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Adding integration test to ReduceReads coreduction 

DEV-117 #resolve
This commit is contained in:
Mauricio Carneiro 2012-10-22 16:09:49 -04:00
parent 118da1cd1c
commit bbf7a0fb09
1 changed files with 9 additions and 0 deletions
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9
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
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@ -14,6 +14,9 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
final String DIVIDEBYZERO_BAM = validationDataLocation + "ReduceReadsDivideByZeroBug.bam";
final String DIVIDEBYZERO_L = " -L " + validationDataLocation + "ReduceReadsDivideByZeroBug.intervals";
final String L = " -L 20:10,100,000-10,120,000 ";
final String COREDUCTION_BAM_A = validationDataLocation + "coreduction.test.A.bam";
final String COREDUCTION_BAM_B = validationDataLocation + "coreduction.test.B.bam";
final String COREDUCTION_L = " -L 1:1,853,860-1,854,354 -L 1:1,884,131-1,892,057";
private void RRTest(String testName, String args, String md5) {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, BAM) + " -o %s ";
@ -77,5 +80,11 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
executeTest("testDivideByZero", new WalkerTestSpec(base, Arrays.asList("d8d066304f7c187f182bfb50f39baa0c")));
}
@Test(enabled = true)
public void testCoReduction() {
String base = String.format("-T ReduceReads %s -npt -R %s -I %s -I %s", COREDUCTION_L, REF, COREDUCTION_BAM_A, COREDUCTION_BAM_B) + " -o %s ";
executeTest("testCoReduction", new WalkerTestSpec(base, Arrays.asList("")));
}
}