BridgeAddVertex pass test
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
index ca7f67d..cc7e0ac 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
@@ -22,7 +22,7 @@
     private JobConf conf = new JobConf();
     private static final String ACTUAL_RESULT_DIR = "actual";
     private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
-    private static final String DATA_PATH = "data/webmap/AdjSplitRepeat.txt";
+    private static final String DATA_PATH = "data/webmap/RemoveBridge.txt";
     private static final String HDFS_PATH = "/webmap";
     private static final String RESULT_PATH = "/result";
     
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
index a6b5169..f56fbf9 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
@@ -8,8 +8,6 @@
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 import edu.uci.ics.pregelix.api.util.BspUtils;
-import edu.uci.ics.genomix.oldtype.PositionListWritable;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
 import edu.uci.ics.genomix.pregelix.client.Client;
 import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
 import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
@@ -79,7 +77,7 @@
                 Vertex vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
                 vertex.getMsgList().clear();
                 vertex.getEdges().clear();
-                VertexValueWritable vertexValue = new VertexValueWritable();
+                VertexValueWritable vertexValue = new VertexValueWritable(kmerSize);
                 /**
                  * set the src vertex id
                  */
@@ -99,9 +97,12 @@
                 vertex.setVertexValue(vertexValue);
                 
                 addVertex(vertexId, vertex);
+            } 
+            else if(getVertexId().toString().equals("ACG")){
+                KmerBytesWritable brdgeVertexId = new KmerBytesWritable(kmerSize);
+                brdgeVertexId.setByRead("GTA".getBytes(), 0);
+                getVertexValue().getRFList().append(brdgeVertexId);
             }
-            if(getVertexId().getReadID() == 2 && getVertexId().getPosInRead() == 2)
-                getVertexValue().getRRList().append(3, (byte)1);
         }
         voteToHalt();
     }
@@ -115,7 +116,7 @@
         job.setVertexInputFormatClass(GraphCleanInputFormat.class);
         job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputKeyClass(KmerBytesWritable.class);
         job.setOutputValueClass(VertexValueWritable.class);
         Client.run(args, job);
     }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index 4648bc0..c49332e 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -162,22 +162,22 @@
 //                + "TipRemoveGraph.xml");
 //    }
 //    
-//    private static void generateBridgeAddGraphJob(String jobName, String outputPath) throws IOException {
-//        PregelixJob job = new PregelixJob(jobName);
-//        job.setVertexClass(BridgeAddVertex.class);
-//        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-//        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
-//        job.setDynamicVertexValueSize(true);
-//        job.setOutputKeyClass(PositionWritable.class);
-//        job.setOutputValueClass(VertexValueWritable.class);
-//        job.getConfiguration().setInt(BridgeAddVertex.KMER_SIZE, 3);
-//        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-//    }
-//
-//    private static void genBridgeAddGraph() throws IOException {
-//        generateBridgeAddGraphJob("BridgeAddGraph", outputBase
-//                + "BridgeAddGraph.xml");
-//    }
+    private static void generateBridgeAddGraphJob(String jobName, String outputPath) throws IOException {
+        PregelixJob job = new PregelixJob(jobName);
+        job.setVertexClass(BridgeAddVertex.class);
+        job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+        job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(KmerBytesWritable.class);
+        job.setOutputValueClass(VertexValueWritable.class);
+        job.getConfiguration().setInt(BridgeAddVertex.KMER_SIZE, 3);
+        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+    }
+
+    private static void genBridgeAddGraph() throws IOException {
+        generateBridgeAddGraphJob("BridgeAddGraph", outputBase
+                + "BridgeAddGraph.xml");
+    }
 //
 //    private static void generateBridgeRemoveGraphJob(String jobName, String outputPath) throws IOException {
 //        PregelixJob job = new PregelixJob(jobName);
@@ -244,6 +244,7 @@
 //        genMapReduceGraph();
         genSplitRepeatGraph();
         genTipAddGraph();
+        genBridgeAddGraph();
     }
 
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeAddSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeAddSmallTestSuite.java
index 221a76a..c4f0963 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeAddSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeAddSmallTestSuite.java
@@ -43,20 +43,9 @@
 public class BridgeAddSmallTestSuite extends TestSuite {
     private static final Logger LOGGER = Logger.getLogger(BridgeAddSmallTestSuite.class.getName());
 
-    public static final String PreFix = "data/input"; //"graphbuildresult";
+    public static final String PreFix = "data/AddBridge"; 
     public static final String[] TestDir = { PreFix + File.separator
-    + "tworeads"};/*, PreFix + File.separator
-            /*+ "CyclePath"};, PreFix + File.separator
-            + "SimplePath", PreFix + File.separator
-            + "SinglePath", PreFix + File.separator
-            + "TreePath"};*/
-           /* + "2", PreFix + File.separator + "3", PreFix + File.separator + "4", PreFix + File.separator + "5",
-            PreFix + File.separator + "6", PreFix + File.separator + "7", PreFix + File.separator + "8",
-            PreFix + File.separator + "9", PreFix + File.separator + "TwoKmer", PreFix + File.separator + "ThreeKmer",
-            PreFix + File.separator + "SinglePath", PreFix + File.separator + "SimplePath",
-            PreFix + File.separator + "Path", PreFix + File.separator + "BridgePath",
-            PreFix + File.separator + "CyclePath", PreFix + File.separator + "RingPath",
-            PreFix + File.separator + "LongPath", PreFix + File.separator + "TreePath" };*/
+    + "SimpleTest"};
     private static final String ACTUAL_RESULT_DIR = "data/actual/bridgeadd";
     private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
     private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";