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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.
This commit is contained in:
David Roazen 2012-01-03 10:42:41 -05:00
parent 1b6d52817e
commit f3f01da1af
1 changed files with 15 additions and 3 deletions
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18
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
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@ -118,6 +118,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
Arrays.asList(md5)); Arrays.asList(md5));
executeTest("testTableRecalibrator1", spec); executeTest("testTableRecalibrator1", spec);
} }
else {
throw new IllegalStateException("testTableRecalibrator1: paramsFile was null");
}
} }
@Test @Test
@ -144,7 +147,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
} }
} }
@Test @Test(dependsOnMethods = "testCountCovariates1")
public void testTableRecalibratorMaxQ70() { public void testTableRecalibratorMaxQ70() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0b7123ae9f4155484b68e4a4f96c5504" ); e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0b7123ae9f4155484b68e4a4f96c5504" );
@ -170,6 +173,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
Arrays.asList(md5)); Arrays.asList(md5));
executeTest("testTableRecalibratorMaxQ70", spec); 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() { public void testTableRecalibratorSolidIndelsRemoveRefBias() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "2ad4c17ac3ed380071137e4e53a398a5" ); e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "2ad4c17ac3ed380071137e4e53a398a5" );
@ -224,6 +230,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
Arrays.asList(md5)); Arrays.asList(md5));
executeTest("testTableRecalibratorSolidIndelsRemoveRefBias", spec); 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() { public void testTableRecalibratorNoIndex() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "991f093a0e610df235d28ada418ebf33" ); 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)); Arrays.asList(md5));
executeTest("testTableRecalibratorNoIndex", spec); executeTest("testTableRecalibratorNoIndex", spec);
} }
else {
throw new IllegalStateException("testTableRecalibratorNoIndex: paramsFile was null");
}
} }
} }