diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
index ca6a3e4..29e27b9 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
@@ -71,7 +71,6 @@
              * set the vertex value
              */
             node.set(getRecordReader().getCurrentValue());
-            vertexValue.setNodeIdList(node.getNodeIdList());
             vertexValue.setFFList(node.getEdgeList(DirectionFlag.DIR_FF));
             vertexValue.setFRList(node.getEdgeList(DirectionFlag.DIR_FR));
             vertexValue.setRFList(node.getEdgeList(DirectionFlag.DIR_RF));
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
index 91f0109..a4b6f4f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
@@ -50,7 +50,7 @@
                 gv.addln(outputEdge);
                 /** add readIdSet **/
                 outputNode += " [shape=record, label = \"<f0> " + key.toString() 
-                        + "|<f1> " + value.getNodeIdList().printReadIdSet()
+                        + "|<f1> " + value.getThreadList(DirectionFlag.DIR_FF).printReadIdSet()
                         + "\"]\n";
                 gv.addln(outputNode);
             }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirectionFlag.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirFlag.java
similarity index 80%
rename from genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirectionFlag.java
rename to genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirFlag.java
index 4785205..5e262ba 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirectionFlag.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/DirFlag.java
@@ -2,7 +2,7 @@
 
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
 
-public class DirectionFlag extends State {
+public class DirFlag extends State {
 //    public static final byte DIR_NO = 0b000 << 0;
     public static final byte DIR_FF = 0b001 << 0;
     public static final byte DIR_FR = 0b010 << 0;
@@ -10,6 +10,4 @@
     public static final byte DIR_RR = 0b100 << 0;
     public static final byte DIR_MASK = 0b111 << 0;
     public static final byte DIR_CLEAR = 0b1111000 << 0;
-    
-//    public static final byte DIR_FROM_DEADVERTEX = 0b101 << 0;
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
index 3ce6c5a..58f12f9 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
@@ -1,6 +1,6 @@
 package edu.uci.ics.genomix.pregelix.type;
 
-public class MessageFlag extends DirectionFlag {
+public class MessageFlag extends DirFlag {
     
     public static String getFlagAsString(byte code) {
         // TODO: allow multiple flags to be set