From f3f01da1afee5390afa46431eeb7c697a67aa177 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Tue, 3 Jan 2012 10:42:41 -0500
Subject: [PATCH] Enforce serial dependencies in
 RecalibrationWalkersIntegrationTest

Some tests in this class were intermittently not being executed due
to being randomly scheduled before tests whose results they depend on.
Now the serial dependencies are enforced to avoid problematic orderings.
---
 .../RecalibrationWalkersIntegrationTest.java   | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index 3976231ef..65de6697b 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -118,6 +118,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                     Arrays.asList(md5));
             executeTest("testTableRecalibrator1", spec);
         }
+        else {
+            throw new IllegalStateException("testTableRecalibrator1: paramsFile was null");
+        }
     }
 
     @Test
@@ -144,7 +147,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-    @Test
+    @Test(dependsOnMethods = "testCountCovariates1")
     public void testTableRecalibratorMaxQ70() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0b7123ae9f4155484b68e4a4f96c5504" );
@@ -170,6 +173,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                         Arrays.asList(md5));
                 executeTest("testTableRecalibratorMaxQ70", spec);
             }
+            else {
+                throw new IllegalStateException("testTableRecalibratorMaxQ70: paramsFile was null");
+            }
         }
     }
 
@@ -199,7 +205,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-    @Test
+    @Test(dependsOnMethods = "testCountCovariatesSolidIndelsRemoveRefBias")
     public void testTableRecalibratorSolidIndelsRemoveRefBias() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "2ad4c17ac3ed380071137e4e53a398a5" );
@@ -224,6 +230,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                         Arrays.asList(md5));
                 executeTest("testTableRecalibratorSolidIndelsRemoveRefBias", spec);
             }
+            else {
+                throw new IllegalStateException("testTableRecalibratorSolidIndelsRemoveRefBias: paramsFile was null");
+            }
         }
     }
 
@@ -305,7 +314,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-    @Test
+    @Test(dependsOnMethods = "testCountCovariatesNoIndex")
     public void testTableRecalibratorNoIndex() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "991f093a0e610df235d28ada418ebf33" );
@@ -329,6 +338,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                         Arrays.asList(md5));
                 executeTest("testTableRecalibratorNoIndex", spec);
             }
+            else {
+                throw new IllegalStateException("testTableRecalibratorNoIndex: paramsFile was null");
+            }
         }
     }