From 45081c32d7d593523993f99f692d56fa7f571dc4 Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 28 Apr 2011 13:30:57 +0000 Subject: [PATCH] continuing from last night, the integration tests weren't covering the right behavior either git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5706 348d0f76-0448-11de-a6fe-93d51630548a --- .../PickSequenomProbesIntegrationTest.java | 29 +++++++------------ 1 file changed, 11 insertions(+), 18 deletions(-) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java index 3f6688fbf..850a3113e 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java @@ -17,25 +17,18 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest { @Test public void testProbesUsingDbSNPMask() { - String testVCF = validationDataLocation + "pickSeqIntegrationTest.vcf"; - String testArgs = "-snp_mask " + GATKDataLocation + "/dbsnp_130_b36.rod -R " - + b36KGReference + " -omitWindow -nameConvention " - + "-project_id 1kgp3_s4_lf -T PickSequenomProbes -L " + validationDataLocation + - "pickSeqIntegrationTest.interval_list -B:input,VCF "+testVCF+" -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, - Arrays.asList("e50162490d0597c8f00d2d20b1463661")); - executeTest("Test probes", spec); - } - @Test - public void testProbesUsingDbSNPMaskWithNMW1() { - String testVCF = validationDataLocation + "pickSeqIntegrationTest.vcf"; - String testArgs = "-snp_mask " + GATKDataLocation + "/dbsnp_130_b36.rod -R " + String md5 = "46d53491af1d3aa0ee1f1e13d68b732d"; + String testVCF = validationDataLocation + "pickSeqIntegrationTest.vcf"; + + String testArgs = "-snp_mask " + validationDataLocation + "pickSeqIntegrationTest.bed -R " + b36KGReference + " -omitWindow -nameConvention " - + "-nmw 1 -project_id 1kgp3_s4_lf -T PickSequenomProbes -L " + validationDataLocation + - "pickSeqIntegrationTest.interval_list -B:input,VCF "+testVCF+" -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, - Arrays.asList("e50162490d0597c8f00d2d20b1463661")); - executeTest("Test probes", spec); + + "-project_id 1kgp3_s4_lf -T PickSequenomProbes -B:input,VCF "+testVCF+" -o %s"; + WalkerTestSpec spec1 = new WalkerTestSpec(testArgs, 1, Arrays.asList(md5)); + executeTest("Test probes", spec1); + + testArgs += " -nmw 1"; + WalkerTestSpec spec2 = new WalkerTestSpec(testArgs, 1, Arrays.asList(md5)); + executeTest("Test probes", spec2); } }