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 e901de6..fd4c252 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
@@ -123,7 +123,7 @@
         byte l = 0;
         int bytecount = 0;
         int bcount = this.size - 1;
-        for (int i = start; i < start + kmerlength; i++) {
+        for (int i = start; i < start + kmerlength && i < array.length; i++) {
             byte code = GeneCode.getCodeFromSymbol(array[i]);
             l |= (byte) (code << bytecount);
             bytecount += 2;
@@ -151,7 +151,7 @@
         byte l = 0;
         int bytecount = 0;
         int bcount = size - 1;
-        for (int i = start + kmerlength - 1; i >= 0; i--) {
+        for (int i = start + kmerlength - 1; i >= 0 && i < array.length; i--) {
             byte code = GeneCode.getCodeFromSymbol(array[i]);
             l |= (byte) (code << bytecount);
             bytecount += 2;
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
index b958ec6..abedad6 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
@@ -38,18 +38,18 @@
         super(other);
     }
 
-    public void setSize(int size) {
+    protected void setSize(int size) {
         if (size > getCapacity()) {
             setCapacity((size * 3 / 2));
         }
         this.size = size;
     }
 
-    public int getCapacity() {
+    protected int getCapacity() {
         return bytes.length;
     }
 
-    public void setCapacity(int new_cap) {
+    protected void setCapacity(int new_cap) {
         if (new_cap != getCapacity()) {
             byte[] new_data = new byte[new_cap];
             if (new_cap < size) {
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java
index 4f5b4da..409b434 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java
@@ -1,157 +1,160 @@
-/*
- * Copyright 2009-2012 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package edu.uci.ics.genomix.dataflow;
-
-import java.nio.ByteBuffer;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.hadoop.io.LongWritable;
-import org.apache.hadoop.io.Text;
-
-import edu.uci.ics.genomix.data.std.accessors.ByteSerializerDeserializer;
-import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.hyracks.api.comm.IFrameWriter;
-import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
-import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
-import edu.uci.ics.hyracks.dataflow.common.comm.io.ArrayTupleBuilder;
-import edu.uci.ics.hyracks.dataflow.common.comm.io.FrameTupleAppender;
-import edu.uci.ics.hyracks.dataflow.common.comm.util.FrameUtils;
-import edu.uci.ics.hyracks.hdfs.api.IKeyValueParser;
-import edu.uci.ics.hyracks.hdfs.api.IKeyValueParserFactory;
-
-;
-
-public class ReadsKeyValueParserFactory implements IKeyValueParserFactory<LongWritable, Text> {
-    private static final long serialVersionUID = 1L;
-
-    private KmerBytesWritable kmer;
-    private boolean bReversed;
-
-    public ReadsKeyValueParserFactory(int k, boolean bGenerateReversed) {
-        bReversed = bGenerateReversed;
-        kmer = new KmerBytesWritable(k);
-    }
-
-    @Override
-    public IKeyValueParser<LongWritable, Text> createKeyValueParser(final IHyracksTaskContext ctx) {
-        final ArrayTupleBuilder tupleBuilder = new ArrayTupleBuilder(2);
-        final ByteBuffer outputBuffer = ctx.allocateFrame();
-        final FrameTupleAppender outputAppender = new FrameTupleAppender(ctx.getFrameSize());
-        outputAppender.reset(outputBuffer, true);
-
-        return new IKeyValueParser<LongWritable, Text>() {
-
-            @Override
-            public void parse(LongWritable key, Text value, IFrameWriter writer) throws HyracksDataException {
-                String geneLine = value.toString(); // Read the Real Gene Line
-                Pattern genePattern = Pattern.compile("[AGCT]+");
-                Matcher geneMatcher = genePattern.matcher(geneLine);
-                boolean isValid = geneMatcher.matches();
-                if (isValid) {
-                    SplitReads(geneLine.getBytes(), writer);
-                }
-            }
-
-            private void SplitReads(byte[] array, IFrameWriter writer) {
-                /** first kmer */
-                int k = kmer.getKmerLength();
-                kmer.setByRead(array, 0);
-                byte pre = 0;
-                byte next = GeneCode.getAdjBit(array[k]);
-                InsertToFrame(kmer, pre, next, writer);
-
-                /** middle kmer */
-                for (int i = k; i < array.length - 1; i++) {
-                    pre = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithNextChar(array[i]));
-                    next = GeneCode.getAdjBit(array[i + 1]);
-                    InsertToFrame(kmer, pre, next, writer);
-                }
-
-                /** last kmer */
-                pre = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithNextChar(array[array.length - 1]));
-                next = 0;
-                InsertToFrame(kmer, pre, next, writer);
-
-                if (bReversed) {
-                    /** first kmer */
-                    kmer.setByReadReverse(array, 0);
-                    next = 0;
-                    pre = GeneCode.getAdjBit(array[k]);
-                    InsertToFrame(kmer, pre, next, writer);
-                    /** middle kmer */
-                    for (int i = k; i < array.length - 1; i++) {
-                        next = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithPreChar(array[i]));
-                        pre = GeneCode.getAdjBit(array[i + 1]);
-                        InsertToFrame(kmer, pre, next, writer);
-                    }
-                    /** last kmer */
-                    next = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithPreChar(array[array.length - 1]));
-                    pre = 0;
-                    InsertToFrame(kmer, pre, next, writer);
-                }
-            }
-
-            /**
-             * At this graph building phase, we assume the kmer length are all
-             * the same Thus we didn't output those Kmer length
-             * 
-             * @param kmer
-             *            :input kmer
-             * @param pre
-             *            : pre neighbor code
-             * @param next
-             *            : next neighbor code
-             * @param writer
-             *            : output writer
-             */
-            private void InsertToFrame(KmerBytesWritable kmer, byte pre, byte next, IFrameWriter writer) {
-                try {
-                    byte adj = GeneCode.mergePreNextAdj(pre, next);
-                    tupleBuilder.reset();
-                    tupleBuilder.addField(kmer.getBytes(), 0, kmer.getLength());
-                    tupleBuilder.addField(ByteSerializerDeserializer.INSTANCE, adj);
-
-                    if (!outputAppender.append(tupleBuilder.getFieldEndOffsets(), tupleBuilder.getByteArray(), 0,
-                            tupleBuilder.getSize())) {
-                        FrameUtils.flushFrame(outputBuffer, writer);
-                        outputAppender.reset(outputBuffer, true);
-                        if (!outputAppender.append(tupleBuilder.getFieldEndOffsets(), tupleBuilder.getByteArray(), 0,
-                                tupleBuilder.getSize())) {
-                            throw new IllegalStateException(
-                                    "Failed to copy an record into a frame: the record size is too large.");
-                        }
-                    }
-                } catch (Exception e) {
-                    throw new IllegalStateException(e);
-                }
-            }
-
-            @Override
-            public void open(IFrameWriter writer) throws HyracksDataException {
-                // TODO Auto-generated method stub
-
-            }
-
-            @Override
-            public void close(IFrameWriter writer) throws HyracksDataException {
-                FrameUtils.flushFrame(outputBuffer, writer);
-            }
-        };
-    }
-
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.dataflow;
+
+import java.nio.ByteBuffer;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.Text;
+
+import edu.uci.ics.genomix.data.std.accessors.ByteSerializerDeserializer;
+import edu.uci.ics.genomix.type.GeneCode;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.hyracks.api.comm.IFrameWriter;
+import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
+import edu.uci.ics.hyracks.dataflow.common.comm.io.ArrayTupleBuilder;
+import edu.uci.ics.hyracks.dataflow.common.comm.io.FrameTupleAppender;
+import edu.uci.ics.hyracks.dataflow.common.comm.util.FrameUtils;
+import edu.uci.ics.hyracks.hdfs.api.IKeyValueParser;
+import edu.uci.ics.hyracks.hdfs.api.IKeyValueParserFactory;
+
+;
+
+public class ReadsKeyValueParserFactory implements IKeyValueParserFactory<LongWritable, Text> {
+    private static final long serialVersionUID = 1L;
+
+    private KmerBytesWritable kmer;
+    private boolean bReversed;
+
+    public ReadsKeyValueParserFactory(int k, boolean bGenerateReversed) {
+        bReversed = bGenerateReversed;
+        kmer = new KmerBytesWritable(k);
+    }
+
+    @Override
+    public IKeyValueParser<LongWritable, Text> createKeyValueParser(final IHyracksTaskContext ctx) {
+        final ArrayTupleBuilder tupleBuilder = new ArrayTupleBuilder(2);
+        final ByteBuffer outputBuffer = ctx.allocateFrame();
+        final FrameTupleAppender outputAppender = new FrameTupleAppender(ctx.getFrameSize());
+        outputAppender.reset(outputBuffer, true);
+
+        return new IKeyValueParser<LongWritable, Text>() {
+
+            @Override
+            public void parse(LongWritable key, Text value, IFrameWriter writer) throws HyracksDataException {
+                String geneLine = value.toString(); // Read the Real Gene Line
+                Pattern genePattern = Pattern.compile("[AGCT]+");
+                Matcher geneMatcher = genePattern.matcher(geneLine);
+                boolean isValid = geneMatcher.matches();
+                if (isValid) {
+                    SplitReads(geneLine.getBytes(), writer);
+                }
+            }
+
+            private void SplitReads(byte[] array, IFrameWriter writer) {
+                /** first kmer */
+                int k = kmer.getKmerLength();
+                if (k >= array.length){
+                	return;
+                }
+                kmer.setByRead(array, 0);
+                byte pre = 0;
+                byte next = GeneCode.getAdjBit(array[k]);
+                InsertToFrame(kmer, pre, next, writer);
+
+                /** middle kmer */
+                for (int i = k; i < array.length - 1; i++) {
+                    pre = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithNextChar(array[i]));
+                    next = GeneCode.getAdjBit(array[i + 1]);
+                    InsertToFrame(kmer, pre, next, writer);
+                }
+
+                /** last kmer */
+                pre = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithNextChar(array[array.length - 1]));
+                next = 0;
+                InsertToFrame(kmer, pre, next, writer);
+
+                if (bReversed) {
+                    /** first kmer */
+                    kmer.setByReadReverse(array, 0);
+                    next = 0;
+                    pre = GeneCode.getAdjBit(array[k]);
+                    InsertToFrame(kmer, pre, next, writer);
+                    /** middle kmer */
+                    for (int i = k; i < array.length - 1; i++) {
+                        next = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithPreChar(array[i]));
+                        pre = GeneCode.getAdjBit(array[i + 1]);
+                        InsertToFrame(kmer, pre, next, writer);
+                    }
+                    /** last kmer */
+                    next = GeneCode.getBitMapFromGeneCode(kmer.shiftKmerWithPreChar(array[array.length - 1]));
+                    pre = 0;
+                    InsertToFrame(kmer, pre, next, writer);
+                }
+            }
+
+            /**
+             * At this graph building phase, we assume the kmer length are all
+             * the same Thus we didn't output those Kmer length
+             * 
+             * @param kmer
+             *            :input kmer
+             * @param pre
+             *            : pre neighbor code
+             * @param next
+             *            : next neighbor code
+             * @param writer
+             *            : output writer
+             */
+            private void InsertToFrame(KmerBytesWritable kmer, byte pre, byte next, IFrameWriter writer) {
+                try {
+                    byte adj = GeneCode.mergePreNextAdj(pre, next);
+                    tupleBuilder.reset();
+                    tupleBuilder.addField(kmer.getBytes(), 0, kmer.getLength());
+                    tupleBuilder.addField(ByteSerializerDeserializer.INSTANCE, adj);
+
+                    if (!outputAppender.append(tupleBuilder.getFieldEndOffsets(), tupleBuilder.getByteArray(), 0,
+                            tupleBuilder.getSize())) {
+                        FrameUtils.flushFrame(outputBuffer, writer);
+                        outputAppender.reset(outputBuffer, true);
+                        if (!outputAppender.append(tupleBuilder.getFieldEndOffsets(), tupleBuilder.getByteArray(), 0,
+                                tupleBuilder.getSize())) {
+                            throw new IllegalStateException(
+                                    "Failed to copy an record into a frame: the record size is too large.");
+                        }
+                    }
+                } catch (Exception e) {
+                    throw new IllegalStateException(e);
+                }
+            }
+
+            @Override
+            public void open(IFrameWriter writer) throws HyracksDataException {
+                // TODO Auto-generated method stub
+
+            }
+
+            @Override
+            public void close(IFrameWriter writer) throws HyracksDataException {
+                FrameUtils.flushFrame(outputBuffer, writer);
+            }
+        };
+    }
+
 }
\ No newline at end of file
diff --git a/genomix/genomix-hyracks/src/test/resources/data/webmap/text.txt b/genomix/genomix-hyracks/src/test/resources/data/webmap/text.txt
index f5a05a8..9874fc2 100755
--- a/genomix/genomix-hyracks/src/test/resources/data/webmap/text.txt
+++ b/genomix/genomix-hyracks/src/test/resources/data/webmap/text.txt
@@ -5,4 +5,4 @@
 EDBDB?BEEEDGGEGGGDGGGA>DG@GGD;GD@DG@F?<B<BFFD?
 AATAGAAG
 AATAGAAG
-AATAGAAG
+AATAGAAG
\ No newline at end of file