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.

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");
+            }
         }
     }