diff --git a/genomix/genomix-hadoop/data/webmap/MergeBubble.txt b/genomix/genomix-hadoop/data/webmap/MergeBubble.txt
new file mode 100644
index 0000000..087f43e
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/MergeBubble.txt
@@ -0,0 +1,2 @@
+1	AATAGAA
+2	AATACAA
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
index c35ad7f..a15ceeb 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
@@ -6,7 +6,6 @@
 
 import org.apache.hadoop.io.WritableComparable;
 
-import edu.uci.ics.genomix.oldtype.PositionListWritable;
 import edu.uci.ics.genomix.type.KmerListWritable;
 
 public class AdjacencyListWritable implements WritableComparable<AdjacencyListWritable>{
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
index ebb4f74..f5aa3a1 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
@@ -4,11 +4,10 @@
 import org.apache.hadoop.io.NullWritable;
 
 import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.KmerListWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 import edu.uci.ics.pregelix.api.util.BspUtils;
-import edu.uci.ics.genomix.oldtype.PositionListWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.client.Client;
 import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
@@ -47,7 +46,7 @@
  *  Remove tip or single node when l > constant
  */
 public class BubbleAddVertex extends
-        Vertex<PositionWritable, VertexValueWritable, NullWritable, MessageWritable> {
+        Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
     public static final String KMER_SIZE = "BubbleAddVertex.kmerSize";
     public static int kmerSize = -1;
    
@@ -64,40 +63,42 @@
     public void compute(Iterator<MessageWritable> msgIterator) {
         initVertex(); 
         if(getSuperstep() == 1){
-            if(getVertexId().getReadID() == 1 && getVertexId().getPosInRead() == 2){
-                getVertexValue().getFFList().append(2, (byte)1);
+            if(getVertexId().toString().equals("ATA")){
+                KmerBytesWritable vertexId = new KmerBytesWritable(kmerSize);
+                vertexId.setByRead("GTA".getBytes(), 0);
+                getVertexValue().getFRList().append(vertexId);
                 
-                //add tip vertex
+                //add bridge vertex
                 @SuppressWarnings("rawtypes")
                 Vertex vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
                 vertex.getMsgList().clear();
                 vertex.getEdges().clear();
-                PositionWritable vertexId = new PositionWritable();
-                VertexValueWritable vertexValue = new VertexValueWritable();
+                VertexValueWritable vertexValue = new VertexValueWritable(kmerSize);
                 /**
                  * set the src vertex id
                  */
-                vertexId.set(2, (byte)1);
                 vertex.setVertexId(vertexId);
                 /**
                  * set the vertex value
                  */
-                byte[] array = { 'T', 'A', 'G', 'C', 'C', 'A', 'G'}; //TAGCCAG
-                KmerBytesWritable kmer = new KmerBytesWritable(array.length); 
-                kmer.setByRead(array, 0);
-                vertexValue.setKmer(kmer);
-                PositionListWritable plist = new PositionListWritable();
-                plist.append(new PositionWritable(1, (byte)2));
-                vertexValue.setRRList(plist);
-                PositionListWritable plist2 = new PositionListWritable();
-                plist2.append(new PositionWritable(1, (byte)4));
-                vertexValue.setFFList(plist2);
+                KmerListWritable kmerFRList = new KmerListWritable(kmerSize);
+                kmerFRList.append(getVertexId());
+                vertexValue.setFRList(kmerFRList);
+                KmerBytesWritable otherVertexId = new KmerBytesWritable(kmerSize);
+                otherVertexId.setByRead("AGA".getBytes(), 0);
+                KmerListWritable kmerRFList = new KmerListWritable(kmerSize);
+                kmerRFList.append(otherVertexId);
+                vertexValue.setRFList(kmerRFList);
+                vertexValue.setKmer(vertexId);
                 vertex.setVertexValue(vertexValue);
                 
                 addVertex(vertexId, vertex);
+            } 
+            else if(getVertexId().toString().equals("AGA")){
+                KmerBytesWritable brdgeVertexId = new KmerBytesWritable(kmerSize);
+                brdgeVertexId.setByRead("GTA".getBytes(), 0);
+                getVertexValue().getRFList().append(brdgeVertexId);
             }
-            if(getVertexId().getReadID() == 1 && getVertexId().getPosInRead() == 4)
-                getVertexValue().getRRList().append(2, (byte)1);
         }
         voteToHalt();
     }
@@ -111,7 +112,7 @@
         job.setVertexInputFormatClass(GraphCleanInputFormat.class);
         job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputKeyClass(KmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
index b782294..d630b5f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
@@ -7,6 +7,7 @@
 
 import org.apache.hadoop.io.NullWritable;
 
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.KmerBytesWritableFactory;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
@@ -51,7 +52,7 @@
  * Naive Algorithm for path merge graph
  */
 public class BubbleMergeVertex extends
-        Vertex<PositionWritable, VertexValueWritable, NullWritable, MergeBubbleMessageWritable> {
+        Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MergeBubbleMessageWritable> {
     public static final String KMER_SIZE = "BubbleMergeVertex.kmerSize";
     public static final String ITERATIONS = "BubbleMergeVertex.iteration";
     public static int kmerSize = -1;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
deleted file mode 100644
index fa5ae19..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
+++ /dev/null
@@ -1,58 +0,0 @@
-package edu.uci.ics.genomix.pregelix.sequencefile;
-
-import java.io.File;
-import java.io.IOException;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.io.SequenceFile;
-import org.apache.hadoop.io.SequenceFile.CompressionType;
-
-import edu.uci.ics.genomix.oldtype.NodeWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
-
-
-public class ConvertNodeToIdValue {
-
-    public static void convert(Path inFile, Path outFile)
-            throws IOException {
-        Configuration conf = new Configuration();
-        FileSystem fileSys = FileSystem.get(conf);
-
-        SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
-        SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf, outFile, PositionWritable.class,
-                VertexValueWritable.class, CompressionType.NONE);
-        NodeWritable node = new NodeWritable();
-        NullWritable value = NullWritable.get();
-        PositionWritable outputKey = new PositionWritable();
-        VertexValueWritable outputValue = new VertexValueWritable();
-
-        while(reader.next(node, value)) {
-            System.out.println(node.getNodeID().toString());
-            outputKey.set(node.getNodeID());
-            outputValue.setFFList(node.getFFList());
-            outputValue.setFRList(node.getFRList());
-            outputValue.setRFList(node.getRFList());
-            outputValue.setRRList(node.getRRList());
-            outputValue.setKmer(node.getKmer());
-            outputValue.setState(State.IS_HEAD);
-            writer.append(outputKey, outputValue);
-        }
-        writer.close();
-        reader.close();
-    }
-    
-    public static void main(String[] args) throws IOException {
-        Path dir = new Path("data/test");
-        Path outDir = new Path("data/input");
-        FileUtils.cleanDirectory(new File("data/input"));
-        Path inFile = new Path(dir, "result.graphbuild.txt.bin");
-        Path outFile = new Path(outDir, "out");
-        convert(inFile,outFile);
-    }
-}
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 fbe47ce..ff5f404 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
@@ -195,23 +195,23 @@
         generateBridgeRemoveGraphJob("BridgeRemoveGraph", outputBase
                 + "BridgeRemoveGraph.xml");
     }
-//    
-//    private static void generateBubbleAddGraphJob(String jobName, String outputPath) throws IOException {
-//        PregelixJob job = new PregelixJob(jobName);
-//        job.setVertexClass(BubbleAddVertex.class);
-//        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
-//        job.setDynamicVertexValueSize(true);
-//        job.setOutputKeyClass(PositionWritable.class);
-//        job.setOutputValueClass(VertexValueWritable.class);
-//        job.getConfiguration().setInt(BubbleAddVertex.KMER_SIZE, 3);
-//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-//    }
-//
-//    private static void genBubbleAddGraph() throws IOException {
-//        generateBubbleAddGraphJob("BubbleAddGraph", outputBase
-//                + "BubbleAddGraph.xml");
-//    }
+    
+    private static void generateBubbleAddGraphJob(String jobName, String outputPath) throws IOException {
+        PregelixJob job = new PregelixJob(jobName);
+        job.setVertexClass(BubbleAddVertex.class);
+        job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(KmerBytesWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
+        job.getConfiguration().setInt(BubbleAddVertex.KMER_SIZE, 3);
+        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+    }
+
+    private static void genBubbleAddGraph() throws IOException {
+        generateBubbleAddGraphJob("BubbleAddGraph", outputBase
+                + "BubbleAddGraph.xml");
+    }
 //    
 //    private static void generateBubbleMergeGraphJob(String jobName, String outputPath) throws IOException {
 //        PregelixJob job = new PregelixJob(jobName);
@@ -247,6 +247,7 @@
         genBridgeAddGraph();
         genTipRemoveGraph();
         genBridgeRemoveGraph();
+        genBubbleAddGraph();
     }
 
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddSmallTestSuite.java
new file mode 100644
index 0000000..a9c2774
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddSmallTestSuite.java
@@ -0,0 +1,199 @@
+/*
+ * Copyright 2009-2010 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.pregelix.JobRun;
+
+import java.io.BufferedReader;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+
+import junit.framework.Test;
+import junit.framework.TestResult;
+import junit.framework.TestSuite;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.hdfs.MiniDFSCluster;
+import org.apache.hadoop.mapred.JobConf;
+
+import edu.uci.ics.pregelix.core.jobgen.clusterconfig.ClusterConfig;
+import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
+
+@SuppressWarnings("deprecation")
+public class BubbleAddSmallTestSuite extends TestSuite {
+    private static final Logger LOGGER = Logger.getLogger(BubbleAddSmallTestSuite.class.getName());
+
+    public static final String PreFix = "data/PathMergeTestSet"; 
+    public static final String[] TestDir = { PreFix + File.separator
+    + "5"};
+    private static final String ACTUAL_RESULT_DIR = "data/actual/bubbleadd";
+    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_bubbleadd.txt";
+
+    public static final String HDFS_INPUTPATH = "/PathTestSet";
+
+    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;
+
+    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 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);
+
+        for (String testDir : TestDir) {
+            File src = new File(testDir);
+            Path dest = new Path(HDFS_INPUTPATH + File.separator + src.getName());
+            dfs.mkdirs(dest);
+            //src.listFiles()
+            //src.listFiles((FilenameFilter)(new WildcardFileFilter("part*")))
+            for (File f : src.listFiles()) {
+                dfs.copyFromLocalFile(new Path(f.getAbsolutePath()), dest);
+            }
+        }
+
+        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();
+    }
+
+    public void tearDown() throws Exception {
+        PregelixHyracksIntegrationUtil.deinit();
+        LOGGER.info("Hyracks mini-cluster shut down");
+        cleanupHDFS();
+    }
+
+    public static Test suite() throws Exception {
+        List<String> onlys = getFileList(PATH_TO_ONLY);
+        File testData = new File(PATH_TO_JOBS);
+        File[] queries = testData.listFiles();
+        BubbleAddSmallTestSuite testSuite = new BubbleAddSmallTestSuite();
+        testSuite.setUp();
+        boolean onlyEnabled = false;
+        FileSystem dfs = FileSystem.get(testSuite.conf);
+
+        if (onlys.size() > 0) {
+            onlyEnabled = true;
+        }
+
+        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 + "bin" + File.separator + testDir.getName();
+                        String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+                                + File.separator + "txt" + File.separator + testDir.getName();
+                        testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
+                                .getAbsolutePath().toString(), dfs,
+                                HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName));
+                    }
+                }
+            }
+        }
+        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;
+    }
+
+}