diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java
index 2b41f5d..2eb91c1 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java
@@ -24,7 +24,10 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Iterator;
+import java.util.List;
 
 import org.apache.hadoop.io.WritableComparable;
 
@@ -52,6 +55,13 @@
         setAsCopy(other);
     }
     
+    public EdgeListWritable(List<EdgeWritable> otherList) {
+        this();
+        for (EdgeWritable e : otherList) {
+            add(e);
+        }
+    }
+    
     public void setAsCopy(EdgeListWritable otherEdge){
         reset();
         edges.addAll(otherEdge.edges);
@@ -212,4 +222,36 @@
     public void remove(EdgeWritable toRemove) {
         remove(toRemove, false);
     }
+
+    /**
+     * Adds all edges in edgeList to me.  If I have the same edge as `other`, that entry will be the union of both sets of readIDs.
+     */
+    public void unionUpdate(EdgeListWritable other) {
+        // TODO test this function properly
+        // TODO perhaps there's a more efficient way to do this?
+        HashMap<VKmerBytesWritable, PositionListWritable> unionEdges = new HashMap<VKmerBytesWritable, PositionListWritable>(edges.size() + other.edges.size());
+        
+        for (EdgeWritable e : edges) {
+            VKmerBytesWritable key = e.getKey();
+            if (unionEdges.containsKey(key)) {
+                unionEdges.get(key).unionUpdate(e.getReadIDs());
+            }
+            else {
+                unionEdges.put(key, new PositionListWritable(e.getReadIDs())); // make a new copy of their list
+            }
+        }
+        for (EdgeWritable e : other.edges) {
+            VKmerBytesWritable key = e.getKey();
+            if (unionEdges.containsKey(key)) {
+                unionEdges.get(key).unionUpdate(e.getReadIDs());
+            }
+            else {
+                unionEdges.put(key, new PositionListWritable(e.getReadIDs())); // make a new copy of their list
+            }
+        }
+        edges.clear();
+        for (VKmerBytesWritable key : unionEdges.keySet()) {
+            edges.add(new EdgeWritable(key, unionEdges.get(key)));
+        }
+    }
 }
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
index 1408e60..b647939 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
@@ -45,6 +45,11 @@
         }
     }
   
+    public PositionListWritable(PositionListWritable other) {
+        this();
+        set(other);
+    }
+
     public void setNewReference(byte[] data, int offset) {
         this.valueCount = Marshal.getInt(data, offset);
         this.storage = data;
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
index 535792b..ad7585c 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
@@ -1,6 +1,7 @@
 package edu.uci.ics.genomix.hadoop.contrailgraphbuilding;
 
 import java.io.IOException;
+import java.util.Arrays;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -12,6 +13,8 @@
 import org.apache.hadoop.mapred.OutputCollector;
 import org.apache.hadoop.mapred.Reporter;
 
+import edu.uci.ics.genomix.type.EdgeListWritable;
+import edu.uci.ics.genomix.type.EdgeWritable;
 import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.genomix.type.VKmerListWritable;
@@ -146,29 +149,38 @@
     	switch(curKmerDir){
     		case FORWARD:
     			switch(preKmerDir){
-    				case FORWARD:
-    				    edgeListForPreKmer.reset();
-    				    edgeListForPreKmer.append(preForwardKmer);
-    					outputNode.setEdgeList(DirectionFlag.DIR_RR, edgeListForPreKmer);
+    				case FORWARD:    				    
+//    				    //TODO NOTE this is one way to fix these entries... or you can refactor your code to have these edgeList and edges sitting around
+//    				    edgeListForPreKmer.reset();
+//    				    edgeListForPreKmer.append(preForwardKmer);
+//    					outputNode.setEdgeList(DirectionFlag.DIR_RR, edgeListForPreKmer);
+//    				    outputNode.setThreadList(DirectionFlag.DIR_RR, nodeIdList);
+    				    outputNode.setEdgeList(DirectionFlag.DIR_RR, new EdgeListWritable(Arrays.asList(new EdgeWritable(preForwardKmer, nodeIdList))));
     					break;
     				case REVERSE:
-    				    edgeListForPreKmer.reset();
-    				    edgeListForPreKmer.append(preReverseKmer);
-    					outputNode.setEdgeList(DirectionFlag.DIR_RF, edgeListForPreKmer);
+//    				    edgeListForPreKmer.reset();
+//    				    edgeListForPreKmer.append(preReverseKmer);
+//    					outputNode.setEdgeList(DirectionFlag.DIR_RF, edgeListForPreKmer);
+//    					outputNode.setThreadList(DirectionFlag.DIR_RF, nodeIdList);
+    				    outputNode.setEdgeList(DirectionFlag.DIR_RF, new EdgeListWritable(Arrays.asList(new EdgeWritable(preReverseKmer, nodeIdList))));
     					break;
     			}
     			break;
     		case REVERSE:
     			switch(preKmerDir){
     				case FORWARD:
-    				    edgeListForPreKmer.reset();
-    				    edgeListForPreKmer.append(preForwardKmer);
-    					outputNode.setEdgeList(DirectionFlag.DIR_FR, edgeListForPreKmer);
+//    				    edgeListForPreKmer.reset();
+//    				    edgeListForPreKmer.append(preForwardKmer);
+//    					outputNode.setEdgeList(DirectionFlag.DIR_FR, edgeListForPreKmer);
+//    					outputNode.setThreadList(DirectionFlag.DIR_FR, nodeIdList);
+    				    outputNode.setEdgeList(DirectionFlag.DIR_FR, new EdgeListWritable(Arrays.asList(new EdgeWritable(preForwardKmer, nodeIdList))));
     					break;
     				case REVERSE:
-    				    edgeListForPreKmer.reset();
-    				    edgeListForPreKmer.append(preReverseKmer);
-    					outputNode.setEdgeList(DirectionFlag.DIR_FF, edgeListForPreKmer);
+//    				    edgeListForPreKmer.reset();
+//    				    edgeListForPreKmer.append(preReverseKmer);
+//    					outputNode.setEdgeList(DirectionFlag.DIR_FF, edgeListForPreKmer);
+//    					outputNode.setThreadList(DirectionFlag.DIR_FF, nodeIdList);
+    				    outputNode.setEdgeList(DirectionFlag.DIR_FR, new EdgeListWritable(Arrays.asList(new EdgeWritable(preReverseKmer, nodeIdList))));
     					break;
     			}
     			break;
@@ -180,28 +192,36 @@
     		case FORWARD:
     			switch(nextKmerDir){
     				case FORWARD:
-    					edgeListForNextKmer.reset();
-    					edgeListForNextKmer.append(nextForwardKmer);
-    					outputNode.setEdgeList(DirectionFlag.DIR_FF, edgeListForNextKmer);
+//    					edgeListForNextKmer.reset();
+//    					edgeListForNextKmer.append(nextForwardKmer);
+//    					outputNode.setEdgeList(DirectionFlag.DIR_FF, edgeListForNextKmer);
+//    					outputNode.setThreadList(DirectionFlag.DIR_FF, nodeIdList);
+    					outputNode.setEdgeList(DirectionFlag.DIR_FF, new EdgeListWritable(Arrays.asList(new EdgeWritable(nextForwardKmer, nodeIdList))));
     					break;
     				case REVERSE:
-    					edgeListForNextKmer.reset();
-    					edgeListForNextKmer.append(nextReverseKmer);
-    					outputNode.setEdgeList(DirectionFlag.DIR_FR, edgeListForNextKmer);
+//    					edgeListForNextKmer.reset();
+//    					edgeListForNextKmer.append(nextReverseKmer);
+//    					outputNode.setEdgeList(DirectionFlag.DIR_FR, edgeListForNextKmer);
+//    					outputNode.setThreadList(DirectionFlag.DIR_FR, nodeIdList);
+    					outputNode.setEdgeList(DirectionFlag.DIR_FR, new EdgeListWritable(Arrays.asList(new EdgeWritable(nextReverseKmer, nodeIdList))));
     					break;
     			}
     			break;
     		case REVERSE:
     			switch(nextKmerDir){
     				case FORWARD:
-    					edgeListForNextKmer.reset();
-    					edgeListForNextKmer.append(nextForwardKmer);
-    					outputNode.setEdgeList(DirectionFlag.DIR_RF, edgeListForNextKmer);
+//    					edgeListForNextKmer.reset();
+//    					edgeListForNextKmer.append(nextForwardKmer);
+//    					outputNode.setEdgeList(DirectionFlag.DIR_RF, edgeListForNextKmer);
+//    					outputNode.setThreadList(DirectionFlag.DIR_RF, nodeIdList);
+    					outputNode.setEdgeList(DirectionFlag.DIR_RF, new EdgeListWritable(Arrays.asList(new EdgeWritable(nextForwardKmer, nodeIdList))));
     					break;
     				case REVERSE:
-    					edgeListForNextKmer.reset();
-    					edgeListForNextKmer.append(nextReverseKmer);
-    					outputNode.setEdgeList(DirectionFlag.DIR_RR, edgeListForNextKmer);
+//    					edgeListForNextKmer.reset();
+//    					edgeListForNextKmer.append(nextReverseKmer);
+//    					outputNode.setEdgeList(DirectionFlag.DIR_RR, edgeListForNextKmer);
+//    					outputNode.setThreadList(DirectionFlag.DIR_RR, nodeIdList);
+    					outputNode.setEdgeList(DirectionFlag.DIR_RR, new EdgeListWritable(Arrays.asList(new EdgeWritable(nextReverseKmer, nodeIdList))));
     					break;
     			}
     			break;
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
index 7ce1ce9..4a669c3 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
@@ -37,10 +37,12 @@
 		averageCoverage = 0;
 		
 		while (values.hasNext()) {
-		    tmpNode.set(values.next());
+		    tmpNode.setAsCopy(values.next());
 		    for (byte d: DirectionFlag.values) {
+		        // TODO NOTE why a *unionupdate* on the edges here?  why not just a simple append?
+//		        outputNode.getEdgeList(d).unionUpdate(tmpNode.getEdgeList(d));
+//		        outputNode.getThreadList(d).unionUpdate(tmpNode.getThreadList(d));
 		        outputNode.getEdgeList(d).unionUpdate(tmpNode.getEdgeList(d));
-		        outputNode.getThreadList(d).unionUpdate(tmpNode.getThreadList(d));
 		    }
 		    outputNode.getStartReads().unionUpdate(tmpNode.getStartReads());
 		    outputNode.getEndReads().unionUpdate(tmpNode.getEndReads());
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graph/GenerateGraphViz.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graph/GenerateGraphViz.java
index fb343e9..8531326 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graph/GenerateGraphViz.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graph/GenerateGraphViz.java
@@ -10,6 +10,7 @@
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.SequenceFile;
 
+import edu.uci.ics.genomix.type.EdgeWritable;
 import edu.uci.ics.genomix.type.NodeWritable;
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
@@ -68,30 +69,30 @@
 
     public static String convertEdgeToGraph(String outputNode, NodeWritable value) {
         String outputEdge = "";
-        Iterator<VKmerBytesWritable> kmerIterator;
-        kmerIterator = value.getEdgeList(DirectionFlag.DIR_FF).iterator();
-        while (kmerIterator.hasNext()) {
-            VKmerBytesWritable edge = kmerIterator.next();
-            outputEdge += outputNode + " -> " + edge.toString() + "[color = \"black\" label =\"FF: "
-                    + value.getThreadList(DirectionFlag.DIR_FF).printReadIdSet() + "\"]\n";
+        Iterator<EdgeWritable> edgeIterator;
+        edgeIterator = value.getEdgeList(DirectionFlag.DIR_FF).iterator();
+        while(edgeIterator.hasNext()){
+            EdgeWritable edge = edgeIterator.next(); 
+            outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"black\" label =\"FF: " +
+                    edge.getReadIDs().toString() + "\"]\n";
         }
-        kmerIterator = value.getEdgeList(DirectionFlag.DIR_FR).iterator();
-        while (kmerIterator.hasNext()) {
-            VKmerBytesWritable edge = kmerIterator.next();
-            outputEdge += outputNode + " -> " + edge.toString() + "[color = \"blue\" label =\"FR: "
-                    + value.getThreadList(DirectionFlag.DIR_FR).printReadIdSet() + "\"]\n";
+        edgeIterator = value.getEdgeList(DirectionFlag.DIR_FR).iterator();
+        while(edgeIterator.hasNext()){
+            EdgeWritable edge = edgeIterator.next();
+            outputEdge += outputNode + " -> " + edge.toString() + "[color = \"blue\" label =\"FR: " +
+                    edge.getReadIDs().toString() + "\"]\n";
         }
-        kmerIterator = value.getEdgeList(DirectionFlag.DIR_RF).iterator();
-        while (kmerIterator.hasNext()) {
-            VKmerBytesWritable edge = kmerIterator.next();
-            outputEdge += outputNode + " -> " + edge.toString() + "[color = \"green\" label =\"RF: "
-                    + value.getThreadList(DirectionFlag.DIR_RF).printReadIdSet() + "\"]\n";
+        edgeIterator = value.getEdgeList(DirectionFlag.DIR_RF).iterator();
+        while(edgeIterator.hasNext()){
+            EdgeWritable edge = edgeIterator.next();
+            outputEdge += outputNode + " -> " + edge.toString() + "[color = \"green\" label =\"RF: " +
+                    edge.getReadIDs().toString() + "\"]\n";
         }
-        kmerIterator = value.getEdgeList(DirectionFlag.DIR_RR).iterator();
-        while (kmerIterator.hasNext()) {
-            VKmerBytesWritable edge = kmerIterator.next();
-            outputEdge += outputNode + " -> " + edge.toString() + "[color = \"red\" label =\"RR: "
-                    + value.getThreadList(DirectionFlag.DIR_RR).printReadIdSet() + "\"]\n";
+        edgeIterator = value.getEdgeList(DirectionFlag.DIR_RR).iterator();
+        while(edgeIterator.hasNext()){
+            EdgeWritable edge = edgeIterator.next();
+            outputEdge += outputNode + " -> " + edge.toString() + "[color = \"red\" label =\"RR: " +
+                    edge.getReadIDs().toString() + "\"]\n";
         }
         //TODO should output actualKmer instead of kmer
         if (outputEdge == "")
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java
index 448d8b7..34675a7 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java
@@ -139,7 +139,7 @@
                     curForwardKmer.setAsCopy(nextForwardKmer);
                     curReverseKmer.setAsCopy(nextReverseKmer);
                     curKmerDir = nextKmerDir;
-                    curNode.set(nextNode);
+                    curNode.setAsCopy(nextNode);
                     nextNode.reset();
                     nextNode.setAvgCoverage(1);
                     nextKmerDir = setNextKmer(nextForwardKmer, nextReverseKmer, array[i]);