diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/ENodeInitialReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/ENodeInitialReducer.java
deleted file mode 100644
index 66cae9b..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/ENodeInitialReducer.java
+++ /dev/null
@@ -1,59 +0,0 @@
-package edu.uci.ics.pathmergingh2;
-
-import java.io.IOException;
-import java.util.Iterator;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.MapReduceBase;
-import org.apache.hadoop.mapred.OutputCollector;
-import org.apache.hadoop.mapred.Reducer;
-import org.apache.hadoop.mapred.Reporter;
-import edu.uci.ics.genomix.type.KmerUtil;
-
-@SuppressWarnings("deprecation")
-public class ENodeInitialReducer extends MapReduceBase implements
-        Reducer<BytesWritable, MergePathValueWritable, BytesWritable, MergePathValueWritable> {
-    public BytesWritable outputKmer = new BytesWritable();
-    public MergePathValueWritable outputAdjList = new MergePathValueWritable();
-    
-
-    @Override
-    public void reduce(BytesWritable key, Iterator<MergePathValueWritable> values,
-            OutputCollector<BytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-        outputAdjList = values.next();
-        outputKmer.set(key);
-        if (values.hasNext() == true) {
-            byte bitFlag = outputAdjList.getFlag();
-            bitFlag = (byte) (bitFlag & 0xFE);
-            if (bitFlag == 2) {
-                bitFlag =  (byte) (0x80 | outputAdjList.getFlag());
-                outputAdjList.set(null, 0, 0, outputAdjList.getAdjBitMap(), bitFlag, outputAdjList.getKmerSize());
-                output.collect(outputKmer, outputAdjList);
-
-            } else {
-                boolean flag = false;
-                while (values.hasNext()) {
-                    outputAdjList = values.next();
-                    if (outputAdjList.getFlag() == 2) {
-                        flag = true;
-                        break;
-                    }
-                }
-                if (flag == true) {
-                    bitFlag =  (byte) (0x80 | outputAdjList.getFlag());
-                    outputAdjList.set(null, 0, 0, outputAdjList.getAdjBitMap(), bitFlag, outputAdjList.getKmerSize());
-                    output.collect(outputKmer, outputAdjList);
-                }
-            }
-        } else {
-            byte bitFlag = outputAdjList.getFlag();
-            bitFlag = (byte) (bitFlag & 0xFE);
-            if (bitFlag == 2) {
-                bitFlag = 0;
-                outputAdjList.set(null, 0, 0, outputAdjList.getAdjBitMap(), bitFlag, outputAdjList.getKmerSize());
-                output.collect(outputKmer, outputAdjList);
-            } 
-        }
-    }
-}
-
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Driver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Driver.java
deleted file mode 100644
index e90e7a4..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Driver.java
+++ /dev/null
@@ -1,150 +0,0 @@
-package edu.uci.ics.pathmergingh2;
-
-import java.io.IOException;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.mapred.FileInputFormat;
-import org.apache.hadoop.mapred.FileOutputFormat;
-import org.apache.hadoop.mapred.JobClient;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.SequenceFileInputFormat;
-import org.apache.hadoop.mapred.SequenceFileOutputFormat;
-import org.apache.hadoop.mapred.TextOutputFormat;
-import org.apache.hadoop.mapred.lib.MultipleOutputs;
-import org.apache.hadoop.mapred.lib.MultipleSequenceFileOutputFormat;
-import org.apache.hadoop.mapred.lib.MultipleTextOutputFormat;
-import org.kohsuke.args4j.CmdLineParser;
-import org.kohsuke.args4j.Option;
-
-@SuppressWarnings("deprecation")
-public class MergePathH2Driver {
-    
-    private static class Options {
-        @Option(name = "-inputpath", usage = "the input path", required = true)
-        public String inputPath;
-
-        @Option(name = "-outputpath", usage = "the output path", required = true)
-        public String outputPath;
-
-        @Option(name = "-mergeresultpath", usage = "the merging results path", required = true)
-        public String mergeResultPath;
-        
-        @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;
-        
-        @Option(name = "-merge-rounds", usage = "the while rounds of merging", required = true)
-        public int mergeRound;
-
-    }
-
-
-    public void run(String inputPath, String outputPath, String mergeResultPath, int numReducers, int sizeKmer, int mergeRound, String defaultConfPath)
-            throws IOException{
-
-        JobConf conf = new JobConf(MergePathH2Driver.class);
-        conf.setInt("sizeKmer", sizeKmer);
-        
-        if (defaultConfPath != null) {
-            conf.addResource(new Path(defaultConfPath));
-        }
-        conf.setJobName("Initial Path-Starting-Points Table");
-        conf.setMapperClass(SNodeInitialMapper.class); 
-        conf.setReducerClass(SNodeInitialReducer.class);
-        
-        conf.setMapOutputKeyClass(BytesWritable.class);
-        conf.setMapOutputValueClass(MergePathValueWritable.class);
-        
-        conf.setInputFormat(SequenceFileInputFormat.class);
-        conf.setOutputFormat(SequenceFileOutputFormat.class);
-        
-        conf.setOutputKeyClass(BytesWritable.class);
-        conf.setOutputValueClass(MergePathValueWritable.class);
-        
-        FileInputFormat.setInputPaths(conf, new Path(inputPath));
-        FileOutputFormat.setOutputPath(conf, new Path(inputPath + "-step1"));
-        conf.setNumReduceTasks(numReducers);
-        FileSystem dfs = FileSystem.get(conf);
-        dfs.delete(new Path(inputPath + "-step1"), true);
-        JobClient.runJob(conf);
-/****************************************************************/
-        conf = new JobConf(MergePathH2Driver.class);
-        conf.setInt("sizeKmer", sizeKmer);
-        if (defaultConfPath != null) {
-            conf.addResource(new Path(defaultConfPath));
-        }
-        conf.setJobName("Initial Path-Starting-Points Table");
-        conf.setMapperClass(ENodeInitialMapper.class); 
-        conf.setReducerClass(ENodeInitialReducer.class);
-        
-        conf.setMapOutputKeyClass(BytesWritable.class);
-        conf.setMapOutputValueClass(MergePathValueWritable.class);
-        
-        conf.setInputFormat(SequenceFileInputFormat.class);
-        conf.setOutputFormat(SequenceFileOutputFormat.class);
-        
-        conf.setOutputKeyClass(BytesWritable.class);
-        conf.setOutputValueClass(MergePathValueWritable.class);
-        
-        FileInputFormat.setInputPaths(conf, new Path(inputPath + "-step1"));
-        FileOutputFormat.setOutputPath(conf, new Path(inputPath + "-step2"));
-        conf.setNumReduceTasks(numReducers);
-        dfs.delete(new Path(inputPath + "-step2"), true);
-        JobClient.runJob(conf);
-//       int iMerge = 0;
-/*----------------------------------------------------------------------*/
-/*        for(iMerge = 0; iMerge < mergeRound; iMerge ++){
-        
-            conf = new JobConf(MergePathDriver.class);
-            conf.setInt("sizeKmer", sizeKmer);
-            conf.setInt("iMerge", iMerge);
-            
-            if (defaultConfPath != null) {
-                conf.addResource(new Path(defaultConfPath));
-            }
-            conf.setJobName("Path Merge");
-            
-            conf.setMapperClass(MergePathMapper.class);
-            conf.setReducerClass(MergePathReducer.class);
-            
-            conf.setMapOutputKeyClass(BytesWritable.class);
-            conf.setMapOutputValueClass(MergePathValueWritable.class);
-            
-            conf.setInputFormat(SequenceFileInputFormat.class);
-            
-            String uncomplete = "uncomplete" + iMerge;
-            String complete = "complete" + iMerge;
-           
-            MultipleOutputs.addNamedOutput(conf, uncomplete,
-                    MergePathMultiSeqOutputFormat.class, BytesWritable.class,
-                    MergePathValueWritable.class);
-
-            MultipleOutputs.addNamedOutput(conf, complete,
-                    MergePathMultiSeqOutputFormat.class, BytesWritable.class,
-                    MergePathValueWritable.class);
-            
-            conf.setOutputKeyClass(BytesWritable.class);
-            conf.setOutputValueClass(MergePathValueWritable.class);
-            
-            FileInputFormat.setInputPaths(conf, new Path(inputPath + "-step1"));
-            FileOutputFormat.setOutputPath(conf, new Path(outputPath));
-            conf.setNumReduceTasks(numReducers);
-            dfs.delete(new Path(outputPath), true);
-            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));
-        }*/
-    }
-
-    public static void main(String[] args) throws Exception {
-        Options options = new Options();
-        CmdLineParser parser = new CmdLineParser(options);
-        parser.parseArgument(args);
-        MergePathH2Driver driver = new MergePathH2Driver();
-        driver.run(options.inputPath, options.outputPath, options.mergeResultPath, options.numReducers, options.sizeKmer, options.mergeRound, null);
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Mapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Mapper.java
deleted file mode 100644
index 1d8a98b..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Mapper.java
+++ /dev/null
@@ -1,83 +0,0 @@
-package edu.uci.ics.pathmergingh2;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.BytesWritable;
-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;
-
-import edu.uci.ics.genomix.type.Kmer;
-import edu.uci.ics.genomix.type.KmerUtil;
-import edu.uci.ics.genomix.type.Kmer.GENE_CODE;
-import edu.uci.ics.pathmerging.MergePathValueWritable;
-
-public class MergePathH2Mapper extends MapReduceBase implements
-        Mapper<BytesWritable, MergePathValueWritable, BytesWritable, MergePathValueWritable> {
-
-    public static int KMER_SIZE;
-    public BytesWritable outputKmer = new BytesWritable();
-    public MergePathValueWritable outputAdjList = new MergePathValueWritable();
-
-    public void configure(JobConf job) {
-        KMER_SIZE = job.getInt("sizeKmer", 0);
-    }
-
-    @Override
-    public void map(BytesWritable key, MergePathValueWritable value,
-            OutputCollector<BytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-        byte bitFlag = value.getFlag();
-        byte bitStartEnd = (byte) (0x81 & bitFlag);
-        byte succeed = (byte) 0x0F;
-        byte adjBitMap = value.getAdjBitMap();
-        succeed = (byte) (succeed & adjBitMap);
-        byte[] kmerValue = key.getBytes();
-        int kmerLength = key.getLength();
-        switch (bitStartEnd) {
-            case 0x01:
-                byte succeedCode = GENE_CODE.getGeneCodeFromBitMap(succeed);
-                int originalByteNum = Kmer.getByteNumFromK(KMER_SIZE);
-                byte[] tmpKmer = KmerUtil.getLastKmerFromChain(KMER_SIZE, value.getKmerSize(), kmerValue, 0, kmerLength);
-                byte[] newKmer = KmerUtil.shiftKmerWithNextCode(KMER_SIZE, tmpKmer, 0, tmpKmer.length, succeedCode);
-                outputKmer.set(newKmer, 0, originalByteNum);
-
-                int mergeByteNum = Kmer.getByteNumFromK(value.getKmerSize() - (KMER_SIZE - 1));
-                byte[] mergeKmer = KmerUtil.getFirstKmerFromChain(value.getKmerSize() - (KMER_SIZE - 1),
-                        value.getKmerSize(), kmerValue, 0, kmerLength);
-
-                bitFlag = (byte) (bitFlag | 0x08);
-                outputAdjList.set(mergeKmer, 0, mergeByteNum, adjBitMap, bitFlag, value.getKmerSize() - (KMER_SIZE - 1));
-                output.collect(outputKmer, outputAdjList);
-                break;
-            case (byte) 0x80:
-                outputKmer.set(key);
-                outputAdjList.set(value);
-                output.collect(outputKmer, outputAdjList);
-                break;
-            case 0x00:
-                succeedCode = GENE_CODE.getGeneCodeFromBitMap(succeed);
-                originalByteNum = Kmer.getByteNumFromK(KMER_SIZE);
-                tmpKmer = KmerUtil.getLastKmerFromChain(KMER_SIZE, value.getKmerSize(), kmerValue, 0, kmerLength);
-                newKmer = KmerUtil.shiftKmerWithNextCode(KMER_SIZE, tmpKmer, 0, tmpKmer.length, succeedCode);
-                outputKmer.set(newKmer, 0, originalByteNum);
-
-                mergeByteNum = Kmer.getByteNumFromK(value.getKmerSize() - (KMER_SIZE - 1));
-                mergeKmer = KmerUtil.getFirstKmerFromChain(value.getKmerSize() - (KMER_SIZE - 1), value.getKmerSize(),
-                        kmerValue, 0, kmerLength);
-
-                bitFlag = (byte) (bitFlag | 0x08);
-                outputAdjList
-                        .set(mergeKmer, 0, mergeByteNum, adjBitMap, bitFlag, value.getKmerSize() - (KMER_SIZE - 1));
-                output.collect(outputKmer, outputAdjList);
-
-                outputKmer.set(key);
-                outputAdjList.set(value);
-                output.collect(outputKmer, outputAdjList);
-                break;
-            case (byte) 0x81:
-                break;
-        }
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Reducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Reducer.java
deleted file mode 100644
index 0551bd3..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Reducer.java
+++ /dev/null
@@ -1,105 +0,0 @@
-package edu.uci.ics.pathmergingh2;
-
-import java.io.IOException;
-import java.util.Iterator;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.MapReduceBase;
-import org.apache.hadoop.mapred.OutputCollector;
-import org.apache.hadoop.mapred.Reducer;
-import org.apache.hadoop.mapred.Reporter;
-import org.apache.hadoop.mapred.lib.MultipleOutputs;
-
-import edu.uci.ics.genomix.type.Kmer;
-import edu.uci.ics.genomix.type.KmerUtil;
-import edu.uci.ics.pathmerging.MergePathValueWritable;
-
-public class MergePathH2Reducer extends MapReduceBase implements
-        Reducer<BytesWritable, MergePathValueWritable, BytesWritable, MergePathValueWritable> {
-    public BytesWritable outputKmer = new BytesWritable();
-    public static int KMER_SIZE;
-    public MergePathValueWritable outputAdjList = new MergePathValueWritable();
-    MultipleOutputs mos = null;
-    public static int I_MERGE;
-
-    public void configure(JobConf job) {
-        mos = new MultipleOutputs(job);
-        I_MERGE = Integer.parseInt(job.get("iMerge"));
-        KMER_SIZE = job.getInt("sizeKmer", 0);
-    }
-
-    public void reduce(BytesWritable key, Iterator<MergePathValueWritable> values,
-            OutputCollector<BytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-        outputKmer.set(key);
-        outputAdjList = values.next();
-        if (values.hasNext() == true) {
-            byte[] keyBytes = key.getBytes();
-            int keyLength = key.getLength();
-            byte bitFlag = outputAdjList.getFlag();
-            byte bitStartEnd = (byte) (0x81 & bitFlag);
-            byte bitPosiNegative = (byte) (0x18 & bitFlag);
-            byte succeed = (byte) 0x0F;
-            byte adjBitMap = outputAdjList.getAdjBitMap();
-
-            switch (bitPosiNegative) {
-                case (byte) 0x08:
-                    succeed = (byte) (succeed & adjBitMap);
-                    if (bitStartEnd == 0x10) {
-                        output.collect(outputKmer, outputAdjList);
-                    }
-                    int kmerSize = outputAdjList.getKmerSize();
-                    int mergeByteNum = Kmer.getByteNumFromK(KMER_SIZE + kmerSize);
-                    byte[] valueBytes = outputAdjList.getBytes();
-                    int valueLength = outputAdjList.getLength();
-                    byte[] mergeKmer = KmerUtil.mergeTwoKmer(outputAdjList.getKmerSize(), valueBytes, 0, valueLength,
-                            KMER_SIZE, keyBytes, 0, keyLength);
-                    outputAdjList = values.next();
-                    valueBytes = outputAdjList.getBytes();
-                    valueLength = outputAdjList.getLength();
-                    adjBitMap = outputAdjList.getAdjBitMap();
-                    mergeKmer = KmerUtil.mergeTwoKmer(outputAdjList.getKmerSize(), valueBytes, 0, valueLength,
-                            KMER_SIZE + kmerSize, mergeKmer, 0, mergeByteNum);
-                    outputKmer.set(mergeKmer, 0, mergeByteNum);
-
-                    adjBitMap = (byte) (adjBitMap & 0xF0);
-                    adjBitMap = (byte) (adjBitMap | succeed);
-                    byte flag = (byte) (bitFlag | 0x80);//zhe you wen ti
-                    outputAdjList.set(null, 0, 0, adjBitMap, flag, KMER_SIZE + kmerSize + outputAdjList.getKmerSize());
-                    mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputAdjList);
-                    break;
-                case (byte) 0x10:
-                    byte[] haha = new byte[outputAdjList.getLength()];
-                    for (int i = 0; i < haha.length; i++) {
-                        haha[i] = outputAdjList.getBytes()[i];
-                    }
-                    byte trueadj = outputAdjList.getAdjBitMap();
-                    int trueKmersize = outputAdjList.getKmerSize();
-                    outputAdjList = values.next();
-                    succeed = (byte) (succeed & adjBitMap);
-                    if (bitStartEnd == 0x10) {
-                        output.collect(outputKmer, outputAdjList);
-                    }
-                    kmerSize = outputAdjList.getKmerSize();
-                    mergeByteNum = Kmer.getByteNumFromK(KMER_SIZE + kmerSize);
-                    valueBytes = outputAdjList.getBytes();
-                    valueLength = outputAdjList.getLength();
-                    mergeKmer = KmerUtil.mergeTwoKmer(outputAdjList.getKmerSize(), valueBytes, 0, valueLength,
-                            KMER_SIZE, keyBytes, 0, keyLength);
-                    mergeKmer = KmerUtil.mergeTwoKmer(trueKmersize, haha, 0, haha.length,
-                            KMER_SIZE + kmerSize, mergeKmer, 0, mergeByteNum);
-                    outputKmer.set(mergeKmer, 0, mergeByteNum);
-                    
-                    trueadj = (byte) (adjBitMap & 0xF0);
-                    trueadj = (byte) (adjBitMap | succeed);
-//                    byte flag = (byte) (bitFlag | 0x80);
-                    outputAdjList.set(null, 0, 0, trueadj, bitFlag, KMER_SIZE + kmerSize + outputAdjList.getKmerSize());
-                    mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputAdjList);
-                    break;
-            }
-        }
-        else{
-            //shi bu shi yijing jieshu ---> complete
-        }
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiSeqOutputFormat.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiSeqOutputFormat.java
deleted file mode 100644
index cbde512..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiSeqOutputFormat.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * 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.pathmergingh2;
-
-import java.io.File;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.mapred.lib.MultipleSequenceFileOutputFormat;
-
-
-public class MergePathMultiSeqOutputFormat extends MultipleSequenceFileOutputFormat<BytesWritable, MergePathValueWritable>{
-    @Override
-    protected String generateLeafFileName(String name) {
-        // TODO Auto-generated method stub System.out.println(name); 
-        String[] names = name.split("-");
-        return names[0] + File.separator + name;
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiTextOutputFormat.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiTextOutputFormat.java
deleted file mode 100644
index d6176e2..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiTextOutputFormat.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * 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.pathmergingh2;
-
-import java.io.File;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.mapred.lib.MultipleTextOutputFormat;
-
-public class MergePathMultiTextOutputFormat extends MultipleTextOutputFormat<Text, Text>{
-    @Override
-    protected String generateLeafFileName(String name) {
-        // TODO Auto-generated method stub System.out.println(name); 
-        String[] names = name.split("-");
-        return names[0] + File.separator + name;
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathValueWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathValueWritable.java
deleted file mode 100644
index 7e944ff..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathValueWritable.java
+++ /dev/null
@@ -1,151 +0,0 @@
-/*
- * 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.pathmergingh2;
-
-import java.io.IOException;
-import java.io.DataInput;
-import java.io.DataOutput;
-import org.apache.hadoop.io.BinaryComparable;
-import org.apache.hadoop.io.WritableComparable;
-
-import edu.uci.ics.genomix.type.Kmer;
-
-public class MergePathValueWritable extends BinaryComparable implements WritableComparable<BinaryComparable> {
-
-    private static final byte[] EMPTY_BYTES = {};
-    private int size;
-    private byte[] bytes;
-
-    private byte adjBitMap;
-    private byte flag;
-    private int kmerSize;
-
-    public MergePathValueWritable() {
-        this((byte) 0, (byte) 0, (byte) 0, EMPTY_BYTES);
-    }
-
-    public MergePathValueWritable(byte adjBitMap, byte flag, byte kmerSize, byte[] bytes) {
-        this.adjBitMap = adjBitMap;
-        this.flag = flag;
-        this.kmerSize = kmerSize;
-
-        this.bytes = bytes;
-        this.size = bytes.length;
-    }
-
-    public void setSize(int size) {
-        if (size > getCapacity()) {
-            setCapacity(size * 3 / 2);
-        }
-        this.size = size;
-    }
-
-    public int getCapacity() {
-        return bytes.length;
-    }
-
-    public void setCapacity(int new_cap) {
-        if (new_cap != getCapacity()) {
-            byte[] new_data = new byte[new_cap];
-            if (new_cap < size) {
-                size = new_cap;
-            }
-            if (size != 0) {
-                System.arraycopy(bytes, 0, new_data, 0, size);
-            }
-            bytes = new_data;
-        }
-    }
-
-    public void set(MergePathValueWritable newData) {
-        set(newData.bytes, 0, newData.size, newData.adjBitMap, newData.flag, newData.kmerSize);
-    }
-
-    public void set(byte[] newData, int offset, int length, byte adjBitMap, byte flag, int kmerSize) {
-        setSize(0);        
-        if (length != 0) {
-            setSize(length);
-            System.arraycopy(newData, offset, bytes, 0, size);
-        }
-            this.adjBitMap = adjBitMap;
-            this.flag = flag;
-            this.kmerSize = kmerSize;
-    }
-
-    @Override
-    public void readFields(DataInput arg0) throws IOException {
-        // TODO Auto-generated method stub
-        setSize(0); // clear the old data
-        setSize(arg0.readInt());
-        if(size != 0){
-        arg0.readFully(bytes, 0, size);
-        }
-        adjBitMap = arg0.readByte();
-        flag = arg0.readByte();
-        kmerSize = arg0.readInt();
-    }
-
-    @Override
-    public void write(DataOutput arg0) throws IOException {
-        // TODO Auto-generated method stub
-        arg0.writeInt(size);
-        arg0.write(bytes, 0, size);
-        arg0.writeByte(adjBitMap);
-        arg0.writeByte(flag);
-        arg0.writeInt(kmerSize);
-    }
-
-    @Override
-    public byte[] getBytes() {
-        // TODO Auto-generated method stub
-        return bytes;
-    }
-
-    @Override
-    public int getLength() {
-        // TODO Auto-generated method stub
-        return size;
-    }
-
-    public byte getAdjBitMap() {
-        return this.adjBitMap;
-    }
-
-    public byte getFlag() {
-        return this.flag;
-    }
-
-    public int getKmerSize() {
-        return this.kmerSize;
-    }
-
-    public String toString() {
-        StringBuffer sb = new StringBuffer(3 * size);
-        for (int idx = 0; idx < size; idx++) {
-            // if not the first, put a blank separator in
-            if (idx != 0) {
-                sb.append(' ');
-            }
-            String num = Integer.toHexString(0xff & bytes[idx]);
-            // if it is only one digit, add a leading 0.
-            if (num.length() < 2) {
-                sb.append('0');
-            }
-            sb.append(num);
-        }
-        return Kmer.GENE_CODE.getSymbolFromBitMap(adjBitMap) + '\t' + String.valueOf(flag) + '\t' + sb.toString();
-    }
-}
-
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialMapper.java
deleted file mode 100644
index b58202c..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialMapper.java
+++ /dev/null
@@ -1,130 +0,0 @@
-package edu.uci.ics.pathmergingh2;
-
-import java.io.IOException;
-import org.apache.hadoop.io.ByteWritable;
-import org.apache.hadoop.io.BytesWritable;
-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;
-import edu.uci.ics.genomix.type.KmerUtil;
-import edu.uci.ics.genomix.type.Kmer.GENE_CODE;
-
-@SuppressWarnings("deprecation")
-public class SNodeInitialMapper extends MapReduceBase implements
-        Mapper<BytesWritable, ByteWritable, BytesWritable, MergePathValueWritable> {
-
-    public static int KMER_SIZE;
-    public BytesWritable outputKmer = new BytesWritable();
-    public MergePathValueWritable outputAdjList = new MergePathValueWritable();
-
-    public void configure(JobConf job) {
-        KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
-    }
-
-    boolean measureDegree(byte adjacent) {
-        boolean result = true;
-        switch (adjacent) {
-            case 0:
-                result = true;
-                break;
-            case 1:
-                result = false;
-                break;
-            case 2:
-                result = false;
-                break;
-            case 3:
-                result = true;
-                break;
-            case 4:
-                result = false;
-                break;
-            case 5:
-                result = true;
-                break;
-            case 6:
-                result = true;
-                break;
-            case 7:
-                result = true;
-                break;
-            case 8:
-                result = false;
-                break;
-            case 9:
-                result = true;
-                break;
-            case 10:
-                result = true;
-                break;
-            case 11:
-                result = true;
-                break;
-            case 12:
-                result = true;
-                break;
-            case 13:
-                result = true;
-                break;
-            case 14:
-                result = true;
-                break;
-            case 15:
-                result = true;
-                break;
-        }
-        return result;
-    }
-
-    @Override
-    public void map(BytesWritable key, ByteWritable value,
-            OutputCollector<BytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-        byte precursor = (byte) 0xF0;
-        byte succeed = (byte) 0x0F;
-        byte adjBitMap = value.get();
-        byte bitFlag = (byte) 0;
-        precursor = (byte) (precursor & adjBitMap);
-        precursor = (byte) ((precursor & 0xff) >> 4);
-        succeed = (byte) (succeed & adjBitMap);
-        boolean inDegree = measureDegree(precursor);
-        boolean outDegree = measureDegree(succeed);
-        byte[] kmerValue = key.getBytes();
-        int kmerLength = key.getLength();
-        if (inDegree == false && outDegree == false) {//bitflag = 2, it means that it has no need to store the precurCode.
-            outputKmer.set(key);
-            bitFlag = (byte) 2;
-            outputAdjList.set(null, 0, 0, adjBitMap, bitFlag, KMER_SIZE);
-            output.collect(outputKmer, outputAdjList);
-        }
-        else{
-            for(int i = 0 ; i < 4; i ++){
-                byte temp = 0x01;
-                temp  = (byte)(temp << i);
-                temp = (byte) (succeed & temp);
-                if(temp != 0 ){
-                    byte succeedCode = GENE_CODE.getGeneCodeFromBitMap(temp);
-                    byte[] newKmer = KmerUtil.shiftKmerWithNextCode(KMER_SIZE, kmerValue, 0, kmerLength, succeedCode);
-                    outputKmer.set(newKmer, 0, kmerLength);
-                    bitFlag = (byte) 0x80;
-                    outputAdjList.set(null, 0, 0, (byte)0, bitFlag, KMER_SIZE);
-                    output.collect(outputKmer, outputAdjList);
-                }
-            }
-            for(int i = 0; i < 4;i ++){
-                byte temp = 0x01;
-                temp = (byte)(temp << i);
-                temp = (byte)(precursor & temp);
-                if(temp != 0){
-                    byte precurCode = GENE_CODE.getGeneCodeFromBitMap(temp);
-                    byte[] newKmer = KmerUtil.shiftKmerWithPreCode(KMER_SIZE, kmerValue, 0, kmerLength, precurCode);
-                    outputKmer.set(newKmer, 0, kmerLength);
-                    bitFlag = (byte)0x40;
-                    outputAdjList.set(null, 0, 0, (byte)0, bitFlag, KMER_SIZE);
-                    output.collect(outputKmer, outputAdjList);
-                }
-            }
-        }
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialReducer.java
deleted file mode 100644
index 7b918b6..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialReducer.java
+++ /dev/null
@@ -1,72 +0,0 @@
-package edu.uci.ics.pathmergingh2;
-
-import java.io.IOException;
-import java.util.Iterator;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.MapReduceBase;
-import org.apache.hadoop.mapred.OutputCollector;
-import org.apache.hadoop.mapred.Reducer;
-import org.apache.hadoop.mapred.Reporter;
-
-import edu.uci.ics.genomix.type.KmerUtil;
-
-@SuppressWarnings("deprecation")
-public class SNodeInitialReducer extends MapReduceBase implements
-        Reducer<BytesWritable, MergePathValueWritable, BytesWritable, MergePathValueWritable> {
-    public BytesWritable outputKmer = new BytesWritable();
-    public MergePathValueWritable outputAdjList = new MergePathValueWritable();
-    public static int KMER_SIZE;
-
-    public void configure(JobConf job) {
-        KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
-    }
-    @Override
-    public void reduce(BytesWritable key, Iterator<MergePathValueWritable> values,
-            OutputCollector<BytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-        outputAdjList = values.next();
-        outputKmer.set(key);
-        byte[] kmerValue = key.getBytes();
-        int kmerLength = key.getLength();
-        if (values.hasNext() == true) {
-            if (outputAdjList.getFlag() == 2) {
-                byte bitFlag = 1;
-                outputAdjList.set(null, 0, 0, outputAdjList.getAdjBitMap(), bitFlag, outputAdjList.getKmerSize());
-                output.collect(outputKmer, outputAdjList);
-            } else {
-                boolean flag = false;
-                while (values.hasNext()) {
-                    outputAdjList = values.next();
-                    if (outputAdjList.getFlag() == 2) {
-                        flag = true;
-                        break;
-                    }
-                    else{
-                        
-                    }
-                }
-                if (flag == true) {
-                    byte bitFlag = 1;
-                    outputAdjList.set(null, 0, 0, outputAdjList.getAdjBitMap(), bitFlag, outputAdjList.getKmerSize());
-                    output.collect(outputKmer, outputAdjList);
-                }
-            }
-        } else {
-            if (outputAdjList.getFlag() == 2) {
-                byte bitFlag = 0;
-                outputAdjList.set(null, 0, 0, outputAdjList.getAdjBitMap(), bitFlag, outputAdjList.getKmerSize());
-                output.collect(outputKmer, outputAdjList);
-            }
-            else {
-                byte bitFlag = outputAdjList.getFlag();
-                byte adjBitMap = outputAdjList.getAdjBitMap();
-                byte precurCode = (byte) ((0xC0 & bitFlag) >> 6);
-                bitFlag = 0;
-                byte[] newKmer = KmerUtil.shiftKmerWithPreCode(KMER_SIZE, kmerValue, 0, kmerLength, precurCode);
-                outputKmer.set(newKmer, 0, kmerLength);
-                outputAdjList.set(null, 0, 0, adjBitMap, bitFlag, kmerLength);
-                output.collect(outputKmer, outputAdjList);
-            }
-        }
-    }
-}
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmergingh2/MergePathH2Test.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmergingh2/MergePathH2Test.java
deleted file mode 100644
index 3e66214..0000000
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmergingh2/MergePathH2Test.java
+++ /dev/null
@@ -1,103 +0,0 @@
-package edu.uci.ics.pathmergingh2;
-
-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;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.hdfs.MiniDFSCluster;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.SequenceFile;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.MiniMRCluster;
-import org.apache.hadoop.util.ReflectionUtils;
-import org.junit.Test;
-import edu.uci.ics.utils.TestUtils;
-
-@SuppressWarnings("deprecation")
-public class MergePathH2Test {
-    private static final String ACTUAL_RESULT_DIR = "actual3";
-    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 = "actual2" + "/result2" + "/part-00000";
-    private static final String HDFS_PATH = "/webmap";
-    private static final String HDFA_PATH_DATA = "/webmapdata";
-    
-    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 int COUNT_REDUCER = 4;
-    private static final int SIZE_KMER = 3;
-
-    private MiniDFSCluster dfsCluster;
-    private MiniMRCluster mrCluster;
-    private FileSystem dfs;
-
-    @SuppressWarnings("resource")
-    @Test
-    public void test() throws Exception {
-        FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
-        FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
-        startHadoop();
-
-        MergePathH2Driver tldriver = new MergePathH2Driver();
-
-        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(HDFA_PATH_DATA + "/complete2" + "/complete2-r-00000");
-        reader = new SequenceFile.Reader(dfs, path, conf);
-        BytesWritable key = (BytesWritable) 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));
-        while (reader.next(key, value)) {
-            bw.write(key.toString() + "\t" + value.getAdjBitMap() + "\t" + value.getFlag());
-            bw.newLine();
-        }
-        bw.close();
-
-        dumpResult();
-        TestUtils.compareWithResult(new File(TEST_SOURCE_DIR), new File(EXPECTED_PATH));
-*/
-        cleanupHadoop();
-
-    }
-    private void startHadoop() throws IOException {
-        FileSystem lfs = FileSystem.getLocal(new Configuration());
-        lfs.delete(new Path("build"), true);
-        System.setProperty("hadoop.log.dir", "logs");
-        dfsCluster = new MiniDFSCluster(conf, 2, true, null);
-        dfs = dfsCluster.getFileSystem();
-        mrCluster = new MiniMRCluster(4, dfs.getUri().toString(), 2);
-
-        Path src = new Path(DATA_PATH);
-        Path dest = new Path(HDFS_PATH + "/");
-        dfs.mkdirs(dest);
-        dfs.copyFromLocalFile(src, dest);
-        Path data = new Path(HDFA_PATH_DATA + "/");
-        dfs.mkdirs(data);
-   
-        DataOutputStream confOutput = new DataOutputStream(new FileOutputStream(new File(HADOOP_CONF_PATH)));
-        conf.writeXml(confOutput);
-        confOutput.flush();
-        confOutput.close();
-    }
-
-    private void cleanupHadoop() throws IOException {
-        mrCluster.shutdown();
-        dfsCluster.shutdown();
-    }
-
-    private void dumpResult() throws IOException {
-        Path src = new Path(HDFA_PATH_DATA + "/" + "complete2");
-        Path dest = new Path(ACTUAL_RESULT_DIR + "/");
-        dfs.copyToLocalFile(src, dest);
-    }
-}