Integration test for SelectVariants. Tests a complex case with an explicit sample selection, sample selection by regex, exclusion of non-variant and filtered loci, and JEXL selection on low allele-frequency variants

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3976 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -0,0 +1,25 @@
+package org.broadinstitute.sting.gatk.walkers.variantutils;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.junit.Test;
+
+import java.util.Arrays;
+
+public class SelectVariantsIntegrationTest extends WalkerTest {
+    public static String baseTestString(String args) {
+        return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s" + args;
+    }
+
+    @Test
+    public void testComplexSelection() {
+        String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+            baseTestString(" -sn A -sn [CDEH] -env -ef -select 'AF < 0.2' -B variant,VCF," + testfile),
+            1,
+            Arrays.asList("3a15628b5980031c629c0c33e7e60b40")
+        );
+
+        executeTest("testComplexSelection--" + testfile, spec);
+    }
+}