diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java
index 416ab49..be65d55 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java
@@ -15,6 +15,8 @@
 
 package edu.uci.ics.genomix.type;
 
+import javax.management.RuntimeErrorException;
+
 public class GeneCode {
     public final static byte[] GENE_SYMBOL = { 'A', 'C', 'G', 'T' };
     /**
@@ -51,7 +53,7 @@
     
     public static byte getPairedGeneCode(byte genecode){
         if ( genecode < 0 || genecode > 3){
-            throw new IllegalArgumentException("Invalid genecode");
+            throw new IllegalArgumentException("Invalid genecode: " + genecode);
         }
         return (byte) (3- genecode);
     }
@@ -66,4 +68,30 @@
         }
         return GENE_SYMBOL[code];
     }
+    
+    public static String reverseComplement(String kmer) {
+        StringBuilder sb = new StringBuilder();
+        for (char letter : kmer.toCharArray()) {
+            sb.append(complement(letter));
+        }
+        return sb.reverse().toString();
+    }
+    
+    public static char complement(char ch) {
+        switch (ch) {
+            case 'A':
+            case 'a':
+                return 'T';
+            case 'C':
+            case 'c':
+                return 'G';
+            case 'G':
+            case 'g':
+                return 'C';
+            case 'T':
+            case 't':
+                return 'A';
+        }
+        throw new RuntimeException("Invalid character given in complement: " + ch);
+    }
 }
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
index 1a875d4..46e1065 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
@@ -267,7 +267,8 @@
         byte l = 0;
         int bytecount = 0;
         int bcount = size - 1;
-        for (int i = start + kmerlength - 1; i >= 0 && i < array.length; i--) {
+//        for (int i = start + kmerlength - 1; i >= 0 && i < array.length; i--) {
+        for (int i = start + kmerlength - 1; i >= start && i < array.length; i--) {
             byte code = GeneCode.getPairedCodeFromSymbol(array[i]);
             l |= (byte) (code << bytecount);
             bytecount += 2;
@@ -384,36 +385,32 @@
      *            : the next kmer
      */
     public void mergeWithFRKmer(int initialKmerSize, KmerBytesWritable kmer) {
-        int preKmerLength = kmerlength;
         int preSize = size;
+        int preKmerLength = kmerlength;
         this.kmerlength += kmer.kmerlength - initialKmerSize + 1;
         setSize(KmerUtil.getByteNumFromK(kmerlength));
-        
         // copy prefix into right-side of buffer
         for (int i = 1; i <= preSize; i++) {
             bytes[offset + size - i] = bytes[offset + preSize - i];
         }
-        
-        // copy complement of suffix in reverse order into left side of buffer.
-        // we read two bits (one letter) at a time from leading bits of kmer, copying their complement 
-        // into my trailing bits
-        byte destByte = 0x00;
-        int destPosn = 0;
-        for (; destPosn < kmer.getKmerLength(); destPosn++) {
-            // srcPosn starts at the end of kmer, but excludes the last (initialKmerSize - 1) letters
-            // there are +1 and -1 terms in there that cancel out :P
-            int srcPosn = kmer.getKmerLength() - destPosn - initialKmerSize;
-            byte compLetter = GeneCode.getPairedCodeFromSymbol(kmer.getGeneCodeAtPosition(srcPosn));
-            if ((destPosn % 4) == 0 && destPosn >= 4) {
-                // byte is full.  write the complete byte to storage
-                bytes[offset + preSize - (destPosn / 4)] = destByte;
-                destByte &= 0x00;
-            }
-            destByte = (byte) ((destByte << 2) | compLetter);
-        }
-        // fill in the leading, partial byte
-        bytes[offset + preSize - (destPosn / 4)] = destByte;
-        clearLeadBit();
+
+        int bytecount = (preKmerLength % 4) * 2;
+        int bcount = size - preSize - bytecount / 8;  // may overlap previous kmer
+        byte l = bcount == size - preSize ? bytes[offset + bcount] : 0x00;
+        bytecount %= 8;
+        for (int i = kmer.kmerlength - initialKmerSize; i >= 0; i--) {
+          byte code = GeneCode.getPairedGeneCode(kmer.getGeneCodeAtPosition(i));
+          l |= (byte) (code << bytecount);
+          bytecount += 2;
+          if (bytecount == 8) {
+              bytes[offset + bcount--] = l;
+              l = 0;
+              bytecount = 0;
+          }
+      }
+      if (bcount >= 0) {
+          bytes[offset] = l;
+      }
     }
 
     /**
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
index 8438a44..c172994 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
@@ -15,6 +15,10 @@
 
 package edu.uci.ics.genomix.data.test;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+
 import junit.framework.Assert;
 
 import org.junit.Test;
@@ -115,7 +119,7 @@
     }
 
     @Test
-    public void TestMergeNextKmer() {
+    public void TestMergeFFKmer() {
         byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
         String text = "AGCTGACCGT";
         KmerBytesWritable kmer1 = new KmerBytesWritable(8);
@@ -154,9 +158,86 @@
             }
         }
     }
+    
+    @Test
+    public void TestMergeFRKmer() {
+        int kmerSize = 3;
+        String result = "AAGCTAACAACC";
+        byte[] resultArray = result.getBytes();
+        
+        String text1 = "AAGCTAA";
+        KmerBytesWritable kmer1 = new KmerBytesWritable(text1.length());
+        kmer1.setByRead(resultArray, 0);
+        Assert.assertEquals(text1, kmer1.toString());
+        
+        // kmer2 is the rc of the end of the read
+        String text2 = "GGTTGTT";
+        KmerBytesWritable kmer2 = new KmerBytesWritable(text2.length());
+        kmer2.setByReadReverse(resultArray, result.length() - text2.length());
+        Assert.assertEquals(text2, kmer2.toString());
+        
+        KmerBytesWritable merge = new KmerBytesWritable(kmer1);
+        merge.mergeWithFRKmer(kmerSize, kmer2);
+        Assert.assertEquals(result, merge.toString());
+        
+        int i = 1;
+        merge.set(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAAAACAACC", merge.toString());
+        
+        i = 2;
+        merge.set(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAAACAACC", merge.toString());
+        
+        i = 3;
+        merge.set(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAACAACC", merge.toString());
+    }
+    
+    
+    @Test
+    public void TestMergeRFKmer() {
+        int kmerSize = 3;
+        String result = "AAGCTAACAACC";
+        byte[] resultArray = result.getBytes();
+        
+        String text1 = "AAGCTAA";
+        KmerBytesWritable kmer1 = new KmerBytesWritable(text1.length());
+        kmer1.setByRead(resultArray, 0);
+        Assert.assertEquals(text1, kmer1.toString());
+        
+        // kmer2 is the rc of the end of the read
+        String text2 = "GGTTGTT";
+        KmerBytesWritable kmer2 = new KmerBytesWritable(text2.length());
+        kmer2.setByReadReverse(resultArray, result.length() - text2.length());
+        Assert.assertEquals(text2, kmer2.toString());
+        
+        KmerBytesWritable merge = new KmerBytesWritable(kmer1);
+        merge.mergeWithFRKmer(kmerSize, kmer2);
+        Assert.assertEquals(result, merge.toString());
+        
+        int i = 1;
+        merge.set(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAAAACAACC", merge.toString());
+        
+        i = 2;
+        merge.set(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAAACAACC", merge.toString());
+        
+        i = 3;
+        merge.set(kmer1);
+        merge.mergeWithFRKmer(i, kmer2);
+        Assert.assertEquals("AAGCTAACAACC", merge.toString());
+    }
+    
+    
 
     @Test
-    public void TestMergePreKmer() {
+    public void TestMergeRRKmer() {
         byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
         String text = "AGCTGACCGT";
         KmerBytesWritable kmer1 = new KmerBytesWritable(8);