diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/.DS_Store
deleted file mode 100644
index f5eb144..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/.DS_Store
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/ResultsCheckingDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/ResultsCheckingDriver.java
deleted file mode 100644
index 132f6e0..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/ResultsCheckingDriver.java
+++ /dev/null
@@ -1,96 +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.gbresultschecking;
-
-import java.io.IOException;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.Text;
-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.TextOutputFormat;
-import org.kohsuke.args4j.CmdLineParser;
-import org.kohsuke.args4j.Option;
-
-@SuppressWarnings("deprecation")
-public class ResultsCheckingDriver {
-    private static class Options {
-        @Option(name = "-inputpath1", usage = "the input path", required = true)
-        public String inputPath1;
-
-        @Option(name = "-inputpath2", usage = "the input path", required = true)
-        public String inputPath2;
-
-        @Option(name = "-outputpath", usage = "the output path", required = true)
-        public String outputPath;
-
-        @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 inputPath1, String inputPath2, String outputPath, int numReducers, int sizeKmer,
-            String defaultConfPath) throws IOException {
-
-        JobConf conf = new JobConf(ResultsCheckingDriver.class);
-
-        conf.setInt("sizeKmer", sizeKmer);
-
-        if (defaultConfPath != null) {
-            conf.addResource(new Path(defaultConfPath));
-        }
-
-        conf.setJobName("Results Checking");
-        conf.setMapperClass(ResultsCheckingMapper.class);
-        conf.setReducerClass(ResultsCheckingReducer.class);
-
-        conf.setMapOutputKeyClass(Text.class);
-        conf.setMapOutputValueClass(Text.class);
-
-        conf.setInputFormat(SequenceFileInputFormat.class);
-        conf.setOutputFormat(TextOutputFormat.class);
-
-        conf.setOutputKeyClass(Text.class);
-        conf.setOutputValueClass(Text.class);
-
-        Path[] inputList = new Path[2];
-        inputList[0] = new Path(inputPath1);
-        inputList[1] = new Path(inputPath2);
-
-        FileInputFormat.setInputPaths(conf, inputList);
-        FileOutputFormat.setOutputPath(conf, new Path(outputPath));
-        conf.setNumReduceTasks(numReducers);
-
-        FileSystem dfs = FileSystem.get(conf);
-        dfs.delete(new Path(outputPath), true);
-        JobClient.runJob(conf);
-    }
-
-    public static void main(String[] args) throws Exception {
-        Options options = new Options();
-        CmdLineParser parser = new CmdLineParser(options);
-        parser.parseArgument(args);
-        ResultsCheckingDriver driver = new ResultsCheckingDriver();
-        driver.run(options.inputPath1, options.inputPath2, options.outputPath, options.numReducers, options.sizeKmer,
-                null);
-    }
-
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/ResultsCheckingMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/ResultsCheckingMapper.java
deleted file mode 100644
index dca3808..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/ResultsCheckingMapper.java
+++ /dev/null
@@ -1,56 +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.gbresultschecking;
-
-import java.io.IOException;
-import org.apache.hadoop.io.ByteWritable;
-import org.apache.hadoop.io.IntWritable;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.mapred.FileInputFormat;
-import org.apache.hadoop.mapred.FileSplit;
-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.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerCountValue;
-
-@SuppressWarnings({ "unused", "deprecation" })
-public class ResultsCheckingMapper extends MapReduceBase implements Mapper<KmerBytesWritable, KmerCountValue, Text, Text> {
-    KmerBytesWritable valWriter;
-    private final static IntWritable one = new IntWritable(1);
-    public static Text textkey = new Text();
-    public static Text textvalue = new Text();
-    public static String INPUT_PATH;
-    public static int KMER_SIZE;
-
-    public void configure(JobConf job) {
-        KMER_SIZE = job.getInt("sizeKmer", 0);
-        valWriter= new KmerBytesWritable(KMER_SIZE);
-    }
-
-    @Override
-    public void map(KmerBytesWritable key, KmerCountValue value, OutputCollector<Text, Text> output, Reporter reporter)
-            throws IOException {
-
-        FileSplit fileSplit = (FileSplit) reporter.getInputSplit();
-        String filename = fileSplit.getPath().getName();
-        textkey.set(key.toString() + "\t" + value.toString());
-        textvalue.set(filename);
-        output.collect(textkey, textvalue);
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/ResultsCheckingReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/ResultsCheckingReducer.java
deleted file mode 100644
index 6f02136..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/ResultsCheckingReducer.java
+++ /dev/null
@@ -1,40 +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.gbresultschecking;
-
-import java.io.IOException;
-import java.util.Iterator;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.mapred.MapReduceBase;
-import org.apache.hadoop.mapred.OutputCollector;
-import org.apache.hadoop.mapred.Reducer;
-import org.apache.hadoop.mapred.Reporter;
-
-@SuppressWarnings("deprecation")
-public class ResultsCheckingReducer extends MapReduceBase implements Reducer<Text, Text, Text, Text> {
-
-    public static Text textkey = new Text();
-    public static Text textvalue = new Text();
-
-    @Override
-    public void reduce(Text key, Iterator<Text> values, OutputCollector<Text, Text> output, Reporter reporter)
-            throws IOException {
-        textkey.set(key);
-        textvalue.set(values.next());
-        if (values.hasNext() == false) {
-            output.collect(textkey, textvalue);
-        }
-    }
-}
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
deleted file mode 100755
index 09a1bf1..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixCombiner.java
+++ /dev/null
@@ -1,56 +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.graphbuilding;
-
-import java.io.IOException;
-import java.util.Iterator;
-
-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.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerCountValue;
-
-/**
- * This class implement the combiner operator of Mapreduce model
- */
-@SuppressWarnings("deprecation")
-public class GenomixCombiner extends MapReduceBase implements
-        Reducer<KmerBytesWritable, KmerCountValue, KmerBytesWritable, KmerCountValue> {
-    private KmerCountValue vaWriter = new KmerCountValue();
-
-    @Override
-    public void reduce(KmerBytesWritable key, Iterator<KmerCountValue> values,
-            OutputCollector<KmerBytesWritable, KmerCountValue> output, Reporter reporter) throws IOException {
-        byte groupByAdjList = 0;
-        int count = 0;
-        byte bytCount = 0;
-        while (values.hasNext()) {
-            //Merge By the all adjacent Nodes;
-            KmerCountValue geneValue = values.next();
-            groupByAdjList = (byte) (groupByAdjList | geneValue.getAdjBitMap());
-            count = count + (int) geneValue.getCount();
-        }
-        if (count >= 127)
-            bytCount = (byte) 127;
-        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
deleted file mode 100755
index e2f0f85..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixDriver.java
+++ /dev/null
@@ -1,92 +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.graphbuilding;
-
-import java.io.IOException;
-
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-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.SequenceFileOutputFormat;
-import org.apache.hadoop.mapred.TextInputFormat;
-import org.kohsuke.args4j.CmdLineParser;
-import org.kohsuke.args4j.Option;
-
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerCountValue;
-
-/**
- * This class implement driver which start the mapreduce program for graphbuilding
- */
-@SuppressWarnings("deprecation")
-public class GenomixDriver {
-    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 = "-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, int sizeKmer, String defaultConfPath)
-            throws IOException {
-
-        JobConf conf = new JobConf(GenomixDriver.class);
-        conf.setInt("sizeKmer", sizeKmer);
-
-        if (defaultConfPath != null) {
-            conf.addResource(new Path(defaultConfPath));
-        }
-
-        conf.setJobName("Genomix Graph Building");
-        conf.setMapperClass(GenomixMapper.class);
-        conf.setReducerClass(GenomixReducer.class);
-        conf.setCombinerClass(GenomixCombiner.class);
-
-        conf.setMapOutputKeyClass(KmerBytesWritable.class);
-        conf.setMapOutputValueClass(KmerCountValue.class);
-
-        conf.setInputFormat(TextInputFormat.class);
-        conf.setOutputFormat(SequenceFileOutputFormat.class);
-        conf.setOutputKeyClass(KmerBytesWritable.class);
-        conf.setOutputValueClass(KmerCountValue.class);
-        FileInputFormat.setInputPaths(conf, new Path(inputPath));
-        FileOutputFormat.setOutputPath(conf, new Path(outputPath));
-        conf.setNumReduceTasks(numReducers);
-
-        FileSystem dfs = FileSystem.get(conf);
-        dfs.delete(new Path(outputPath), true);
-        JobClient.runJob(conf);
-    }
-
-    public static void main(String[] args) throws Exception {
-        Options options = new Options();
-        CmdLineParser parser = new CmdLineParser(options);
-        parser.parseArgument(args);
-        GenomixDriver driver = new GenomixDriver();
-        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
deleted file mode 100755
index f3f4584..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixMapper.java
+++ /dev/null
@@ -1,104 +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.graphbuilding;
-
-import java.io.IOException;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.hadoop.io.LongWritable;
-import org.apache.hadoop.io.Text;
-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.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerCountValue;
-
-/**
- * This class implement mapper operator of mapreduce model
- */
-@SuppressWarnings("deprecation")
-public class GenomixMapper extends MapReduceBase implements
-        Mapper<LongWritable, Text, KmerBytesWritable, KmerCountValue> {
-
-    public class CurrenByte {
-        public byte curByte;
-        public byte preMarker;
-    }
-
-    public static int KMER_SIZE;
-    public KmerCountValue outputAdjList; 
-    public KmerBytesWritable outputKmer; 
-
-    @Override
-    public void configure(JobConf job) {
-        KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
-        outputAdjList = new KmerCountValue();
-        outputKmer = new KmerBytesWritable(KMER_SIZE);
-    }
-
-    /*succeed node
-      A 00000001 1
-      C 00000010 2
-      G 00000100 4
-      T 00001000 8
-      precursor node
-      A 00010000 16
-      C 00100000 32
-      G 01000000 64
-      T 10000000 128*/
-    @Override
-    public void map(LongWritable key, Text value, OutputCollector<KmerBytesWritable, KmerCountValue> output,
-            Reporter reporter) throws IOException {
-        /* A 00
-           C 01
-           G 10
-           T 11*/
-        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) {
-            /** first kmer */
-            byte count = 1;
-            byte[] array = geneLine.getBytes();
-            outputKmer.setByRead( array, 0);
-            byte pre = 0;
-            byte next = GeneCode.getAdjBit(array[KMER_SIZE]);
-            byte adj = GeneCode.mergePreNextAdj(pre, next);
-            outputAdjList.set(adj, count);
-            output.collect(outputKmer, outputAdjList);
-            /** middle kmer */
-            for (int i = KMER_SIZE; i < array.length - 1; i++) {
-                pre = GeneCode.getBitMapFromGeneCode(outputKmer.shiftKmerWithNextChar(array[i]));
-                next = GeneCode.getAdjBit(array[i + 1]);
-                adj = GeneCode.mergePreNextAdj(pre, next);
-                outputAdjList.set(adj, count);
-                output.collect(outputKmer, outputAdjList);
-            }
-            /** last kmer */
-            pre = GeneCode.getBitMapFromGeneCode(outputKmer.shiftKmerWithNextChar(array[array.length - 1]));
-            next = 0;
-            adj = GeneCode.mergePreNextAdj(pre, next);
-            outputAdjList.set(adj, count);
-            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
deleted file mode 100755
index 1fba709..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphbuilding/GenomixReducer.java
+++ /dev/null
@@ -1,56 +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.graphbuilding;
-
-import java.io.IOException;
-import java.util.Iterator;
-
-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.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerCountValue;
-
-/**
- * This class implement reducer operator of mapreduce model
- */
-@SuppressWarnings("deprecation")
-public class GenomixReducer extends MapReduceBase implements
-        Reducer<KmerBytesWritable, KmerCountValue, KmerBytesWritable, KmerCountValue> {
-    KmerCountValue valWriter = new KmerCountValue();
-    static enum MyCounters { NUM_RECORDS };
-    @Override
-    public void reduce(KmerBytesWritable key, Iterator<KmerCountValue> values,
-            OutputCollector<KmerBytesWritable, KmerCountValue> output, Reporter reporter) throws IOException {
-        byte groupByAdjList = 0;
-        int count = 0;
-        byte bytCount = 0;
-        while (values.hasNext()) {
-            //Merge By the all adjacent Nodes;
-            KmerCountValue geneValue = values.next();            
-            groupByAdjList = (byte) (groupByAdjList | geneValue.getAdjBitMap());
-            count = count + (int) geneValue.getCount();
-        }
-        if (count >= 127)
-            bytCount = (byte) 127;
-        else
-            bytCount = (byte) count;
-        valWriter.set(groupByAdjList, bytCount);
-        output.collect(key, valWriter);
-        reporter.incrCounter(MyCounters.NUM_RECORDS, 1);
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphcountfilter/CountFilterDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphcountfilter/CountFilterDriver.java
deleted file mode 100644
index d54eca2..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphcountfilter/CountFilterDriver.java
+++ /dev/null
@@ -1,89 +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.graphcountfilter;
-
-import java.io.IOException;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.ByteWritable;
-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.kohsuke.args4j.CmdLineParser;
-import org.kohsuke.args4j.Option;
-
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-
-@SuppressWarnings("deprecation")
-public class CountFilterDriver {
-    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 = "-num-reducers", usage = "the number of reducers", required = true)
-        public int numReducers;
-
-        @Option(name = "-count-threshold", usage = "the threshold of count", required = true)
-        public int countThreshold;
-    }
-   
-    public void run(String inputPath, String outputPath, int numReducers, int countThreshold, String defaultConfPath)
-            throws IOException {
-
-        JobConf conf = new JobConf(CountFilterDriver.class);
-        conf.setInt("countThreshold", countThreshold);
-
-        if (defaultConfPath != null) {
-            conf.addResource(new Path(defaultConfPath));
-        }
-
-        conf.setJobName("Count Filter");
-        conf.setMapperClass(CountFilterMapper.class);
-        conf.setReducerClass(CountFilterReducer.class);
-        conf.setCombinerClass(CountFilterReducer.class);
-
-        conf.setMapOutputKeyClass(KmerBytesWritable.class);
-        conf.setMapOutputValueClass(ByteWritable.class);
-
-        conf.setInputFormat(SequenceFileInputFormat.class);
-        conf.setOutputFormat(SequenceFileOutputFormat.class);
-        
-        conf.setOutputKeyClass(KmerBytesWritable.class);
-        conf.setOutputValueClass(ByteWritable.class);
-        
-        FileInputFormat.setInputPaths(conf, new Path(inputPath));
-        FileOutputFormat.setOutputPath(conf, new Path(outputPath));
-        conf.setNumReduceTasks(numReducers);
-
-        FileSystem dfs = FileSystem.get(conf);
-        dfs.delete(new Path(outputPath), true);
-        JobClient.runJob(conf);
-    }
-
-    public static void main(String[] args) throws Exception {
-        Options options = new Options();
-        CmdLineParser parser = new CmdLineParser(options);
-        parser.parseArgument(args);
-        CountFilterDriver driver = new CountFilterDriver();
-        driver.run(options.inputPath, options.outputPath, options.numReducers, options.countThreshold, null);
-    }
-
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphcountfilter/CountFilterMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphcountfilter/CountFilterMapper.java
deleted file mode 100644
index 2a54217..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphcountfilter/CountFilterMapper.java
+++ /dev/null
@@ -1,46 +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.graphcountfilter;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.ByteWritable;
-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.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerCountValue;
-
-
-@SuppressWarnings({ "deprecation" })
-public class CountFilterMapper extends MapReduceBase implements
-        Mapper<KmerBytesWritable, KmerCountValue, KmerBytesWritable, ByteWritable> {
-    private int THRESHOLD;
-    private ByteWritable adjByte = new ByteWritable();
-    @Override
-    public void configure(JobConf job) {
-        THRESHOLD = Integer.parseInt(job.get("countThreshold"));
-    }
-    public void map(KmerBytesWritable key, KmerCountValue value, OutputCollector<KmerBytesWritable, ByteWritable> output,
-            Reporter reporter) throws IOException {
-        if(value.getCount() >= THRESHOLD){
-            adjByte.set(value.getAdjBitMap());
-            output.collect(key, adjByte );
-        }
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphcountfilter/CountFilterReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphcountfilter/CountFilterReducer.java
deleted file mode 100644
index dd33451..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/graphcountfilter/CountFilterReducer.java
+++ /dev/null
@@ -1,35 +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.graphcountfilter;
-
-import java.io.IOException;
-import java.util.Iterator;
-import org.apache.hadoop.io.ByteWritable;
-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.KmerBytesWritable;
-
-@SuppressWarnings("deprecation")
-public class CountFilterReducer extends MapReduceBase implements
-        Reducer<KmerBytesWritable, ByteWritable, KmerBytesWritable, ByteWritable> {
-    @Override
-    public void reduce(KmerBytesWritable key, Iterator<ByteWritable> values,
-            OutputCollector<KmerBytesWritable, ByteWritable> output, Reporter reporter) throws IOException {
-        output.collect(key, values.next()); //Output the Pair
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/.DS_Store
deleted file mode 100644
index f9e3926..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/.DS_Store
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathDriver.java
deleted file mode 100644
index 36c12ae..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathDriver.java
+++ /dev/null
@@ -1,182 +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.pathmerging;
-
-import java.io.IOException;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-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;
-
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-
-@SuppressWarnings("deprecation")
-public class MergePathDriver {
-    
-    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(MergePathDriver.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(KmerBytesWritable.class);
-        conf.setMapOutputValueClass(MergePathValueWritable.class);
-        
-        conf.setInputFormat(SequenceFileInputFormat.class);
-        conf.setOutputFormat(SequenceFileOutputFormat.class);
-        
-        conf.setOutputKeyClass(VKmerBytesWritable.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);
-        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(VKmerBytesWritable.class);
-            conf.setMapOutputValueClass(MergePathValueWritable.class);
-            
-            conf.setInputFormat(SequenceFileInputFormat.class);
-            
-            String uncomplete = "uncomplete" + iMerge;
-            String complete = "complete" + iMerge;
-           
-            MultipleOutputs.addNamedOutput(conf, uncomplete,
-                    MergePathMultiSeqOutputFormat.class, VKmerBytesWritable.class,
-                    MergePathValueWritable.class);
-
-            MultipleOutputs.addNamedOutput(conf, complete,
-                    MergePathMultiSeqOutputFormat.class, VKmerBytesWritable.class,
-                    MergePathValueWritable.class);
-            
-            conf.setOutputKeyClass(VKmerBytesWritable.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));
-        }
-        /*----------------------------------------*/
-        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(VKmerBytesWritable.class);
-        conf.setMapOutputValueClass(MergePathValueWritable.class);
-        
-        conf.setInputFormat(SequenceFileInputFormat.class);
-        
-        String uncomplete = "uncomplete" + iMerge;
-        String complete = "complete" + iMerge;
-       
-        MultipleOutputs.addNamedOutput(conf, uncomplete,
-                MergePathMultiSeqOutputFormat.class, VKmerBytesWritable.class,
-                MergePathValueWritable.class);
-
-        MultipleOutputs.addNamedOutput(conf, complete,
-                MergePathMultiSeqOutputFormat.class, VKmerBytesWritable.class,
-                MergePathValueWritable.class);
-        
-        conf.setOutputKeyClass(VKmerBytesWritable.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);
-        MergePathDriver driver = new MergePathDriver();
-        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/pathmerging/MergePathMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java
deleted file mode 100644
index 0c7dcc1..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java
+++ /dev/null
@@ -1,70 +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.pathmerging;
-
-import java.io.IOException;
-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.GeneCode;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
-
-@SuppressWarnings("deprecation")
-public class MergePathMapper extends MapReduceBase implements
-        Mapper<VKmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
-    private int KMER_SIZE;
-    private VKmerBytesWritableFactory outputKmerFactory;
-    private MergePathValueWritable outputValue; 
-    private VKmerBytesWritable tmpKmer;
-    private VKmerBytesWritable outputKmer;
-
-
-    public void configure(JobConf job) {
-        KMER_SIZE = job.getInt("sizeKmer", 0);
-        outputKmerFactory = new VKmerBytesWritableFactory(KMER_SIZE);
-        outputValue = new MergePathValueWritable();
-        tmpKmer = new VKmerBytesWritable(KMER_SIZE);
-        outputKmer = new VKmerBytesWritable(KMER_SIZE);
-    }
-
-    @Override
-    public void map(VKmerBytesWritable key, MergePathValueWritable value,
-            OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-
-        byte precursor = (byte) 0xF0;
-        byte succeed = (byte) 0x0F;
-        byte adjBitMap = value.getAdjBitMap();
-        byte bitFlag = value.getFlag();
-        precursor = (byte) (precursor & adjBitMap);
-        precursor = (byte) ((precursor & 0xff) >> 4);
-        succeed = (byte) (succeed & adjBitMap);
-       if (bitFlag == 1) {
-            byte succeedCode = GeneCode.getGeneCodeFromBitMap(succeed);
-            tmpKmer.set(outputKmerFactory.getLastKmerFromChain(KMER_SIZE, key));
-            outputKmer.set(outputKmerFactory.shiftKmerWithNextCode(tmpKmer, succeedCode));
-            
-            tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(key.getKmerLength() - (KMER_SIZE - 1), key));
-            outputValue.set(adjBitMap, bitFlag, tmpKmer);
-            output.collect(outputKmer, outputValue);
-        } else {
-            outputKmer.set(key);
-            outputValue.set(value);
-            output.collect(key, outputValue);
-        }
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMultiSeqOutputFormat.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMultiSeqOutputFormat.java
deleted file mode 100644
index bd4cd2a..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMultiSeqOutputFormat.java
+++ /dev/null
@@ -1,30 +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.pathmerging;
-
-import java.io.File;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.mapred.lib.MultipleSequenceFileOutputFormat;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-
-
-public class MergePathMultiSeqOutputFormat extends MultipleSequenceFileOutputFormat<VKmerBytesWritable, 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/pathmerging/MergePathMultiTextOutputFormat.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMultiTextOutputFormat.java
deleted file mode 100644
index 29d3b68..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/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.pathmerging;
-
-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/pathmerging/MergePathReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java
deleted file mode 100644
index 52abc1c..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java
+++ /dev/null
@@ -1,141 +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.pathmerging;
-
-import java.io.IOException;
-import java.util.Iterator;
-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.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
-
-@SuppressWarnings("deprecation")
-public class MergePathReducer extends MapReduceBase implements
-        Reducer<VKmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
-    private VKmerBytesWritableFactory kmerFactory;
-    private VKmerBytesWritable outputKmer;
-    private VKmerBytesWritable tmpKmer;
-    private int KMER_SIZE;
-    private MergePathValueWritable outputValue;
-    private MergePathValueWritable tmpOutputValue;
-    MultipleOutputs mos = null;
-    private 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);
-        outputValue = new MergePathValueWritable();
-        tmpOutputValue = new MergePathValueWritable();
-        kmerFactory = new VKmerBytesWritableFactory(KMER_SIZE);
-        outputKmer = new VKmerBytesWritable(KMER_SIZE);
-        tmpKmer = new VKmerBytesWritable(KMER_SIZE);
-    }
-
-    @SuppressWarnings("unchecked")
-    @Override
-    public void reduce(VKmerBytesWritable key, Iterator<MergePathValueWritable> values,
-            OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-        outputValue = values.next();
-        if (values.hasNext() == true) {
-            if (outputValue.getFlag() != 1) {
-                byte nextAdj = outputValue.getAdjBitMap();
-                byte succeed = (byte) 0x0F;
-                succeed = (byte) (succeed & nextAdj);
-
-                outputValue = values.next();
-                byte adjBitMap = outputValue.getAdjBitMap();
-                byte flag = outputValue.getFlag();
-                if (outputValue.getKmerLength() != 0)
-                    outputKmer.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), key));
-                else
-                    outputKmer.set(key);
-
-                adjBitMap = (byte) (adjBitMap & 0xF0);
-                adjBitMap = (byte) (adjBitMap | succeed);
-                outputValue.set(adjBitMap, flag, null);
-                mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputValue);
-            } else {
-                tmpOutputValue.set(outputValue);
-                byte tmpAdjMap = tmpOutputValue.getAdjBitMap();
-
-                outputValue = values.next();
-                if (outputValue.getFlag() != 1) {
-                    if (tmpOutputValue.getKmerLength() != 0)
-                        outputKmer.set(kmerFactory.mergeTwoKmer(tmpOutputValue.getKmer(), key));
-                    else
-                        outputKmer.set(key);
-
-                    byte nextAdj = outputValue.getAdjBitMap();
-                    byte succeed = (byte) 0x0F;
-                    succeed = (byte) (succeed & nextAdj);
-                    tmpAdjMap = (byte) (tmpAdjMap & 0xF0);
-                    tmpAdjMap = (byte) (tmpAdjMap | succeed);
-                    outputValue.set(tmpAdjMap, tmpOutputValue.getFlag(), null);
-                    mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputValue);
-                } else {
-
-                    tmpKmer.set(kmerFactory.getFirstKmerFromChain(KMER_SIZE - 1, key));
-                    if (tmpOutputValue.getKmerLength() != 0)
-                        outputKmer.set(kmerFactory.mergeTwoKmer(tmpOutputValue.getKmer(), tmpKmer));
-                    else
-                        outputKmer.set(tmpKmer);
-                    tmpOutputValue.set(tmpAdjMap, tmpOutputValue.getFlag(), null);
-                    mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, tmpOutputValue);
-
-                    tmpKmer.set(kmerFactory.getFirstKmerFromChain(KMER_SIZE - 1, key));
-                    if (outputValue.getKmerLength() != 0)
-                        outputKmer.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), tmpKmer));
-                    else
-                        outputKmer.set(tmpKmer);
-                    outputValue.set(outputValue.getAdjBitMap(), outputValue.getFlag(), null);
-                    mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputValue);
-
-                    while (values.hasNext()) {
-                        outputValue = values.next();
-                        tmpKmer.set(kmerFactory.getFirstKmerFromChain(KMER_SIZE - 1, key));
-                        if (outputValue.getKmerLength() != 0)
-                            outputKmer.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), tmpKmer));
-                        else
-                            outputKmer.set(tmpKmer);
-                        outputValue.set(outputValue.getAdjBitMap(), outputValue.getFlag(), null);
-                        mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputValue);
-                    }
-                }
-            }
-        } else {
-            if (outputValue.getFlag() != 0) {
-                tmpKmer.set(kmerFactory.getFirstKmerFromChain(KMER_SIZE - 1, key));
-                if (outputValue.getKmerLength() != 0)
-                    outputKmer.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), tmpKmer));
-                else
-                    outputKmer.set(tmpKmer);
-                outputValue.set(outputValue.getAdjBitMap(), outputValue.getFlag(), null);
-                mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputValue);
-
-            } else
-                mos.getCollector("uncomplete" + I_MERGE, reporter).collect(key, outputValue);
-        }
-    }
-
-    public void close() throws IOException {
-        // TODO Auto-generated method stub
-        mos.close();
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathValueWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathValueWritable.java
deleted file mode 100644
index 9686c18..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathValueWritable.java
+++ /dev/null
@@ -1,110 +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.pathmerging;
-
-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> {
-
-    private static final byte[] EMPTY_BYTES = {};
-    private byte adjBitMap;
-    private byte flag;
-    private VKmerBytesWritable kmer;
-
-    public MergePathValueWritable() {
-        this((byte) 0, (byte) 0, 0, EMPTY_BYTES);
-    }
-
-    public MergePathValueWritable(byte adjBitMap, byte flag, int kmerSize, byte[] bytes) {
-        this.adjBitMap = adjBitMap;
-        this.flag = flag;
-        this.kmer = new VKmerBytesWritable(kmerSize, bytes);
-        kmer.set(bytes, 0, bytes.length);
-    }
-
-    public void set(MergePathValueWritable right) {
-        set(right.getAdjBitMap(), right.getFlag(), right.getKmer());
-    }
-
-    public void set(byte adjBitMap, byte flag, VKmerBytesWritable kmer) {
-        this.kmer.set(kmer);
-        this.adjBitMap = adjBitMap;
-        this.flag = flag;
-    }
-
-    @Override
-    public void readFields(DataInput arg0) throws IOException {
-        // TODO Auto-generated method stub
-        kmer.readFields(arg0);
-        adjBitMap = arg0.readByte();
-        flag = arg0.readByte();
-    }
-
-    @Override
-    public void write(DataOutput arg0) throws IOException {
-        // TODO Auto-generated method stub
-
-        kmer.write(arg0);
-        arg0.writeByte(adjBitMap);
-        arg0.writeByte(flag);
-    }
-
-    public VKmerBytesWritable getKmer() {
-        if (kmer.getLength() != 0) {
-            return kmer;
-        }
-        return null;
-    }
-
-    public byte getAdjBitMap() {
-        return this.adjBitMap;
-    }
-
-    public byte getFlag() {
-        return this.flag;
-    }
-
-    public String toString() {
-        return GeneCode.getSymbolFromBitMap(adjBitMap) + '\t' + String.valueOf(flag);
-    }
-
-    @Override
-    public byte[] getBytes() {
-        // TODO Auto-generated method stub
-        if (kmer.getLength() != 0) {
-            return kmer.getBytes();
-        } else
-            return null;
-
-    }
-
-    public int getKmerLength() {
-        return kmer.getKmerLength();
-    }
-
-    @Override
-    public int getLength() {
-        return kmer.getLength();
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java
deleted file mode 100644
index 1058fda..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java
+++ /dev/null
@@ -1,132 +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.pathmerging;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.ByteWritable;
-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.KmerBytesWritable;
-import edu.uci.ics.genomix.type.GeneCode;
-
-@SuppressWarnings("deprecation")
-public class SNodeInitialMapper extends MapReduceBase implements
-        Mapper<KmerBytesWritable, ByteWritable, KmerBytesWritable, MergePathValueWritable> {
-
-    public int KMER_SIZE;
-    public KmerBytesWritable outputKmer;
-    public MergePathValueWritable outputAdjList;
-
-    public void configure(JobConf job) {
-        KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
-        outputKmer = new KmerBytesWritable(KMER_SIZE);
-        outputAdjList = new MergePathValueWritable();
-    }
-
-    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(KmerBytesWritable key, ByteWritable value,
-            OutputCollector<KmerBytesWritable, 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);
-        if (inDegree == false && outDegree == false) {
-            outputKmer.set(key);
-            bitFlag = (byte) 2;
-            outputAdjList.set(adjBitMap, bitFlag, null);///~~~~~kmersize----->0
-            output.collect(outputKmer, outputAdjList);
-        }
-        else{
-            for(int i = 0 ; i < 4; i ++){
-                byte temp = 0x01;
-                byte shiftedCode = 0;
-                temp  = (byte)(temp << i);
-                temp = (byte) (succeed & temp);
-                if(temp != 0 ){
-                    byte succeedCode = GeneCode.getGeneCodeFromBitMap(temp);
-                    shiftedCode = key.shiftKmerWithNextCode(succeedCode);
-                    outputKmer.set(key);
-                    outputAdjList.set((byte)0, bitFlag, null);
-                    output.collect(outputKmer, outputAdjList);
-                    key.shiftKmerWithPreCode(shiftedCode);
-                }
-            }
-        }
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialReducer.java
deleted file mode 100644
index 07cc32f..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialReducer.java
+++ /dev/null
@@ -1,66 +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.pathmerging;
-
-import java.io.IOException;
-import java.util.Iterator;
-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.KmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-
-@SuppressWarnings("deprecation")
-public class SNodeInitialReducer extends MapReduceBase implements
-        Reducer<KmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
-    private VKmerBytesWritable outputKmer = new VKmerBytesWritable();
-    private MergePathValueWritable outputValue = new MergePathValueWritable();
-
-
-    @Override
-    public void reduce(KmerBytesWritable key, Iterator<MergePathValueWritable> values,
-            OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-        outputKmer.set(key);
-        outputValue = values.next();
-        if (values.hasNext() == true) {
-            if (outputValue.getFlag() == 2) {
-                byte bitFlag = 1;
-                outputValue.set(outputValue.getAdjBitMap(), bitFlag, null);///outputValue.getKmerLength()
-                output.collect(outputKmer, outputValue);
-            } else {
-                boolean flag = false;
-                while (values.hasNext()) {
-                    outputValue = values.next();
-                    if (outputValue.getFlag() == 2) {
-                        flag = true;
-                        break;
-                    }
-                }
-                if (flag == true) {
-                    byte bitFlag = 1;
-                    outputValue.set(outputValue.getAdjBitMap(), bitFlag, null);
-                    output.collect(outputKmer, outputValue);
-                }
-            }
-        } else {
-            if (outputValue.getFlag() == 2) {
-                byte bitFlag = 0;
-                outputValue.set(outputValue.getAdjBitMap(), bitFlag, null);
-                output.collect(outputKmer, outputValue);
-            }
-        }
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/.DS_Store
deleted file mode 100644
index 7c4ae29..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/.DS_Store
+++ /dev/null
Binary files differ
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 1f9bc82..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/ENodeInitialReducer.java
+++ /dev/null
@@ -1,58 +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(outputAdjList.getAdjBitMap(), bitFlag, null);
-                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(outputAdjList.getAdjBitMap(), bitFlag, null);
-                    output.collect(outputKmer, outputAdjList);
-                }
-            }
-        } else {
-            byte bitFlag = outputAdjList.getFlag();
-            bitFlag = (byte) (bitFlag & 0xFE);
-            if (bitFlag == 2) {
-                bitFlag = 0;
-                outputAdjList.set(outputAdjList.getAdjBitMap(), bitFlag, null);
-                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 2898a90..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Driver.java
+++ /dev/null
@@ -1,168 +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.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;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-
-
-@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(KmerBytesWritable.class);
-        conf.setMapOutputValueClass(MergePathValueWritable.class);
-        
-        conf.setInputFormat(SequenceFileInputFormat.class);
-        conf.setOutputFormat(SequenceFileOutputFormat.class);
-        
-        conf.setOutputKeyClass(VKmerBytesWritable.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);
-        int iMerge = 0;
-/*----------------------------------------------------------------------*/
-        for(iMerge = 0; iMerge < mergeRound; iMerge ++){
-            if(!dfs.exists(new Path(inputPath + "-step1")))
-                break;
-            conf = new JobConf(MergePathH2Driver.class);
-            conf.setInt("sizeKmer", sizeKmer);
-            conf.setInt("iMerge", iMerge);
-            
-            if (defaultConfPath != null) {
-                conf.addResource(new Path(defaultConfPath));
-            }
-            conf.setJobName("Path Merge");
-            
-            conf.setMapperClass(MergePathH2Mapper.class);
-            conf.setReducerClass(MergePathH2Reducer.class);
-            
-            conf.setMapOutputKeyClass(VKmerBytesWritable.class);
-            conf.setMapOutputValueClass(MergePathValueWritable.class);
-            
-            conf.setInputFormat(SequenceFileInputFormat.class);
-            
-            String uncomplete = "uncomplete" + iMerge;
-            String complete = "complete" + iMerge;
-           
-            MultipleOutputs.addNamedOutput(conf, uncomplete,
-                    MergePathMultiSeqOutputFormat.class, VKmerBytesWritable.class,
-                    MergePathValueWritable.class);
-
-            MultipleOutputs.addNamedOutput(conf, complete,
-                    MergePathMultiTextOutputFormat.class, VKmerBytesWritable.class,
-                    MergePathValueWritable.class);
-            
-            conf.setOutputKeyClass(VKmerBytesWritable.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));
-        }
-/*        conf = new JobConf(MergePathH2Driver.class);
-        conf.setInt("sizeKmer", sizeKmer);
-        conf.setInt("iMerge", iMerge);
-        
-        if (defaultConfPath != null) {
-            conf.addResource(new Path(defaultConfPath));
-        }
-        conf.setJobName("Path Merge");
-        
-        conf.setMapperClass(MergePathH2Mapper.class);
-        conf.setReducerClass(MergePathH2Reducer.class);
-        
-        conf.setMapOutputKeyClass(VKmerBytesWritable.class);
-        conf.setMapOutputValueClass(MergePathValueWritable.class);
-        
-        conf.setInputFormat(SequenceFileInputFormat.class);
-        
-        String uncomplete = "uncomplete" + iMerge;
-        String complete = "complete" + iMerge;
-       
-        MultipleOutputs.addNamedOutput(conf, uncomplete,
-                MergePathMultiTextOutputFormat.class, VKmerBytesWritable.class,
-                MergePathValueWritable.class);
-
-        MultipleOutputs.addNamedOutput(conf, complete,
-                MergePathMultiTextOutputFormat.class, VKmerBytesWritable.class,
-                MergePathValueWritable.class);
-        
-        conf.setOutputKeyClass(VKmerBytesWritable.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 6ea9dd3..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Mapper.java
+++ /dev/null
@@ -1,87 +0,0 @@
-package edu.uci.ics.pathmergingh2;
-
-import java.io.IOException;
-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.GeneCode;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
-
-@SuppressWarnings("deprecation")
-public class MergePathH2Mapper extends MapReduceBase implements
-        Mapper<VKmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
-
-    private int KMER_SIZE;
-    private VKmerBytesWritableFactory outputKmerFactory;
-    private MergePathValueWritable outputValue;
-    private VKmerBytesWritable tmpKmer;
-    private VKmerBytesWritable outputKmer;
-
-    public void configure(JobConf job) {
-        KMER_SIZE = job.getInt("sizeKmer", 0);
-        outputKmerFactory = new VKmerBytesWritableFactory(KMER_SIZE);
-        outputValue = new MergePathValueWritable();
-        tmpKmer = new VKmerBytesWritable(KMER_SIZE);
-        outputKmer = new VKmerBytesWritable(KMER_SIZE);
-    }
-
-    @Override
-    public void map(VKmerBytesWritable key, MergePathValueWritable value,
-            OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-        byte precursor = (byte) 0xF0;
-        byte succeed = (byte) 0x0F;
-        byte adjBitMap = value.getAdjBitMap();
-        byte bitFlag = value.getFlag();
-        precursor = (byte) (precursor & adjBitMap);
-        precursor = (byte) ((precursor & 0xff) >> 4);
-        succeed = (byte) (succeed & adjBitMap);
-        byte bitStartEnd = (byte) (0x81 & bitFlag);
-
-        switch (bitStartEnd) {
-            case (byte) 0x01:
-                byte succeedCode = GeneCode.getGeneCodeFromBitMap(succeed);
-                tmpKmer.set(outputKmerFactory.getLastKmerFromChain(KMER_SIZE, key));
-                outputKmer.set(outputKmerFactory.shiftKmerWithNextCode(tmpKmer, succeedCode));
-
-                tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(key.getKmerLength() - (KMER_SIZE - 1), key));
-                bitFlag = (byte) (bitFlag | 0x08);
-                outputValue.set(adjBitMap, bitFlag, tmpKmer);
-                output.collect(outputKmer, outputValue);
-                break;
-            case (byte) 0x80:
-                tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(KMER_SIZE, key));
-                outputKmer.set(tmpKmer);
-                tmpKmer.set(outputKmerFactory.getLastKmerFromChain(key.getKmerLength() - KMER_SIZE, key));
-                bitFlag = (byte) (bitFlag | 0x10);
-                outputValue.set(adjBitMap, bitFlag, tmpKmer);
-                output.collect(outputKmer, outputValue);
-                break;
-            case (byte) 0x00:
-                succeedCode = GeneCode.getGeneCodeFromBitMap(succeed);
-                tmpKmer.set(outputKmerFactory.getLastKmerFromChain(KMER_SIZE, key));
-                outputKmer.set(outputKmerFactory.shiftKmerWithNextCode(tmpKmer, succeedCode));
-
-                tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(key.getKmerLength() - (KMER_SIZE - 1), key));
-                bitFlag = (byte) (bitFlag | 0x08);
-                outputValue.set(adjBitMap, bitFlag, tmpKmer);
-                output.collect(outputKmer, outputValue);
-
-                bitFlag = (byte) (bitFlag & 0xF7);
-                tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(KMER_SIZE, key));
-                outputKmer.set(tmpKmer);
-                tmpKmer.set(outputKmerFactory.getLastKmerFromChain(key.getKmerLength() - KMER_SIZE, key));
-                bitFlag = (byte) (bitFlag | 0x10);
-                outputValue.set(adjBitMap, bitFlag, tmpKmer);
-                output.collect(outputKmer, outputValue);
-                break;
-            case (byte) 0x81:
-                outputKmer.set(key);
-                outputValue.set(adjBitMap, bitFlag, null);
-                output.collect(outputKmer, outputValue);
-                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 0bf7708..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Reducer.java
+++ /dev/null
@@ -1,119 +0,0 @@
-package edu.uci.ics.pathmergingh2;
-
-import java.io.IOException;
-import java.util.Iterator;
-
-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.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
-
-@SuppressWarnings("deprecation")
-public class MergePathH2Reducer extends MapReduceBase implements
-        Reducer<VKmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
-    private VKmerBytesWritableFactory kmerFactory;
-    private VKmerBytesWritable outputKmer;
-    private VKmerBytesWritable tmpKmer1;
-    private VKmerBytesWritable tmpKmer2;
-    private int KMER_SIZE;
-    private MergePathValueWritable outputValue;
-    private MergePathValueWritable tmpOutputValue;
-
-    MultipleOutputs mos = null;
-    private 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);
-        outputValue = new MergePathValueWritable();
-        tmpOutputValue = new MergePathValueWritable();
-        kmerFactory = new VKmerBytesWritableFactory(KMER_SIZE);
-        outputKmer = new VKmerBytesWritable(KMER_SIZE);
-        tmpKmer1 = new VKmerBytesWritable(KMER_SIZE);
-        tmpKmer2 = new VKmerBytesWritable(KMER_SIZE);
-    }
-
-    @SuppressWarnings("unchecked")
-    public void reduce(VKmerBytesWritable key, Iterator<MergePathValueWritable> values,
-            OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-        outputValue = values.next();
-        outputKmer.set(key);
-        if (values.hasNext() == true) {
-            byte bitFlag = outputValue.getFlag();
-            byte bitStartEnd = (byte) (0x81 & bitFlag);
-            byte bitPosiNegative = (byte) (0x18 & bitFlag);
-            byte succeed = (byte) 0x0F;
-            switch (bitPosiNegative) {
-                case (byte) 0x08:
-                    if (outputValue.getKmerLength() != 0)
-                        tmpKmer1.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), key));
-                    else
-                        tmpKmer1.set(key);
-                    byte adjBitMap = outputValue.getAdjBitMap();
-                    outputValue = values.next();
-                    bitStartEnd = (byte) (0x81 & outputValue.getFlag());
-                    if (bitStartEnd == (byte) 0x80) {
-                        if (outputValue.getKmerLength() != 0)
-                            tmpKmer2.set(kmerFactory.mergeTwoKmer(key, outputValue.getKmer()));
-                        else
-                            tmpKmer2.set(key);
-                        byte tmpFlag = (byte) 0x80;
-                        tmpOutputValue.set(outputValue.getAdjBitMap(), tmpFlag, null);
-                        mos.getCollector("uncomplete" + I_MERGE, reporter).collect(tmpKmer2, tmpOutputValue);
-                    }
-                    if (outputValue.getKmerLength() != 0)
-                        outputKmer.set(kmerFactory.mergeTwoKmer(tmpKmer1, outputValue.getKmer()));
-                    else
-                        outputKmer.set(tmpKmer1);
-                    succeed = (byte) (succeed & outputValue.getAdjBitMap());
-                    adjBitMap = (byte) (adjBitMap & 0xF0);
-                    adjBitMap = (byte) (adjBitMap | succeed);
-                    byte outputFlag = (byte) (0x81 & bitFlag);
-                    outputFlag = (byte) (outputFlag | ((byte) 0x81 & outputValue.getFlag()));
-                    outputValue.set(adjBitMap, outputFlag, null);
-                    mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputValue);
-                    break;
-                case (byte) 0x10:
-                    if (outputValue.getKmerLength() != 0)
-                        tmpKmer1.set(kmerFactory.mergeTwoKmer(key, outputValue.getKmer()));
-                    else
-                        tmpKmer1.set(key);
-                    if (bitStartEnd == (byte) 0x80) {
-                        byte tmpFlag = (byte) 0x80;
-                        tmpOutputValue.set(outputValue.getAdjBitMap(), tmpFlag, null);
-                        mos.getCollector("uncomplete" + I_MERGE, reporter).collect(tmpKmer1, tmpOutputValue);
-                    }
-                    succeed = (byte) (succeed & outputValue.getAdjBitMap());
-                    outputValue = values.next();
-                    if (outputValue.getKmerLength() != 0)
-                        outputKmer.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), tmpKmer1));
-                    else
-                        outputKmer.set(tmpKmer1);
-                    adjBitMap = outputValue.getAdjBitMap();
-                    adjBitMap = (byte) (adjBitMap & 0xF0);
-                    adjBitMap = (byte) (adjBitMap | succeed);                    
-                    outputFlag = (byte) (0x81 & bitFlag);
-                    outputFlag = (byte) (outputFlag | ((byte) 0x81 & outputValue.getFlag()));
-                    outputValue.set(adjBitMap, outputFlag, null);
-                    mos.getCollector("uncomplete" + I_MERGE, reporter).collect(outputKmer, outputValue);
-                    break;
-            }
-        } else {
-            byte bitFlag = outputValue.getFlag();
-            byte bitStartEnd = (byte) (0x81 & bitFlag);
-            if (bitStartEnd == (byte) 0x81) {
-                outputKmer.set(key);
-                mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputValue);
-            }
-        }
-    }
-    public void close() throws IOException {
-        // TODO Auto-generated method stub
-        mos.close();
-    }
-}
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 5e6f008..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathMultiSeqOutputFormat.java
+++ /dev/null
@@ -1,31 +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;
-
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-
-
-public class MergePathMultiSeqOutputFormat extends MultipleSequenceFileOutputFormat<VKmerBytesWritable, 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 2f1869d..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathValueWritable.java
+++ /dev/null
@@ -1,115 +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.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.VKmerBytesWritable;
-
-public class MergePathValueWritable extends BinaryComparable implements WritableComparable<BinaryComparable> {
-
-    private static final byte[] EMPTY_BYTES = {};
-    private byte adjBitMap;
-    private byte flag;
-    private VKmerBytesWritable kmer;
-
-    public MergePathValueWritable() {
-        this((byte) 0, (byte) 0, 0, EMPTY_BYTES);
-    }
-    
-    public MergePathValueWritable(int k) {
-        this.adjBitMap = 0;
-        this.flag = 0;
-        this.kmer = new VKmerBytesWritable(k);
-    }
-    
-    public MergePathValueWritable(byte adjBitMap, byte flag, int kmerSize, byte[] bytes) {
-        this.adjBitMap = adjBitMap;
-        this.flag = flag;
-        this.kmer = new VKmerBytesWritable(kmerSize, bytes);
-        kmer.set(bytes, 0, bytes.length);
-    }
-
-    public void set(MergePathValueWritable right) {
-        set(right.getAdjBitMap(), right.getFlag(), right.getKmer());
-    }
-
-    public void set(byte adjBitMap, byte flag, VKmerBytesWritable kmer) {
-        this.kmer.set(kmer);
-        this.adjBitMap = adjBitMap;
-        this.flag = flag;
-    }
-
-    @Override
-    public void readFields(DataInput arg0) throws IOException {
-        // TODO Auto-generated method stub
-        kmer.readFields(arg0);
-        adjBitMap = arg0.readByte();
-        flag = arg0.readByte();
-    }
-
-    @Override
-    public void write(DataOutput arg0) throws IOException {
-        // TODO Auto-generated method stub
-
-        kmer.write(arg0);
-        arg0.writeByte(adjBitMap);
-        arg0.writeByte(flag);
-    }
-
-    public VKmerBytesWritable getKmer() {
-        if (kmer.getLength() != 0) {
-            return kmer;
-        }
-        return null;
-    }
-
-    public byte getAdjBitMap() {
-        return this.adjBitMap;
-    }
-
-    public byte getFlag() {
-        return this.flag;
-    }
-
-    public String toString() {
-        return GeneCode.getSymbolFromBitMap(adjBitMap) + '\t' + String.valueOf(flag);
-    }
-
-    @Override
-    public byte[] getBytes() {
-        // TODO Auto-generated method stub
-        if (kmer.getLength() != 0) {
-            return kmer.getBytes();
-        } else
-            return null;
-
-    }
-
-    public int getKmerLength() {
-        return kmer.getKmerLength();
-    }
-
-    @Override
-    public int getLength() {
-        return kmer.getLength();
-    }
-}
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 4c05dac..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialMapper.java
+++ /dev/null
@@ -1,141 +0,0 @@
-package edu.uci.ics.pathmergingh2;
-
-import java.io.IOException;
-import org.apache.hadoop.io.ByteWritable;
-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.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-
-@SuppressWarnings("deprecation")
-public class SNodeInitialMapper extends MapReduceBase implements
-        Mapper<KmerBytesWritable, ByteWritable, KmerBytesWritable, MergePathValueWritable> {
-
-    public int KMER_SIZE;
-    public KmerBytesWritable outputKmer;
-    public MergePathValueWritable outputAdjList;
-
-    public void configure(JobConf job) {
-        KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
-        outputKmer = new KmerBytesWritable(KMER_SIZE);
-        outputAdjList = new MergePathValueWritable();
-    }
-
-    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(KmerBytesWritable key, ByteWritable value,
-            OutputCollector<KmerBytesWritable, 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);
-        if (key.toString().equals("CGC")) {
-            int a = 2;
-            int b = a;
-        }
-        if (key.toString().equals("TCG")) {
-            int a = 2;
-            int b = a;
-        }
-        if (inDegree == false && outDegree == false) {
-            outputKmer.set(key);
-            System.out.println(outputKmer.hashCode());
-            bitFlag = (byte) 2;
-            outputAdjList.set(adjBitMap, bitFlag, null);
-            output.collect(outputKmer, outputAdjList);
-        } else {
-            for (int i = 0; i < 4; i++) {
-                byte temp = (byte) 0x01;
-                byte shiftedCode = 0;
-                temp = (byte) (temp << i);
-                temp = (byte) (precursor & temp);
-                if (temp != 0) {
-                    byte precurCode = GeneCode.getGeneCodeFromBitMap(temp);
-                    shiftedCode = key.shiftKmerWithPreCode(precurCode);
-                    outputKmer.set(key);
-                    bitFlag = (byte) 0x80;
-                    outputAdjList.set((byte) 0, bitFlag, null);
-                    output.collect(outputKmer, outputAdjList);
-                    key.shiftKmerWithNextCode(shiftedCode);
-                }
-            }
-            for (int i = 0; i < 4; i++) {
-                byte temp = (byte) 0x01;
-                byte shiftedCode = 0;
-                temp = (byte) (temp << i);
-                temp = (byte) (succeed & temp);
-                if (temp != 0) {
-                    byte succeedCode = GeneCode.getGeneCodeFromBitMap(temp);
-                    shiftedCode = key.shiftKmerWithNextCode(succeedCode);
-                    outputKmer.set(key);
-                    bitFlag = (byte) 0x01;
-                    outputAdjList.set((byte) 0, bitFlag, null);
-                    output.collect(outputKmer, outputAdjList);
-                    key.shiftKmerWithPreCode(shiftedCode);
-                }
-            }
-        }
-    }
-}
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 7fd7a2e..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialReducer.java
+++ /dev/null
@@ -1,80 +0,0 @@
-package edu.uci.ics.pathmergingh2;
-
-import java.io.IOException;
-import java.util.Iterator;
-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.KmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-
-@SuppressWarnings("deprecation")
-public class SNodeInitialReducer extends MapReduceBase implements
-        Reducer<KmerBytesWritable, MergePathValueWritable, VKmerBytesWritable, MergePathValueWritable> {
-    private VKmerBytesWritable outputKmer = new VKmerBytesWritable();
-    private MergePathValueWritable outputValue = new MergePathValueWritable();
-
-    @Override
-    public void reduce(KmerBytesWritable key, Iterator<MergePathValueWritable> values,
-            OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-        outputKmer.set(key);
-        outputValue = values.next();
-        byte startFlag = 0x00;
-        byte endFlag = 0x00;
-        byte targetPointFlag = 0x00;
-        byte targetAdjList = 0x00;
-        byte outputFlag = 0x00;
-        if(key.toString().equals("TCG")){
-            int a = 2;
-            int b = a;
-        }
-        if (values.hasNext() == true) {
-            switch (outputValue.getFlag()) {
-                case (byte) 0x01:
-                    startFlag = (byte) 0x01;
-                    break;
-                case (byte) 0x80:
-                    endFlag = (byte) 0x80;
-                    break;
-                case (byte) 0x02:
-                    targetPointFlag = (byte) 0x02;
-                    targetAdjList = outputValue.getAdjBitMap();
-                    break;
-            }
-            while (values.hasNext()) {
-                outputValue = values.next();
-                switch (outputValue.getFlag()) {
-                    case (byte) 0x01:
-                        startFlag = (byte) 0x01;
-                        break;
-                    case (byte) 0x80:
-                        endFlag = (byte) 0x80;
-                        break;
-                    case (byte) 0x02:
-                        targetPointFlag = (byte) 0x02;
-                        targetAdjList = outputValue.getAdjBitMap();
-                        break;
-                }
-                if(startFlag != (byte) 0x00 && endFlag!= (byte) 0x00 && targetPointFlag != (byte) 0x00)
-                    break;
-            }
-            if(targetPointFlag == (byte) 0x02) {
-                if(startFlag == (byte) 0x01) {
-                    outputFlag = (byte) (outputFlag | startFlag);
-                }
-                if(endFlag == (byte) 0x80) {
-                    outputFlag = (byte) (outputFlag | endFlag);
-                }
-                outputValue.set(targetAdjList, outputFlag, null);
-                output.collect(outputKmer, outputValue);
-            }
-        } else {
-            if (outputValue.getFlag() == 2) {
-                byte bitFlag = 0;
-                outputValue.set(outputValue.getAdjBitMap(), bitFlag, null);
-                output.collect(outputKmer, outputValue);
-            }
-        }
-    }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/statistics/GenomixStatDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/statistics/GenomixStatDriver.java
deleted file mode 100644
index efe1589..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/statistics/GenomixStatDriver.java
+++ /dev/null
@@ -1,86 +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.statistics;
-
-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.kohsuke.args4j.CmdLineParser;
-import org.kohsuke.args4j.Option;
-
-import edu.uci.ics.genomix.type.KmerCountValue;
-
-@SuppressWarnings("deprecation")
-public class GenomixStatDriver {
-    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 = "-num-reducers", usage = "the number of reducers", required = true)
-        public int numReducers;
-
-    }
-   
-    public void run(String inputPath, String outputPath, int numReducers, String defaultConfPath)
-            throws IOException {
-
-        JobConf conf = new JobConf(GenomixStatDriver.class);
-
-        if (defaultConfPath != null) {
-            conf.addResource(new Path(defaultConfPath));
-        }
-
-        conf.setJobName("Genomix Statistics");
-        conf.setMapperClass(GenomixStatMapper.class);
-        conf.setReducerClass(GenomixStatReducer.class);
-        conf.setCombinerClass(GenomixStatReducer.class);
-
-        conf.setMapOutputKeyClass(BytesWritable.class);
-        conf.setMapOutputValueClass(KmerCountValue.class);
-
-        conf.setInputFormat(SequenceFileInputFormat.class);
-        conf.setOutputFormat(SequenceFileOutputFormat.class);
-        
-        conf.setOutputKeyClass(BytesWritable.class);
-        conf.setOutputValueClass(KmerCountValue.class);
-        
-        FileInputFormat.setInputPaths(conf, new Path(inputPath));
-        FileOutputFormat.setOutputPath(conf, new Path(outputPath));
-        conf.setNumReduceTasks(numReducers);
-
-        FileSystem dfs = FileSystem.get(conf);
-        dfs.delete(new Path(outputPath), true);
-        JobClient.runJob(conf);
-    }
-
-    public static void main(String[] args) throws Exception {
-        Options options = new Options();
-        CmdLineParser parser = new CmdLineParser(options);
-        parser.parseArgument(args);
-        GenomixStatDriver driver = new GenomixStatDriver();
-        driver.run(options.inputPath, options.outputPath, options.numReducers, null);
-    }
-}
\ No newline at end of file
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/statistics/GenomixStatMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/statistics/GenomixStatMapper.java
deleted file mode 100644
index c5feefe..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/statistics/GenomixStatMapper.java
+++ /dev/null
@@ -1,102 +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.statistics;
-
-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.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerCountValue;
-
-@SuppressWarnings({ "unused", "deprecation" })
-public class GenomixStatMapper extends MapReduceBase implements
-        Mapper<BytesWritable, KmerCountValue, BytesWritable, KmerCountValue> {
-    
-    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, KmerCountValue value, OutputCollector<BytesWritable, KmerCountValue> output,
-            Reporter reporter) throws IOException {
-        byte precursor = (byte) 0xF0;
-        byte succeed = (byte) 0x0F;
-        byte adj = value.getAdjBitMap();
-        precursor = (byte) (precursor & adj);
-        precursor = (byte) ((precursor & 0xff) >> 4);
-        succeed = (byte) (succeed & adj);
-        boolean inDegree = measureDegree(precursor);
-        boolean outDegree = measureDegree(succeed);
-        if (inDegree == true && outDegree == false) {
-            output.collect(key, value);
-        }
-    }
-}
\ No newline at end of file
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/statistics/GenomixStatReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/statistics/GenomixStatReducer.java
deleted file mode 100644
index ea9a915..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/statistics/GenomixStatReducer.java
+++ /dev/null
@@ -1,39 +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.statistics;
-
-import java.io.IOException;
-import java.util.Iterator;
-import org.apache.hadoop.io.BytesWritable;
-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.KmerCountValue;
-
-@SuppressWarnings("deprecation")
-public class GenomixStatReducer extends MapReduceBase implements
-        Reducer<BytesWritable, KmerCountValue, BytesWritable, KmerCountValue> {
-    static enum MyCounters { NUM_RECORDS };
-    KmerCountValue valWriter = new KmerCountValue();
-    @Override
-    public void reduce(BytesWritable key, Iterator<KmerCountValue> values,
-            OutputCollector<BytesWritable, KmerCountValue> output, Reporter reporter) throws IOException {
-        reporter.incrCounter(MyCounters.NUM_RECORDS, 1);
-        valWriter = values.next();
-        output.collect(key, valWriter); 
-    }
-}
\ No newline at end of file