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 e = new HashMap(); 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 e = new HashMap(); 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 e = new HashMap(); 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"); + } } }