUtils.compareWithResult(new File(TEST_SOURCE_DIR), new File(EXPECTED_PATH));
+        TestUtils.compareWithResult(new File(TEST_SOURCE_DIR + "/comparesource.txt"), new File(EXPECTED_PATH));
 
         cleanupHadoop();
 
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/pathmergingh1/MergePathTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/pathmergingh1/MergePathTest.java
index c7a1213..109db50 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/pathmergingh1/MergePathTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/pathmergingh1/MergePathTest.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.pathmergingh1;
 
 import java.io.BufferedWriter;
@@ -34,7 +48,7 @@
     
     private static final String RESULT_PATH = "/result3";
     private static final String EXPECTED_PATH = "expected/result3";
-    private static final String TEST_SOURCE_DIR = COMPARE_DIR + RESULT_PATH + "/comparesource.txt";
+    private static final String TEST_SOURCE_DIR = COMPARE_DIR + RESULT_PATH;
     private static final int COUNT_REDUCER = 1;
     private static final int SIZE_KMER = 3;
 
@@ -50,24 +64,24 @@
         startHadoop();
 
         MergePathH1Driver tldriver = new MergePathH1Driver();
-        tldriver.run(HDFS_PATH, RESULT_PATH, HDFA_PATH_DATA, COUNT_REDUCER, SIZE_KMER, 1, HADOOP_CONF_PATH);
+        tldriver.run(HDFS_PATH, RESULT_PATH, HDFA_PATH_DATA, COUNT_REDUCER, SIZE_KMER, 3, HADOOP_CONF_PATH);
         
-/*        SequenceFile.Reader reader = null;
-        Path path = new Path(RESULT_PATH + "/part-00000");
-//        Path path = new Path(RESULT_PATH + "/uncomplete0" + "/uncomplete0-r-00000");
+        SequenceFile.Reader reader = null;
+        Path path = new Path(HDFA_PATH_DATA + "/complete2" + "/complete2-r-00000");
         reader = new SequenceFile.Reader(dfs, path, conf);
         VKmerBytesWritable key = (VKmerBytesWritable) ReflectionUtils.newInstance(reader.getKeyClass(), conf);
         MergePathValueWritable value = (MergePathValueWritable) ReflectionUtils.newInstance(reader.getValueClass(), conf);
         File filePathTo = new File(TEST_SOURCE_DIR);
-        BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
+        FileUtils.forceMkdir(filePathTo);
+        FileUtils.cleanDirectory(filePathTo);
+        BufferedWriter bw = new BufferedWriter(new FileWriter(new File(TEST_SOURCE_DIR + "/comparesource.txt")));
         while (reader.next(key, value)) {
             bw.write(key.toString() + "\t" + value.getAdjBitMap() + "\t" + value.getFlag());
             bw.newLine();
         }
-        bw.close();*/
-        dumpResult();
+        bw.close();
         
-//        TestUtils.compareWithResult(new File(TEST_SOURCE_DIR), new File(EXPECTED_PATH));
+        TestUtils.compareWithResult(new File(TEST_SOURCE_DIR + "/comparesource.txt"), new File(EXPECTED_PATH));
 
         cleanupHadoop();
 
@@ -99,7 +113,6 @@
     }
 
     private void dumpResult() throws IOException {
-//        Path src = new Path(HDFA_PATH_DATA + "/" + "complete2");
         Path src = new Path(RESULT_PATH);
         Path dest = new Path(ACTUAL_RESULT_DIR + "/");
         dfs.copyToLocalFile(src, dest);
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/pathmergingh2/MergePathH2Test.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/pathmergingh2/MergePathH2Test.java
index e72c352..7f871bd 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/pathmergingh2/MergePathH2Test.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/pathmergingh2/MergePathH2Test.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.pathmergingh2;
 
 import java.io.BufferedWriter;
@@ -34,7 +48,7 @@
     
     private static final String RESULT_PATH = "/result4";
     private static final String EXPECTED_PATH = "expected/result4";
-    private static final String TEST_SOURCE_DIR = COMPARE_DIR + RESULT_PATH + "/comparesource.txt";
+    private static final String TEST_SOURCE_DIR = COMPARE_DIR + RESULT_PATH;
     private static final int COUNT_REDUCER = 1;
     private static final int SIZE_KMER = 3;
 
@@ -50,24 +64,24 @@
         startHadoop();
 
         MergePathH2Driver tldriver = new MergePathH2Driver();
-        tldriver.run(HDFS_PATH, RESULT_PATH, HDFA_PATH_DATA, COUNT_REDUCER, SIZE_KMER, 1, HADOOP_CONF_PATH);
+        tldriver.run(HDFS_PATH, RESULT_PATH, HDFA_PATH_DATA, COUNT_REDUCER, SIZE_KMER, 3, HADOOP_CONF_PATH);
         
-/*        SequenceFile.Reader reader = null;
-//        Path path = new Path(RESULT_PATH + "/part-00000");
-        Path path = new Path(RESULT_PATH + "/uncomplete0" + "/uncomplete0-r-00000");
+        SequenceFile.Reader reader = null;
+        Path path = new Path(HDFA_PATH_DATA + "/complete2" + "/complete2-r-00000");
         reader = new SequenceFile.Reader(dfs, path, conf);
         VKmerBytesWritable key = (VKmerBytesWritable) ReflectionUtils.newInstance(reader.getKeyClass(), conf);
         MergePathValueWritable value = (MergePathValueWritable) ReflectionUtils.newInstance(reader.getValueClass(), conf);
         File filePathTo = new File(TEST_SOURCE_DIR);
-        BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
+        FileUtils.forceMkdir(filePathTo);
+        FileUtils.cleanDirectory(filePathTo);
+        BufferedWriter bw = new BufferedWriter(new FileWriter(new File(TEST_SOURCE_DIR + "/comparesource.txt")));
         while (reader.next(key, value)) {
             bw.write(key.toString() + "\t" + value.getAdjBitMap() + "\t" + value.getFlag());
             bw.newLine();
         }
-        bw.close();*/
-//        dumpResult();
+        bw.close();
         
-//        TestUtils.compareWithResult(new File(TEST_SOURCE_DIR), new File(EXPECTED_PATH));
+        TestUtils.compareWithResult(new File(TEST_SOURCE_DIR + "/comparesource.txt"), new File(EXPECTED_PATH));
 
         cleanupHadoop();
 
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/utils/TestUtils.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/utils/TestUtils.java
index 73a7254..1488907 100755
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/utils/TestUtils.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/utils/TestUtils.java
@@ -1,5 +1,3 @@
-package edu.uci.ics.genomix.utils;
-
 /*
  * Copyright 2009-2012 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
@@ -14,6 +12,8 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+package edu.uci.ics.genomix.utils;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;