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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
This commit is contained in:
ebanks 2011-04-28 13:30:57 +00:00
parent f34e6d5b8c
commit 45081c32d7
1 changed files with 11 additions and 18 deletions
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29
java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java
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@ -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);
}
}