From bbf7a0fb091937691551a686171266852dffccca Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Mon, 22 Oct 2012 16:09:49 -0400 Subject: [PATCH] Adding integration test to ReduceReads coreduction DEV-117 #resolve --- .../reducereads/ReduceReadsIntegrationTest.java | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java index 89f251ed4..73b7025c3 100755 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java @@ -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(""))); + } + }