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Modified the SnpEff integration test to run on a much smaller interval.

This commit is contained in:
David Roazen 2011-08-08 21:07:13 -04:00
parent a13bc7b929
commit 28d8c8fcbc
1 changed files with 4 additions and 3 deletions
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7
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -129,10 +129,11 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testSnpEffAnnotations() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -o %s -A SnpEff -B:variant,VCF " + validationDataLocation + "/1000G.exomes.vcf " +
"-B:SnpEff,SnpEff " + validationDataLocation + "/snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out" + " -L 1",
"-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff -B:variant,VCF " +
validationDataLocation + "1000G.exomes.vcf -B:SnpEff,SnpEff " + validationDataLocation +
"snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000",
1,
Arrays.asList("5fe3644744d3c084a179c3d204555333")
Arrays.asList("c08648a078368c80530bff004b3157f1")
);
executeTest("Testing SnpEff annotations", spec);
}