Adding integration test for Flag Stat

public/java/test/org/broadinstitute/sting/gatk/walkers/FlagStatIntegrationTest.java

@@ -0,0 +1,20 @@
+package org.broadinstitute.sting.gatk.walkers;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+public class FlagStatIntegrationTest extends WalkerTest {
+
+    @Test
+    public void testFlagStat() {
+        String md5 = "9c4039662f24bfd23ccf67973cb5df29";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FlagStat -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
+                 1,
+                 Arrays.asList(md5));
+        executeTest("test flag stat", spec);
+    }
+}