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Integration test to ensure VariantFiltration makes . -> PASS/FAIL like VQSR 

Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
This commit is contained in:
Mark DePristo 2012-07-25 08:53:22 -04:00
parent fcefa61bce
commit 16947e93f2
1 changed files with 9 additions and 0 deletions
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9
public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
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@ -99,4 +99,13 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
Arrays.asList("8077eb3bab5ff98f12085eb04176fdc9"));
executeTest("test deletions", spec);
}
@Test
public void testUnfilteredBecomesFilteredAndPass() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+ " --filterExpression 'FS > 60.0' --filterName SNP_FS -V " + privateTestDir + "unfilteredForFiltering.vcf", 1,
Arrays.asList("8ed32a2272bab8043a255362335395ef"));
executeTest("testUnfilteredBecomesFilteredAndPass", spec);
}
}