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Added MendelianViolationEvaluator integration test

This commit is contained in:
Laurent Francioli 2011-11-30 10:09:20 +01:00
parent ab67011791
commit 7d58db626e
1 changed files with 11 additions and 0 deletions
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11
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -291,6 +291,17 @@ public class VariantEvalIntegrationTest extends WalkerTest {
executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
} }
@Test
public void testVEMendelianViolationEvaluator() {
String vcfFile = "/MendelianViolationEval.vcf";
String pedFile = "/MendelianViolationEval.ped";
WalkerTestSpec spec = new WalkerTestSpec("-T VariantEval -R "+b37KGReference+" --eval " + variantEvalTestDataRoot + vcfFile + " -ped "+ variantEvalTestDataRoot + pedFile +" -noEV -EV MendelianViolationEvaluator -L 1:10109-10315 -o %s",
1,
Arrays.asList("85a8fc01a1f50839667bfcd04155f735"));
executeTestParallel("testVEMendelianViolationEvaluator" + vcfFile, spec);
}
@Test @Test
public void testCompVsEvalAC() { public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf"; String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";