Adding integration test for left alignment of indels

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java

@@ -0,0 +1,46 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * 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.gatk.walkers.variantutils;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+/**
+ * Tests LeftAlignVariants
+ */
+public class LeftAlignVariantsIntegrationTest extends WalkerTest {
+
+    @Test
+    public void testLeftAlignment() {
+         WalkerTestSpec spec = new WalkerTestSpec(
+                 "-T LeftAlignVariants -o %s -R " + b37KGReference + " -B:variant,vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf -NO_HEADER",
+                 1,
+                 Arrays.asList("158b1d71b28c52e2789f164500b53732"));
+         executeTest("test left alignment", spec);
+    }
+}