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Merged bug fix from Stable into Unstable

This commit is contained in:
David Roazen 2012-01-03 11:03:30 -05:00
parent 055364d786 f3f01da1af
commit 4984ca5e31
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");
}
} }
} }