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 a7d67d1..fa7d9d5 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
@@ -31,17 +31,19 @@
 
     public PositionListWritable(byte[] data, int offset) {
 //        setNewReference(data, offset);
+        this();
         set(data, offset);
     }
 
     public PositionListWritable(List<PositionWritable> posns) {
         this();
-        setSize(posns.size()); // reserve space for all elements
+        setSize(posns.size() * PositionWritable.LENGTH + HEADER_SIZE); // reserve space for all elements
         for (PositionWritable p : posns) {
             append(p);
         }
     }
 
+//    // TODO: we currently don't track who actually owns each block so variable-length references are impossible. We could track 1) if it's a reference and 2) the size of the original reference block, but that would require a check for every setSize and might be coplicated logic  
 //    public void setNewReference(byte[] data, int offset) {
 //        this.valueCount = Marshal.getInt(data, offset);
 //        this.storage = data;
@@ -112,13 +114,13 @@
         set(otherList.storage, otherList.offset);
     }
 
-    public void set(byte[] newData, int offset) {
-        valueCount = Marshal.getInt(newData, offset);
+    public void set(byte[] newData, int newOffset) {
+        valueCount = Marshal.getInt(newData, newOffset);
         setSize(valueCount * PositionWritable.LENGTH + HEADER_SIZE);
         if (valueCount > 0) {
-            System.arraycopy(newData, offset + HEADER_SIZE, storage, this.offset + HEADER_SIZE, valueCount * PositionWritable.LENGTH);
+            System.arraycopy(newData, newOffset + HEADER_SIZE, storage, this.offset + HEADER_SIZE, valueCount * PositionWritable.LENGTH);
         }
-        Marshal.putInt(valueCount, storage, offset);
+        Marshal.putInt(valueCount, storage, this.offset);
     }
 
     public void reset() {
@@ -154,7 +156,7 @@
         if (i >= valueCount) {
             throw new ArrayIndexOutOfBoundsException("No such positions");
         }
-        posIter.setNewReference(storage, offset + i * PositionWritable.LENGTH);
+        posIter.setNewReference(storage, offset + i * PositionWritable.LENGTH + HEADER_SIZE);
         return posIter;
     }
 
@@ -162,7 +164,7 @@
         if (i >= valueCount) {
             throw new ArrayIndexOutOfBoundsException("No such positions");
         }
-        Marshal.putLong(uuid, storage, offset + i * PositionWritable.LENGTH);
+        Marshal.putLong(uuid, storage, offset + i * PositionWritable.LENGTH + HEADER_SIZE);
     }
 
     public int getCountOfPosition() {
@@ -178,7 +180,7 @@
     }
 
     public int getLength() {
-        return valueCount * PositionWritable.LENGTH;
+        return valueCount * PositionWritable.LENGTH + HEADER_SIZE;
     }
 
     @Override
@@ -200,11 +202,12 @@
             @Override
             public void remove() {
                 if (currentIndex < valueCount)
-                    System.arraycopy(storage, offset + currentIndex * PositionWritable.LENGTH, storage, offset
-                            + (currentIndex - 1) * PositionWritable.LENGTH, (valueCount - currentIndex)
+                    System.arraycopy(storage, offset + currentIndex * PositionWritable.LENGTH + HEADER_SIZE, storage, offset
+                            + (currentIndex - 1) * PositionWritable.LENGTH + HEADER_SIZE, (valueCount - currentIndex)
                             * PositionWritable.LENGTH);
                 valueCount--;
                 currentIndex--;
+                Marshal.putInt(valueCount, storage, offset);
             }
         };
         return it;
@@ -234,14 +237,15 @@
     @Override
     public void write(DataOutput out) throws IOException {
         out.writeInt(valueCount);
-        out.write(storage, offset, valueCount * PositionWritable.LENGTH);
+        out.write(storage, offset + HEADER_SIZE, valueCount * PositionWritable.LENGTH);
     }
 
     @Override
     public void readFields(DataInput in) throws IOException {
         this.valueCount = in.readInt();
-        setSize(valueCount * PositionWritable.LENGTH);
-        in.readFully(storage, offset, valueCount * PositionWritable.LENGTH);
+        setSize(valueCount * PositionWritable.LENGTH + HEADER_SIZE);
+        in.readFully(storage, offset + HEADER_SIZE, valueCount * PositionWritable.LENGTH);
+        Marshal.putInt(valueCount, storage, offset);
     }
 
     @Override
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
index 1079677..03d66a6 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
@@ -119,10 +119,10 @@
     }
     
     /*
-     * String of form "(readId-posID_mate)" where mate is _1 or _2
+     * String of form "(readId-posID_mate)" where mate is _0 or _1
      */
     @Override
     public String toString() {
-        return "(" + this.getReadId() + "-" + this.getPosId() + "_" + (this.getMateId() + 1) + ")";
+        return "(" + this.getReadId() + "-" + this.getPosId() + "_" + (this.getMateId()) + ")";
     }
 }
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionListWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionListWritableTest.java
index fea658d..ac7322e 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionListWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionListWritableTest.java
@@ -41,7 +41,7 @@
         byte [] another = new byte [plist.getLength()*2];
         int start = 20;
         System.arraycopy(plist.getByteArray(), 0, another, start, plist.getLength());
-        PositionListWritable plist2 = new PositionListWritable(plist.getCountOfPosition(),another,start);
+        PositionListWritable plist2 = new PositionListWritable(another,start);
         for( i = 0; i < plist2.getCountOfPosition(); i++){
             Assert.assertEquals(plist.getPosition(i), plist2.getPosition(i));
         }
@@ -84,19 +84,22 @@
             iterator = copyList.iterator();
             PositionWritable deletePos = new PositionWritable();
             deletePos.set((byte)1, (long)j, j);
+            boolean removed = false;
             while(iterator.hasNext()){
                 pos = iterator.next();
                 if(pos.equals(deletePos)){
                     iterator.remove();
+                    removed = true;
                     break;
                 }
             }
+            Assert.assertTrue(removed);
             Assert.assertEquals(5 - 1 - j, copyList.getCountOfPosition());
             while(iterator.hasNext()){
                 pos = iterator.next();
-                Assert.assertTrue(pos.getUUID() != deletePos.getUUID());
-                Assert.assertTrue(pos.getReadId() != deletePos.getReadId());
-                Assert.assertTrue(pos.getPosId() != deletePos.getPosId());
+                Assert.assertTrue(! (pos.getUUID() == deletePos.getUUID() && 
+                                  pos.getReadId() == deletePos.getReadId() && 
+                                  pos.getPosId() == deletePos.getPosId()));
                 i++;
             }
         }