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Adding integration test to BQSR for the csv file

This commit is contained in:
Eric Banks 2012-11-09 09:11:04 -05:00
parent ee776e996a
commit e93d461910
1 changed files with 15 additions and 0 deletions
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15
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
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@ -90,6 +90,21 @@ public class BQSRIntegrationTest extends WalkerTest {
executeTest("testBQSRFailWithoutDBSNP", spec); executeTest("testBQSRFailWithoutDBSNP", spec);
} }
@Test
public void testBQSRCSV() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
" -T BaseRecalibrator" +
" -R " + b36KGReference +
" -I " + validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam" +
" -knownSites " + b36dbSNP129 +
" -L 1:10,000,000-10,200,000" +
" -o /dev/null" +
" --plot_pdf_file /dev/null" +
" --intermediate_csv_file %s",
Arrays.asList("d1c38a3418979400630e2bca1140689c"));
executeTest("testBQSR-CSVfile", spec);
}
@Test @Test
public void testBQSRFailWithSolidNoCall() { public void testBQSRFailWithSolidNoCall() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(