UnitTest for reverseAlleleClipping

-- No code modified yet, just implementing a unit test to ensure correctness of the existing code

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java

@@ -617,6 +617,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
 
         return clipping;
     }
+
     /**
      * clip the alleles, based on the reference
      *

public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFCodecUnitTest.java

@@ -0,0 +1,91 @@
+/*
+ * Copyright (c) 2012, 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.
+ */
+
+// our package
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+
+// the imports for unit testing.
+
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.variantcontext.*;
+import org.testng.Assert;
+import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+
+public class VCFCodecUnitTest extends BaseTest {
+
+    // --------------------------------------------------------------------------------
+    //
+    // Provider
+    //
+    // --------------------------------------------------------------------------------
+
+    private class AlleleClippingTestProvider extends TestDataProvider {
+        final String ref;
+        final List<Allele> alleles = new ArrayList<Allele>();
+        final int expectedClip;
+
+        private AlleleClippingTestProvider(final int expectedClip, final String ref, final String ... alleles) {
+            super(AlleleClippingTestProvider.class);
+            this.ref = ref;
+            for ( final String allele : alleles )
+                this.alleles.add(Allele.create(allele));
+            this.expectedClip = expectedClip;
+        }
+
+        @Override
+        public String toString() {
+            return String.format("ref=%s allele=%s reverse clip %d", ref, alleles, expectedClip);
+        }
+    }
+
+    @DataProvider(name = "AlleleClippingTestProvider")
+    public Object[][] MakeAlleleClippingTest() {
+        // pair clipping
+        new AlleleClippingTestProvider(0, "ATT", "CCG");
+        new AlleleClippingTestProvider(1, "ATT", "CCT");
+        new AlleleClippingTestProvider(2, "ATT", "CTT");
+        new AlleleClippingTestProvider(2, "ATT", "ATT");  // cannot completely clip allele
+
+        // triplets
+        new AlleleClippingTestProvider(0, "ATT", "CTT", "CGG");
+        new AlleleClippingTestProvider(1, "ATT", "CTT", "CGT"); // the T can go
+        new AlleleClippingTestProvider(2, "ATT", "CTT", "CTT"); // both Ts can go
+
+        return AlleleClippingTestProvider.getTests(AlleleClippingTestProvider.class);
+    }
+
+
+    @Test(dataProvider = "AlleleClippingTestProvider")
+    public void TestAlleleClipping(AlleleClippingTestProvider cfg) {
+        int result = AbstractVCFCodec.computeReverseClipping(cfg.alleles, cfg.ref, 0, 1);
+        Assert.assertEquals(result, cfg.expectedClip);
+    }
+}