diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java
new file mode 100644
index 0000000..063c5f7
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java
@@ -0,0 +1,328 @@
+package edu.uci.ics.genomix.hadoop.graphclean.mergepaths.h4;
+
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.Random;
+
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.conf.Configured;
+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.MapReduceBase;
+import org.apache.hadoop.mapred.Mapper;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reducer;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hadoop.mapred.RunningJob;
+import org.apache.hadoop.mapred.SequenceFileInputFormat;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.hadoop.util.Tool;
+import org.apache.hadoop.util.ToolRunner;
+
+import edu.uci.ics.genomix.hadoop.pmcommon.MessageWritableNodeWithFlag;
+import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.genomix.hadoop.graphclean.mergepaths.h3.MergePathsH3.MessageFlag;
+
+@SuppressWarnings("deprecation")
+public class MergePathsH4 extends Configured implements Tool {
+
+    /*
+     * Mapper class: Partition the graph using random pseudoheads.
+     * Heads send themselves to their successors, and all others map themselves.
+     */
+    private static class MergePathsH4Mapper extends MapReduceBase implements
+            Mapper<PositionWritable, MessageWritableNodeWithFlag, PositionWritable, MessageWritableNodeWithFlag> {
+        private static long randSeed;
+        private Random randGenerator;
+        private float probBeingRandomHead;
+
+        private int KMER_SIZE;
+        private PositionWritable outputKey;
+        private MessageWritableNodeWithFlag outputValue;
+        private NodeWritable curNode;
+        private PositionWritable curID;
+        private PositionWritable nextID;
+        private PositionWritable prevID;
+        private boolean hasNext;
+        private boolean hasPrev;
+        private boolean curHead;
+        private boolean nextHead;
+        private boolean prevHead;
+        private boolean willMerge;
+        private byte headFlag;
+        private byte tailFlag;
+        private byte outFlag;
+
+        public void configure(JobConf conf) {
+            randSeed = conf.getLong("randomSeed", 0);
+            randGenerator = new Random(randSeed);
+            probBeingRandomHead = conf.getFloat("probBeingRandomHead", 0.5f);
+
+            KMER_SIZE = conf.getInt("sizeKmer", 0);
+            outputValue = new MessageWritableNodeWithFlag(KMER_SIZE);
+            outputKey = new PositionWritable();
+            curNode = new NodeWritable(KMER_SIZE);
+            curID = new PositionWritable();
+            nextID = new PositionWritable();
+            prevID = new PositionWritable();
+        }
+
+        protected boolean isNodeRandomHead(PositionWritable nodeID) {
+            // "deterministically random", based on node id
+            randGenerator.setSeed(randSeed ^ nodeID.hashCode());
+            return randGenerator.nextFloat() < probBeingRandomHead;
+        }
+
+        /*
+         * set nextID to the element that's next (in the node's FF or FR list), returning true when there is a next neighbor
+         */
+        protected boolean setNextInfo(NodeWritable node) {
+            if (node.getFFList().getCountOfPosition() > 0) {
+                nextID.set(node.getFFList().getPosition(0));
+                nextHead = isNodeRandomHead(nextID);
+                return true;
+            }
+            if (node.getFRList().getCountOfPosition() > 0) {
+                nextID.set(node.getFRList().getPosition(0));
+                nextHead = isNodeRandomHead(nextID);
+                return true;
+            }
+            return false;
+        }
+
+        /*
+         * set prevID to the element that's previous (in the node's RR or RF list), returning true when there is a previous neighbor
+         */
+        protected boolean setPrevInfo(NodeWritable node) {
+            if (node.getRRList().getCountOfPosition() > 0) {
+                prevID.set(node.getRRList().getPosition(0));
+                prevHead = isNodeRandomHead(prevID);
+                return true;
+            }
+            if (node.getRFList().getCountOfPosition() > 0) {
+                prevID.set(node.getRFList().getPosition(0));
+                prevHead = isNodeRandomHead(prevID);
+                return true;
+            }
+            return false;
+        }
+
+        @Override
+        public void map(PositionWritable key, MessageWritableNodeWithFlag value,
+                OutputCollector<PositionWritable, MessageWritableNodeWithFlag> output, Reporter reporter)
+                throws IOException {
+            // only PATH vertices are present. Find the ID's for my neighbors
+            curNode.set(value.getNode());
+            curID.set(curNode.getNodeID());
+            curHead = isNodeRandomHead(curID);
+            hasNext = setNextInfo(curNode);
+            hasPrev = setPrevInfo(curNode);
+            willMerge = false;
+            
+            reporter.setStatus("CHECK ME OUT");
+            System.out.println("mapping node" + curNode.toString() + " next:" + String.valueOf(hasNext) + " prev:" + String.valueOf(hasPrev));
+
+            // TODO: need to update edges in neighboring nodes
+
+            if (hasNext || hasPrev) {
+                // Node may be marked as head b/c it's a real head or a real tail
+                headFlag = (byte) (MessageFlag.IS_HEAD & value.getFlag());
+                tailFlag = (byte) (MessageFlag.IS_TAIL & value.getFlag());
+                outFlag = (byte) (headFlag | tailFlag);
+                if (curHead) {
+                    if (hasNext && !nextHead) {
+                        // compress this head to the forward tail
+                        outFlag |= MessageFlag.FROM_PREDECESSOR;
+                        outputValue.set(outFlag, curNode);
+                        output.collect(nextID, outputValue);
+                        willMerge = true;
+                    } else if (hasPrev && !prevHead) {
+                        // compress this head to the reverse tail
+                        outFlag |= MessageFlag.FROM_SUCCESSOR;
+                        outputValue.set(outFlag, curNode);
+                        output.collect(prevID, outputValue);
+                        willMerge = true;
+                    }
+                } else {
+                    // I'm a tail
+                    if (hasNext && hasPrev) {
+                        if ((!nextHead && !prevHead) && (curID.compareTo(nextID) < 0 && curID.compareTo(prevID) < 0)) {
+                            // tails on both sides, and I'm the "local minimum"
+                            // compress me towards the tail in forward dir
+                            outFlag |= MessageFlag.FROM_PREDECESSOR;
+                            outputValue.set(outFlag, curNode);
+                            output.collect(nextID, outputValue);
+                            willMerge = true;
+                        }
+                    } else if (!hasPrev) {
+                        // no previous node
+                        if (!nextHead && curID.compareTo(nextID) < 0) {
+                            // merge towards tail in forward dir
+                            outFlag |= MessageFlag.FROM_PREDECESSOR;
+                            outputValue.set(outFlag, curNode);
+                            output.collect(nextID, outputValue);
+                            willMerge = true;
+                        }
+                    } else if (!hasNext) {
+                        // no next node
+                        if (!prevHead && curID.compareTo(prevID) < 0) {
+                            // merge towards tail in reverse dir
+                            outFlag |= MessageFlag.FROM_SUCCESSOR;
+                            outputValue.set(outFlag, curNode);
+                            output.collect(prevID, outputValue);
+                            willMerge = true;
+                        }
+                    }
+                }
+            }
+
+            // if we didn't send ourselves to some other node, remap ourselves
+            if (!willMerge) {
+                outFlag |= MessageFlag.FROM_SELF;
+                outputValue.set(outFlag, curNode);
+                output.collect(curID, outputValue);
+            }
+        }
+    }
+
+    /*
+     * Reducer class: merge nodes that co-occur; for singletons, remap the original nodes 
+     */
+    private static class MergePathsH4Reducer extends MapReduceBase implements
+            Reducer<PositionWritable, MessageWritableNodeWithFlag, PositionWritable, MessageWritableNodeWithFlag> {
+
+        private int KMER_SIZE;
+        private MessageWritableNodeWithFlag inputValue;
+        private MessageWritableNodeWithFlag outputValue;
+        private NodeWritable curNode;
+        private NodeWritable prevNode;
+        private NodeWritable nextNode;
+        private boolean sawCurNode;
+        private boolean sawPrevNode;
+        private boolean sawNextNode;
+        private int count;
+        private byte outFlag;
+
+        public void configure(JobConf conf) {
+            KMER_SIZE = conf.getInt("sizeKmer", 0);
+            outputValue = new MessageWritableNodeWithFlag(KMER_SIZE);
+            curNode = new NodeWritable(KMER_SIZE);
+            prevNode = new NodeWritable(KMER_SIZE);
+            nextNode = new NodeWritable(KMER_SIZE);
+        }
+
+        @Override
+        public void reduce(PositionWritable key, Iterator<MessageWritableNodeWithFlag> values,
+                OutputCollector<PositionWritable, MessageWritableNodeWithFlag> output, Reporter reporter)
+                throws IOException {
+
+            inputValue.set(values.next());
+            if (!values.hasNext()) {
+                // all single nodes must be remapped
+                if ((inputValue.getFlag() & MessageFlag.FROM_SELF) == MessageFlag.FROM_SELF) {
+                    // FROM_SELF => remap self
+                    output.collect(key, inputValue);
+                } else if ((inputValue.getFlag() & (MessageFlag.FROM_PREDECESSOR | MessageFlag.FROM_SUCCESSOR)) > 0) {
+                    // FROM_PREDECESSOR | FROM_SUCCESSOR, but singleton?  error here!
+                    throw new IOException("Only one value recieved in merge, but it wasn't from self!");
+                }
+            } else {
+                // multiple inputs => a merge will take place. Aggregate all, then collect the merged path
+                count = 0;
+                outFlag = MessageFlag.EMPTY_MESSAGE;
+                sawCurNode = false;
+                sawPrevNode = false;
+                sawNextNode = false;
+                while (true) { // process values; break when no more
+                    count++;
+                    outFlag |= (inputValue.getFlag() & (MessageFlag.IS_HEAD | MessageFlag.IS_TAIL)); // merged node may become HEAD or TAIL
+                    if ((inputValue.getFlag() & MessageFlag.FROM_PREDECESSOR) > 0) {
+                        prevNode.set(inputValue.getNode());
+                        sawPrevNode = true;
+                    } else if ((inputValue.getFlag() & MessageFlag.FROM_SUCCESSOR) > 0) {
+                        nextNode.set(inputValue.getNode());
+                        sawNextNode = false;
+                    } else {
+                        curNode.set(inputValue.getNode());
+                        sawCurNode = true;
+                    }
+                    if (!values.hasNext()) {
+                        break;
+                    } else {
+                        inputValue.set(values.next());
+                    }
+                }
+                if (count != 2 && count != 3) {
+                    throw new IOException("Expected two or three nodes in MergePathsH4 reduce; saw "
+                            + String.valueOf(count));
+                }
+                if (!sawCurNode) {
+                    throw new IOException("Didn't see node from self in MergePathsH4 reduce!");
+                }
+
+                // merge any received nodes
+                if (sawNextNode) {
+                    curNode.mergeForwardNext(nextNode, KMER_SIZE);
+                    reporter.incrCounter("genomix", "num_merged", 1);
+                }
+                if (sawPrevNode) {
+                    // TODO: fix this merge command!  which one is the right one?
+                    curNode.mergeForwardPre(prevNode, KMER_SIZE);
+                    reporter.incrCounter("genomix", "num_merged", 1);
+                }
+                
+                outputValue.set(outFlag, curNode);
+                if ((outFlag & MessageFlag.IS_HEAD) > 0 && (outFlag & MessageFlag.IS_TAIL) > 0) {
+                    // True heads meeting tails => merge is complete for this node
+                    // TODO: send to the "complete" collector
+                } else {
+                    output.collect(key, outputValue);
+                }
+            }
+        }
+    }
+
+    /*
+     * Run one iteration of the mergePaths algorithm
+     */
+    public RunningJob run(String inputPath, String outputPath, JobConf baseConf) throws IOException {
+        JobConf conf = new JobConf(baseConf);
+        conf.setJarByClass(MergePathsH4.class);
+        conf.setJobName("MergePathsH4 " + inputPath);
+
+        FileInputFormat.addInputPath(conf, new Path(inputPath));
+        FileOutputFormat.setOutputPath(conf, new Path(outputPath));
+
+        conf.setInputFormat(SequenceFileInputFormat.class);
+        conf.setOutputFormat(SequenceFileOutputFormat.class);
+
+        conf.setMapOutputKeyClass(PositionWritable.class);
+        conf.setMapOutputValueClass(MessageWritableNodeWithFlag.class);
+        conf.setOutputKeyClass(PositionWritable.class);
+        conf.setOutputValueClass(MessageWritableNodeWithFlag.class);
+
+        conf.setMapperClass(MergePathsH4Mapper.class);
+        conf.setReducerClass(MergePathsH4Reducer.class);
+
+        FileSystem.get(conf).delete(new Path(outputPath), true);
+
+        return JobClient.runJob(conf);
+    }
+
+    @Override
+    public int run(String[] arg0) throws Exception {
+        // TODO Auto-generated method stub
+        return 0;
+    }
+
+    public static void main(String[] args) throws Exception {
+        int res = ToolRunner.run(new Configuration(), new MergePathsH4(), args);
+        System.out.println("Ran the job fine!");
+        System.exit(res);
+    }
+}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4Driver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4Driver.java
new file mode 100644
index 0000000..155b999
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4Driver.java
@@ -0,0 +1,105 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.genomix.hadoop.graphclean.mergepaths.h4;
+
+import java.io.IOException;
+
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.RunningJob;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.Option;
+
+@SuppressWarnings("deprecation")
+public class MergePathsH4Driver {
+
+    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 maximum number of rounds to merge", required = false)
+        public int mergeRound;
+        
+        @Option(name = "-hadoop-conf", usage = "an (optional) hadoop configuration xml", required = false)
+        public String hadoopConf;
+
+    }
+
+    public void run(String inputPath, String outputPath, int numReducers, int sizeKmer, int mergeRound,
+            String defaultConfPath, JobConf defaultConf) throws IOException {
+        JobConf baseConf = defaultConf == null ? new JobConf() : defaultConf;
+        if (defaultConfPath != null) {
+            baseConf.addResource(new Path(defaultConfPath));
+        }
+        baseConf.setNumReduceTasks(numReducers);
+        baseConf.setInt("sizeKmer", sizeKmer);
+
+        FileSystem dfs = FileSystem.get(baseConf);
+        String prevOutput = inputPath;
+        dfs.delete(new Path(outputPath), true); // clear any previous output
+
+        String tmpOutputPath = "NO_JOBS_DONE";
+        boolean finalMerge = false;
+        for (int iMerge = 1; iMerge <= mergeRound; iMerge++) {
+            baseConf.setInt("iMerge", iMerge);
+            baseConf.setBoolean("finalMerge", finalMerge);
+            MergePathsH4 merger = new MergePathsH4();
+            tmpOutputPath = inputPath + ".mergepathsH3." + String.valueOf(iMerge);
+            RunningJob job = merger.run(prevOutput, tmpOutputPath, baseConf);
+            if (job.getCounters().findCounter("genomix", "num_merged").getValue() == 0) {
+                if (!finalMerge) {
+                    // all of the pseudoheads have found each other.  H3 now behaves like H1
+                    finalMerge = true;
+                } else {
+                    // already in final merge stage and all paths were merged before.  We're done!
+                    break;
+                }
+            }
+        }
+        dfs.rename(new Path(tmpOutputPath), new Path(outputPath)); // save final results
+    }
+
+    public void run(String inputPath, String outputPath, int numReducers, int sizeKmer, int mergeRound,
+            String defaultConfPath) throws IOException {
+        run(inputPath, outputPath, numReducers, sizeKmer, mergeRound, defaultConfPath, null);
+    }
+
+    public void run(String inputPath, String outputPath, int numReducers, int sizeKmer, int mergeRound,
+            JobConf defaultConf) throws IOException {
+        run(inputPath, outputPath, numReducers, sizeKmer, mergeRound, null, defaultConf);
+    }
+
+    public static void main(String[] args) throws Exception {
+        Options options = new Options();
+        CmdLineParser parser = new CmdLineParser(options);
+        parser.parseArgument(args);
+        MergePathsH4Driver driver = new MergePathsH4Driver();
+        driver.run(options.inputPath, options.outputPath, options.numReducers, options.sizeKmer, options.mergeRound,
+                null, null);
+    }
+}
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/TestPathMergeH4.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/TestPathMergeH4.java
new file mode 100644
index 0000000..9e799f3
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/TestPathMergeH4.java
@@ -0,0 +1,72 @@
+package edu.uci.ics.genomix.hadoop.graphclean.mergepaths.h4;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.mapred.FileInputFormat;
+import org.apache.hadoop.mapred.FileOutputFormat;
+import org.apache.hadoop.mapred.JobConf;
+import org.junit.Test;
+
+import edu.uci.ics.genomix.hadoop.graphclean.mergepaths.h3.MergePathsH3Driver;
+import edu.uci.ics.genomix.hadoop.pmcommon.GenomixMiniClusterTest;
+import edu.uci.ics.genomix.hadoop.pmcommon.PathNodeInitial;
+import edu.uci.ics.genomix.hyracks.driver.Driver.Plan;
+import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
+
+@SuppressWarnings("deprecation")
+public class TestPathMergeH4 extends GenomixMiniClusterTest {
+    protected String LOCAL_SEQUENCE_FILE = "src/test/resources/data/webmap/text.txt";
+    protected String HDFS_SEQUENCE = "/00-sequence/";
+    protected String HDFS_GRAPHBUILD = "/01-graphbuild/";
+    protected String HDFS_MARKPATHS = "/02-pathmark/";
+    protected String HDFS_MERGED = "/03-pathmerge/";
+    
+    protected String GRAPHBUILD_FILE = "graphbuild.result";
+    protected String PATHMARKS_FILE = "markpaths.result";
+    protected String PATHMERGE_FILE = "h4.mergepath.result";
+    protected boolean regenerateGraph = true;
+    
+    {
+        KMER_LENGTH = 5;
+        READ_LENGTH = 8;
+        HDFS_PATHS = new ArrayList<String>(Arrays.asList(HDFS_SEQUENCE, HDFS_GRAPHBUILD, HDFS_MARKPATHS, HDFS_MERGED));
+        conf.setInt(GenomixJobConf.KMER_LENGTH, KMER_LENGTH);
+        conf.setInt(GenomixJobConf.READ_LENGTH, READ_LENGTH);
+    }
+
+    @Test
+    public void TestMergeOneIteration() throws Exception {
+        cleanUpOutput();
+        if (regenerateGraph) {
+            copyLocalToDFS(LOCAL_SEQUENCE_FILE, HDFS_SEQUENCE);
+            buildGraph();
+            copyLocalToDFS(ACTUAL_ROOT + GRAPHBUILD_FILE + ".binmerge", HDFS_GRAPHBUILD);
+        } else {
+            copyLocalToDFS(EXPECTED_ROOT + GRAPHBUILD_FILE + ".binmerge", HDFS_GRAPHBUILD);
+        }
+        
+        PathNodeInitial inith4 = new PathNodeInitial();
+        inith4.run(HDFS_GRAPHBUILD, HDFS_MARKPATHS, conf);
+        copyResultsToLocal(HDFS_MARKPATHS, ACTUAL_ROOT + PATHMARKS_FILE, false, conf);
+
+        MergePathsH4Driver h4 = new MergePathsH4Driver();
+        h4.run(HDFS_MARKPATHS, HDFS_MERGED, 2, KMER_LENGTH, 1, conf);
+        copyResultsToLocal(HDFS_MERGED, ACTUAL_ROOT + PATHMERGE_FILE, false, conf);
+    }
+
+
+
+    public void buildGraph() throws Exception {
+        JobConf buildConf = new JobConf(conf);  // use a separate conf so we don't interfere with other jobs 
+        FileInputFormat.setInputPaths(buildConf, HDFS_SEQUENCE);
+        FileOutputFormat.setOutputPath(buildConf, new Path(HDFS_GRAPHBUILD));
+        buildConf.set(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_BINARY);
+        buildConf.set(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
+        driver.runJob(new GenomixJobConf(buildConf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+        String fileFormat = buildConf.get(GenomixJobConf.OUTPUT_FORMAT);
+        boolean resultsAreText = GenomixJobConf.OUTPUT_FORMAT_TEXT.equalsIgnoreCase(fileFormat);
+        copyResultsToLocal(HDFS_GRAPHBUILD, ACTUAL_ROOT + GRAPHBUILD_FILE, resultsAreText, buildConf);
+    }
+}