Integration test for PhaseByTransmission

public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java

@@ -0,0 +1,44 @@
+package org.broadinstitute.sting.gatk.walkers.phasing;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+public class PhaseByTransmissionIntegrationTest extends WalkerTest {
+    private static String phaseByTransmissionTestDataRoot = validationDataLocation + "/PhaseByTransmission";
+    private static String fundamentalTestVCF = phaseByTransmissionTestDataRoot + "/" + "FundamentalsTest.unfiltered.vcf";
+
+    @Test
+    public void testBasicFunctionalityWithoutFilters() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T PhaseByTransmission",
+                        "-R " + b37KGReference,
+                        "-B:variant,VCF " + fundamentalTestVCF,
+                        "-f NA12892+NA12891=NA12878",
+                        "-nofilters",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("")
+        );
+        executeTest("testBasicFunctionalityWithoutFilters", spec);
+    }
+
+    @Test
+    public void testBasicFunctionalityWithFilters() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T PhaseByTransmission",
+                        "-R " + b37KGReference,
+                        "-B:variant,VCF " + fundamentalTestVCF,
+                        "-f NA12892+NA12891=NA12878",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("")
+        );
+        executeTest("testBasicFunctionalityWithFilters", spec);
+    }
+}