diff --git a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
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+++ b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
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+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils;
+
+
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+/**
+ * Basic unit test for Haplotype Class
+ */
+public class HaplotypeUnitTest extends BaseTest {
+    @BeforeClass
+    public void init() {
+    }
+
+    @Test
+    public void testSimpleInsertionAllele() {
+        final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";
+
+        final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
+        h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
+        final Cigar h1Cigar = new Cigar(h1CigarList);
+        String h1bases = "AACTTCTGGTCAACTGGTCAACTGGTCAACTGGTCA";
+        basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases);
+        h1bases = "ACTGGTCACTTAACTGGTCAACTGGTCAACTGGTCA";
+        basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases);
+        h1bases = "ACTGGTCAACTGGTCAAACTTCTGGTCAACTGGTCA";
+        basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases);
+    }
+
+    @Test
+    public void testSimpleDeletionAllele() {
+        final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";
+
+        final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
+        h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
+        final Cigar h1Cigar = new Cigar(h1CigarList);
+        String h1bases = "ATCAACTGGTCAACTGGTCAACTGGTCA";
+        basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases);
+        h1bases = "ACTGGTCGGTCAACTGGTCAACTGGTCA";
+        basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases);
+        h1bases = "ACTGGTCAACTGGTCAATCAACTGGTCA";
+        basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases);
+    }
+
+    @Test
+    public void testSimpleSNPAllele() {
+        final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";
+
+        final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
+        h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
+        final Cigar h1Cigar = new Cigar(h1CigarList);
+        String h1bases = "AGTGGTCAACTGGTCAACTGGTCAACTGGTCA";
+        basicInsertTest("C", "G", 1, h1Cigar, bases, h1bases);
+        h1bases = "ACTGGTCTACTGGTCAACTGGTCAACTGGTCA";
+        basicInsertTest("A", "T", 7, h1Cigar, bases, h1bases);
+        h1bases = "ACTGGTCAACTGGTCAAATGGTCAACTGGTCA";
+        basicInsertTest("C", "A", 17, h1Cigar, bases, h1bases);
+    }
+
+    @Test
+    public void testComplexInsertionAllele() {
+        final String bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+
+        final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
+        h1CigarList.add(new CigarElement(4, CigarOperator.M));
+        h1CigarList.add(new CigarElement(10, CigarOperator.I));
+        h1CigarList.add(new CigarElement(8, CigarOperator.M));
+        h1CigarList.add(new CigarElement(3, CigarOperator.D));
+        h1CigarList.add(new CigarElement(7, CigarOperator.M));
+        h1CigarList.add(new CigarElement(4, CigarOperator.M));
+        final Cigar h1Cigar = new Cigar(h1CigarList);
+        String h1bases = "AACTTTCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+        basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases);
+        h1bases = "ATCG" + "CCGGCCGGCC" + "ATCACTTGATCG" + "AGGGGGA" + "AGGC";
+        basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases);
+        h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGACTTGGGGA" + "AGGC";
+        basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases);
+    }
+
+    @Test
+    public void testComplexDeletionAllele() {
+        final String bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+
+        final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
+        h1CigarList.add(new CigarElement(4, CigarOperator.M));
+        h1CigarList.add(new CigarElement(10, CigarOperator.I));
+        h1CigarList.add(new CigarElement(8, CigarOperator.M));
+        h1CigarList.add(new CigarElement(3, CigarOperator.D));
+        h1CigarList.add(new CigarElement(7, CigarOperator.M));
+        h1CigarList.add(new CigarElement(4, CigarOperator.M));
+        final Cigar h1Cigar = new Cigar(h1CigarList);
+        String h1bases = "A" + "CGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+        basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases);
+        h1bases = "ATCG" + "CCGGCCGGCC" + "ATCG" + "AGGGGGA" + "AGGC";
+        basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases);
+        h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGA" + "AGGC";
+        basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases);
+    }
+
+    @Test
+    public void testComplexSNPAllele() {
+        final String bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+
+        final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
+        h1CigarList.add(new CigarElement(4, CigarOperator.M));
+        h1CigarList.add(new CigarElement(10, CigarOperator.I));
+        h1CigarList.add(new CigarElement(8, CigarOperator.M));
+        h1CigarList.add(new CigarElement(3, CigarOperator.D));
+        h1CigarList.add(new CigarElement(7, CigarOperator.M));
+        h1CigarList.add(new CigarElement(4, CigarOperator.M));
+        final Cigar h1Cigar = new Cigar(h1CigarList);
+        String h1bases = "AGCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+        basicInsertTest("T", "G", 1, h1Cigar, bases, h1bases);
+        h1bases = "ATCG" + "CCGGCCGGCC" + "ATCTATCG" + "AGGGGGA" + "AGGC";
+        basicInsertTest("G", "T", 7, h1Cigar, bases, h1bases);
+        h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGCGGGA" + "AGGC";
+        basicInsertTest("G", "C", 17, h1Cigar, bases, h1bases);
+    }
+
+    private void basicInsertTest(String ref, String alt, int loc, Cigar cigar, String hap, String newHap) {
+        final int INDEL_PADDING_BASE = (ref.length() == alt.length() ? 0 : 1);
+        final Haplotype h = new Haplotype(hap.getBytes());
+        final Allele h1refAllele = Allele.create(ref, true);
+        final Allele h1altAllele = Allele.create(alt, false);
+        final Haplotype h1 = new Haplotype( h.insertAllele(h1refAllele, h1altAllele, loc - INDEL_PADDING_BASE, 0, cigar) );
+        final Haplotype h1expected = new Haplotype(newHap.getBytes());
+        Assert.assertEquals(h1, h1expected);
+
+    }
+}