From 9eaee8c73c4acfc992fec64c9c75166a83f62790 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Tue, 4 Feb 2014 11:45:18 -0500
Subject: [PATCH] Integration test for the -nt race condition corrupting AD and
 PL fields

---
 .../variantutils/SelectVariantsParallelIntegrationTest.java  | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
index 4d7fa28ad..68eb1cc41 100644
--- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
+++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
@@ -92,6 +92,11 @@ public class SelectVariantsParallelIntegrationTest extends WalkerTest {
                 final String args = "-select 'DP > 30' -V " + testfile;
                 new ParallelSelectTestProvider(b37KGReference, args, "c64b45a14d41b1e5cddbe036b47e7519", nt);
             }
+            { // AD and PL decoding race condition
+                final String testfile = privateTestDir + "race_condition.vcf";
+                final String args = "-env -sn SAMPLE -L 1:1-10,000,000 -V " + testfile;
+                new ParallelSelectTestProvider(b37KGReference, args, "62e6156387d6e91bd2b08ef649cb1129", nt);
+            }
         }
 
         return ParallelSelectTestProvider.getTests(ParallelSelectTestProvider.class);