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Added CountCovariates integration test to ensure that it throws an exception if a variant mask isn't provided. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4298 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-09-16 19:18:38 +00:00
parent bf69b5fa21
commit 3a400e3dc0
1 changed files with 23 additions and 0 deletions
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23
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.junit.Test;
import java.util.HashMap;
@ -356,4 +357,26 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
}
}
@Test
public void testCountCovariatesFailWithoutDBSNP() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "3700eaf567e4937f442fc777a226d6ad");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -T CountCovariates" +
" -I " + bam +
" -L 1:10,000,000-10,200,000" +
" -standard" +
" --solid_recal_mode SET_Q_ZERO" +
" -recalFile %s",
1, // just one output file
UserException.CommandLineException.class);
executeTest("testCountCovariatesFailWithoutDBSNP", spec);
}
}
}