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Fixing BQSR integration test

This commit is contained in:
Mauricio Carneiro 2012-07-21 10:52:59 -04:00
parent d7bffb0024
commit df965d4a5a
1 changed files with 3 additions and 3 deletions
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6
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
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@ -59,7 +59,7 @@ public class BQSRIntegrationTest extends WalkerTest {
@Test(dataProvider = "BQSRTest")
public void testBQSR(BQSRTest params) {
WalkerTestSpec spec = new WalkerTestSpec(
"-T BaseQualityScoreRecalibrator" +
" -T BQSR" +
" -R " + params.reference +
" -I " + params.bam +
" -L " + params.interval +
@ -74,8 +74,8 @@ public class BQSRIntegrationTest extends WalkerTest {
@Test
public void testBQSRFailWithoutDBSNP() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -T BaseQualityScoreRecalibrator" +
" -T BQSR" +
" -R " + b36KGReference +
" -I " + validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam" +
" -L 1:10,000,000-10,200,000" +
" --no_plots" +