From 16947e93f24484006252988729a3f9c1656a628d Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 25 Jul 2012 08:53:22 -0400
Subject: [PATCH] Integration test to ensure VariantFiltration makes . ->
 PASS/FAIL like VQSR

Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
---
 .../filters/VariantFiltrationIntegrationTest.java        | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
index ae5128c75..97b985a29 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
@@ -99,4 +99,13 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
                 Arrays.asList("8077eb3bab5ff98f12085eb04176fdc9"));
         executeTest("test deletions", spec);
     }
+
+    @Test
+    public void testUnfilteredBecomesFilteredAndPass() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+            "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+                    + " --filterExpression 'FS > 60.0' --filterName SNP_FS -V " + privateTestDir + "unfilteredForFiltering.vcf", 1,
+                Arrays.asList("8ed32a2272bab8043a255362335395ef"));
+        executeTest("testUnfilteredBecomesFilteredAndPass", spec);
+    }
 }