diff --git a/genomix/genomix-hadoop/actual/conf.xml b/genomix/genomix-hadoop/actual/conf.xml
index b3ca482..a24987c 100755
--- a/genomix/genomix-hadoop/actual/conf.xml
+++ b/genomix/genomix-hadoop/actual/conf.xml
@@ -12,7 +12,7 @@
 <property><name>dfs.namenode.logging.level</name><value>info</value></property>
 <property><name>dfs.datanode.address</name><value>127.0.0.1:0</value></property>
 <property><name>io.skip.checksum.errors</name><value>false</value></property>
-<property><name>fs.default.name</name><value>hdfs://localhost:49297</value></property>
+<property><name>fs.default.name</name><value>hdfs://localhost:55116</value></property>
 <property><name>mapred.child.tmp</name><value>./tmp</value></property>
 <property><name>fs.har.impl.disable.cache</name><value>true</value></property>
 <property><name>dfs.safemode.threshold.pct</name><value>0.999f</value></property>
@@ -125,7 +125,7 @@
 <property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
 <property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
 <property><name>dfs.namenode.decommission.interval</name><value>3</value></property>
-<property><name>dfs.http.address</name><value>localhost:49298</value></property>
+<property><name>dfs.http.address</name><value>localhost:55117</value></property>
 <property><name>dfs.heartbeat.interval</name><value>3</value></property>
 <property><name>mapred.job.tracker</name><value>local</value></property>
 <property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
diff --git a/genomix/genomix-hadoop/actual/result2/.part-00000.crc b/genomix/genomix-hadoop/actual/result2/.part-00000.crc
index 190ef20..7a34e25 100755
--- a/genomix/genomix-hadoop/actual/result2/.part-00000.crc
+++ b/genomix/genomix-hadoop/actual/result2/.part-00000.crc
Binary files differ
diff --git a/genomix/genomix-hadoop/actual/result2/part-00000 b/genomix/genomix-hadoop/actual/result2/part-00000
index bd04159..1f33880 100755
--- a/genomix/genomix-hadoop/actual/result2/part-00000
+++ b/genomix/genomix-hadoop/actual/result2/part-00000
@@ -1,6 +1,6 @@
 1	33	1
 3	1	1
-4	153	1
+4	-103	2
 12	18	1
 16	18	1
 19	16	1
diff --git a/genomix/genomix-hadoop/expected/result2 b/genomix/genomix-hadoop/expected/result2
index 6ead1cc..bc7bc64 100755
--- a/genomix/genomix-hadoop/expected/result2
+++ b/genomix/genomix-hadoop/expected/result2
@@ -1,6 +1,6 @@
 1 33 1
 3 1 1
-4 153 1
+4 -103 2
 12 18 1
 16 18 1
 19 16 1
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java
index 5f4d991..dadbb9a 100755
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java
@@ -1,24 +1,53 @@
 package edu.uci.ics.graphbuilding;
 
+/*
+ * 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.
+ */
 import java.io.IOException;
 import java.util.Iterator;
 
 import org.apache.hadoop.io.IntWritable;
 import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.VLongWritable;
 import org.apache.hadoop.mapred.MapReduceBase;
 import org.apache.hadoop.mapred.OutputCollector;
 import org.apache.hadoop.mapred.Reducer;
 import org.apache.hadoop.mapred.Reporter;
 
+/**
+ * This class implement the combiner operator of Mapreduce model
+ */
 public class GenomixCombiner extends MapReduceBase implements
-        Reducer<LongWritable, IntWritable, LongWritable, IntWritable> {
-    public void reduce(LongWritable key, Iterator<IntWritable> values,
-            OutputCollector<LongWritable, IntWritable> output, Reporter reporter) throws IOException {
-        int groupByAdjList = 0;
+        Reducer<VLongWritable, ValueWritable, VLongWritable, ValueWritable> {
+    public ValueWritable vaWriter = new ValueWritable();
+
+    @Override
+    public void reduce(VLongWritable key, Iterator<ValueWritable> values,
+            OutputCollector<VLongWritable, ValueWritable> output, Reporter reporter) throws IOException {
+        byte groupByAdjList = 0;
+        int count = 0;
+        byte bytCount = 0;
         while (values.hasNext()) {
             //Merge By the all adjacent Nodes;
-            groupByAdjList = groupByAdjList | values.next().get();
+            groupByAdjList = (byte) (groupByAdjList | values.next().getFirst());
+            count = count + 1;
         }
-        output.collect(key, new IntWritable(groupByAdjList));
+        if (count >= 128)
+            bytCount = (byte) 128;
+        else
+            bytCount = (byte) count;
+        vaWriter.set(groupByAdjList, bytCount);
+        output.collect(key, vaWriter);
     }
 }
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java
index 9c8a689..67c4e09 100755
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java
@@ -1,5 +1,19 @@
 package edu.uci.ics.graphbuilding;
 
+/*
+ * 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.
+ */
 import java.io.IOException;
 
 import org.apache.hadoop.fs.FileSystem;
@@ -7,6 +21,7 @@
 import org.apache.hadoop.io.IntWritable;
 import org.apache.hadoop.io.LongWritable;
 import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.VLongWritable;
 import org.apache.hadoop.mapred.FileInputFormat;
 import org.apache.hadoop.mapred.FileOutputFormat;
 import org.apache.hadoop.mapred.JobClient;
@@ -16,6 +31,9 @@
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
 
+/**
+ * This class implement driver which start the mapreduce program for graphbuilding
+ */
 @SuppressWarnings("deprecation")
 public class GenomixDriver {
     private static class Options {
@@ -27,11 +45,17 @@
 
         @Option(name = "-num-reducers", usage = "the number of reducers", required = true)
         public int numReducers;
+
+        @Option(name = "-kmer-size", usage = "the size of kmer", required = true)
+        public int sizeKmer;
     }
 
-    public void run(String inputPath, String outputPath, int numReducers, String defaultConfPath) throws IOException {
+    public void run(String inputPath, String outputPath, int numReducers, int sizeKmer, String defaultConfPath)
+            throws IOException {
 
         JobConf conf = new JobConf(GenomixDriver.class);
+        conf.setInt("sizeKmer", sizeKmer);
+
         if (defaultConfPath != null) {
             conf.addResource(new Path(defaultConfPath));
         }
@@ -41,12 +65,12 @@
         conf.setReducerClass(GenomixReducer.class);
         conf.setCombinerClass(GenomixCombiner.class);
 
-        conf.setMapOutputKeyClass(LongWritable.class);
-        conf.setMapOutputValueClass(IntWritable.class);
+        conf.setMapOutputKeyClass(VLongWritable.class);
+        conf.setMapOutputValueClass(ValueWritable.class);
 
         conf.setInputFormat(TextInputFormat.class);
         conf.setOutputFormat(TextOutputFormat.class);
-        conf.setOutputKeyClass(LongWritable.class);
+        conf.setOutputKeyClass(VLongWritable.class);
         conf.setOutputValueClass(ValueWritable.class);
         FileInputFormat.setInputPaths(conf, new Path(inputPath));
         FileOutputFormat.setOutputPath(conf, new Path(outputPath));
@@ -62,7 +86,7 @@
         CmdLineParser parser = new CmdLineParser(options);
         parser.parseArgument(args);
         GenomixDriver driver = new GenomixDriver();
-        driver.run(options.inputPath, options.outputPath, options.numReducers, null);
+        driver.run(options.inputPath, options.outputPath, options.numReducers, options.sizeKmer, null);
     }
 
 }
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java
index aff4e6d..367370e 100755
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java
@@ -1,85 +1,94 @@
 package edu.uci.ics.graphbuilding;
 
+/*
+ * 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.
+ */
 import java.io.IOException;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.io.IntWritable;
 import org.apache.hadoop.io.LongWritable;
 import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.VLongWritable;
+import org.apache.hadoop.mapred.JobConf;
 import org.apache.hadoop.mapred.MapReduceBase;
 import org.apache.hadoop.mapred.Mapper;
 import org.apache.hadoop.mapred.OutputCollector;
 import org.apache.hadoop.mapred.Reporter;
 
-public class GenomixMapper extends MapReduceBase implements Mapper<LongWritable, Text, LongWritable, IntWritable> {
+/**
+ * This class implement mapper operator of mapreduce model
+ */
+public class GenomixMapper extends MapReduceBase implements Mapper<LongWritable, Text, VLongWritable, ValueWritable> {
 
-    public static final int KMER_SIZE = 3; //User Specify
-    //    private Text Map_Pair_Key = new Text();
+    public static int KMER_SIZE;
+    public ValueWritable outputAdjList = new ValueWritable();
+    public VLongWritable outputKmer = new VLongWritable();
 
-    /*precursor node
+    @Override
+    public void configure(JobConf job) {
+        KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
+    }
+
+    /*succeed node
       A 00000001 1
       G 00000010 2
       C 00000100 4
       T 00001000 8
-      succeed node
+      precursor node
       A 00010000 16
       G 00100000 32
       C 01000000 64
       T 10000000 128*/
-    public void map(LongWritable key, Text value, OutputCollector<LongWritable, IntWritable> output, Reporter reporter)
-            throws IOException {
+    @Override
+    public void map(LongWritable key, Text value, OutputCollector<VLongWritable, ValueWritable> output,
+            Reporter reporter) throws IOException {
         /* A 00
            G 01
            C 10
            T 11*/
-        try {
-            String geneLine = value.toString(); // Read the Real Gene Line
-            Pattern genePattern = Pattern.compile("[AGCT]+");
-            Matcher geneMatcher = genePattern.matcher(geneLine);
-            boolean isValid = geneMatcher.matches();
-            if (isValid == true) {
-                long kmerValue = 0;
-                long PreMarker = -1;
-                //Initialization: get the first kmer of this geneLine 
-                for (int i = 0; i < KMER_SIZE; i++) {
-                    kmerValue = (kmerValue << 2);
-                    switch (geneLine.charAt(i)) {
-                        case 'A':
-                            kmerValue = kmerValue + 0;
-                            break;
-                        case 'G':
-                            kmerValue = kmerValue + 1;
-                            break;
-                        case 'C':
-                            kmerValue = kmerValue + 2;
-                            break;
-                        case 'T':
-                            kmerValue = kmerValue + 3;
-                            break;
-                    }
-                }
-                int i;
-                //Get the next kmer by shiftint one letter every time
-                for (i = KMER_SIZE; i < geneLine.length(); i++) {
-                    LongWritable outputKmer = new LongWritable(kmerValue);
-                    int kmerAdjList = 0;
-                    //Get the precursor node using the premarker
+        String geneLine = value.toString(); // Read the Real Gene Line
+        Pattern genePattern = Pattern.compile("[AGCT]+");
+        Matcher geneMatcher = genePattern.matcher(geneLine);
+        boolean isValid = geneMatcher.matches();
+        int i = 0;
+        if (isValid == true) {
+            long kmerValue = 0;
+            long PreMarker = -1;
+            byte count = 0;
+            //Get the next kmer by shiftint one letter every time
+            for (i = 0; i < geneLine.length(); i++) {
+                byte kmerAdjList = 0;
+                if (i >= KMER_SIZE) {
+                    outputKmer.set(kmerValue);
                     switch ((int) PreMarker) {
                         case -1:
-                            kmerAdjList = kmerAdjList + 0;
+                            kmerAdjList = (byte) (kmerAdjList + 0);
                             break;
                         case 0:
-                            kmerAdjList = kmerAdjList + 16;
+                            kmerAdjList = (byte) (kmerAdjList + 16);
                             break;
                         case 16:
-                            kmerAdjList = kmerAdjList + 32;
+                            kmerAdjList = (byte) (kmerAdjList + 32);
                             break;
                         case 32:
-                            kmerAdjList = kmerAdjList + 64;
+                            kmerAdjList = (byte) (kmerAdjList + 64);
                             break;
                         case 48:
-                            kmerAdjList = kmerAdjList + 128;
+                            kmerAdjList = (byte) (kmerAdjList + 128);
                             break;
                     }
                     //Update the premarker
@@ -91,51 +100,53 @@
                     kmerValue = kmerValue << 2;
                     reset = ~(reset << KMER_SIZE * 2);
                     kmerValue = kmerValue & reset;
-                    switch (geneLine.charAt(i)) {
-                        case 'A':
-                            kmerAdjList = kmerAdjList + 1;
-                            kmerValue = kmerValue + 0;
-                            break;
-                        case 'G':
-                            kmerAdjList = kmerAdjList + 2;
-                            kmerValue = kmerValue + 1;
-                            break;
-                        case 'C':
-                            kmerAdjList = kmerAdjList + 4;
-                            kmerValue = kmerValue + 2;
-                            break;
-                        case 'T':
-                            kmerAdjList = kmerAdjList + 8;
-                            kmerValue = kmerValue + 3;
-                            break;
-                    }
-                    IntWritable outputAdjList = new IntWritable(kmerAdjList);
+                }
+                switch (geneLine.charAt(i)) {
+                    case 'A':
+                        kmerAdjList = (byte) (kmerAdjList + 1);
+                        kmerValue = kmerValue + 0;
+                        break;
+                    case 'G':
+                        kmerAdjList = (byte) (kmerAdjList + 2);
+                        kmerValue = kmerValue + 1;
+                        break;
+                    case 'C':
+                        kmerAdjList = (byte) (kmerAdjList + 4);
+                        kmerValue = kmerValue + 2;
+                        break;
+                    case 'T':
+                        kmerAdjList = (byte) (kmerAdjList + 8);
+                        kmerValue = kmerValue + 3;
+                        break;
+                }
+                if (i >= KMER_SIZE) {
+                    outputAdjList.set(kmerAdjList, count);
                     output.collect(outputKmer, outputAdjList);
                 }
-                // arrive the last letter of this gene line
-                if (i == geneLine.length()) {
-                    int kmerAdjList = 0;
-                    switch ((int) PreMarker) {
-                        case 0:
-                            kmerAdjList = kmerAdjList + 16;
-                            break;
-                        case 16:
-                            kmerAdjList = kmerAdjList + 32;
-                            break;
-                        case 32:
-                            kmerAdjList = kmerAdjList + 64;
-                            break;
-                        case 48:
-                            kmerAdjList = kmerAdjList + 128;
-                            break;
-                    }
-                    IntWritable outputAdjList = new IntWritable(kmerAdjList);
-                    LongWritable outputKmer = new LongWritable(kmerValue);
-                    output.collect(outputKmer, outputAdjList);
-                }
+                if (i < KMER_SIZE - 1)
+                    kmerValue = (kmerValue << 2);
             }
-        } catch (Exception e) {
-            System.out.println("Exception:" + e);
+            // arrive the last letter of this gene line
+            if (i == geneLine.length()) {
+                byte kmerAdjList = 0;
+                switch ((int) PreMarker) {
+                    case 0:
+                        kmerAdjList = (byte) (kmerAdjList + 16);
+                        break;
+                    case 16:
+                        kmerAdjList = (byte) (kmerAdjList + 32);
+                        break;
+                    case 32:
+                        kmerAdjList = (byte) (kmerAdjList + 64);
+                        break;
+                    case 48:
+                        kmerAdjList = (byte) (kmerAdjList + 128);
+                        break;
+                }
+                outputAdjList.set(kmerAdjList, count);
+                outputKmer.set(kmerValue);
+                output.collect(outputKmer, outputAdjList);
+            }
         }
     }
-}
+}
\ No newline at end of file
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java
index 244d058..7358ae0 100755
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java
@@ -1,26 +1,51 @@
 package edu.uci.ics.graphbuilding;
-
+/*
+ * 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.
+ */
 import java.io.IOException;
 import java.util.Iterator;
 
 import org.apache.hadoop.io.IntWritable;
 import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.VLongWritable;
 import org.apache.hadoop.mapred.MapReduceBase;
 import org.apache.hadoop.mapred.OutputCollector;
 import org.apache.hadoop.mapred.Reducer;
 import org.apache.hadoop.mapred.Reporter;
-
+/**
+ * This class implement reducer operator of mapreduce model
+ */
 public class GenomixReducer extends MapReduceBase implements
-        Reducer<LongWritable, IntWritable, LongWritable, ValueWritable> {
-    public void reduce(LongWritable key, Iterator<IntWritable> values,
-            OutputCollector<LongWritable, ValueWritable> output, Reporter reporter) throws IOException {
-        int groupByAdjList = 0;
-        int count = 0;
-        while (values.hasNext()) {
-            //Merge By the all adjacent Nodes;
-            groupByAdjList = groupByAdjList | values.next().get();
-            count++;
-        }
-        output.collect(key, new ValueWritable(groupByAdjList, count));
-    }
+Reducer<VLongWritable, ValueWritable, VLongWritable, ValueWritable> {
+ValueWritable valWriter = new ValueWritable();
+@Override
+public void reduce(VLongWritable key, Iterator<ValueWritable> values,
+    OutputCollector<VLongWritable, ValueWritable> output, Reporter reporter) throws IOException {
+byte groupByAdjList = 0;
+int count = 0;
+byte bytCount = 0;
+while (values.hasNext()) {
+    //Merge By the all adjacent Nodes;
+    ValueWritable geneValue = values.next();
+    groupByAdjList = (byte) (groupByAdjList | geneValue.getFirst());
+    count = count + (int)geneValue.getSecond();
+}
+if(count >= 128)
+    bytCount = (byte)128;
+else
+    bytCount = (byte)count;
+valWriter.set(groupByAdjList, bytCount);
+output.collect(key, valWriter);
+}
 }
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java
index 3adac3c..87d9be6 100755
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/ValueWritable.java
@@ -1,49 +1,65 @@
 package edu.uci.ics.graphbuilding;
-
+/*
+ * 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.
+ */
 import java.io.DataInput;
 import java.io.DataOutput;
 import java.io.IOException;
 
 import org.apache.hadoop.io.WritableComparable;
-
+/**
+ * This class override the writablecomparable class which contain int varable
+ */
 public class ValueWritable implements WritableComparable<ValueWritable> {
-    private int first;
-    private int second;
+    private byte first;
+    private byte second;
 
     public ValueWritable() {
     }
 
-    public ValueWritable(int first, int second) {
+    public ValueWritable(byte first, byte second) {
         set(first, second);
     }
 
-    public void set(int first, int second) {
+    public void set(byte first, byte second) {
         this.first = first;
         this.second = second;
     }
 
-    public int getFirst() {
+    public byte getFirst() {
         return first;
     }
 
-    public int getSecond() {
+    public byte getSecond() {
         return second;
     }
 
+    @Override
     public void write(DataOutput out) throws IOException {
-        out.writeInt(first);
-        out.writeInt(second);
+        out.writeByte(first);
+        out.writeByte(second);
     }
-
+    @Override
     public void readFields(DataInput in) throws IOException {
-        first = in.readInt();
-        second = in.readInt();
+        first = in.readByte();
+        second = in.readByte();
     }
-
+    @Override
     public int hashCode() {
-        return first + second;
+        return (int) first + (int) second;
     }
-
+    @Override
     public boolean equals(Object o) {
         if (o instanceof ValueWritable) {
             ValueWritable tp = (ValueWritable) o;
@@ -51,11 +67,11 @@
         }
         return false;
     }
-
+    @Override
     public String toString() {
         return Integer.toString(first) + "\t" + Integer.toString(second);
     }
-
+    @Override
     public int compareTo(ValueWritable tp) {
         int cmp;
         if (first == tp.first)
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java
index 783ecf4..0095fe9 100755
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/graphbuilding/GraphBuildingTest.java
@@ -1,5 +1,18 @@
 package edu.uci.ics.graphbuilding;
-
+/*
+ * 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.
+ */
 import java.io.DataOutputStream;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -15,7 +28,9 @@
 import org.junit.Test;
 
 import edu.uci.ics.utils.TestUtils;
-
+/**
+ * This class test the correctness of graphbuilding program
+ */
 public class GraphBuildingTest {
 
     private static final String ACTUAL_RESULT_DIR = "actual";
@@ -39,7 +54,7 @@
 
         // run graph transformation tests
         GenomixDriver tldriver = new GenomixDriver();
-        tldriver.run(HDFS_PATH, RESULT_PATH, 2, HADOOP_CONF_PATH);
+        tldriver.run(HDFS_PATH, RESULT_PATH, 2, 3, HADOOP_CONF_PATH);
         dumpResult();
         TestUtils.compareWithResult(new File(DUMPED_RESULT), new File(EXPECTED_PATH));
 
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java
index 0455b14..e63aa5b 100755
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/utils/TestUtils.java
@@ -1,9 +1,24 @@
 package edu.uci.ics.utils;
-
+/*
+ * 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.
+ */
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
-
+/**
+ * This class offer the service for graphbuildingtest.class
+ */
 public class TestUtils {
     public static void compareWithResult(File expectedFile, File actualFile) throws Exception {
         BufferedReader readerExpected = new BufferedReader(new FileReader(expectedFile));