From 1d8b1bae0a77a50ac00d9dc89a88ee47baf6cceb Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 7 Aug 2011 13:32:26 -0400 Subject: [PATCH] Need to rename the integration test argument -mask to -maskName --- .../walkers/filters/VariantFiltrationIntegrationTest.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java index 05c0c0982..f613407e2 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java @@ -31,17 +31,17 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testMasks() { WalkerTestSpec spec1 = new WalkerTestSpec( - baseTestString() + " -mask foo --mask:VCF3 " + validationDataLocation + "vcfexample2.vcf --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -maskName foo --mask:VCF3 " + validationDataLocation + "vcfexample2.vcf --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("578f9e774784c25871678e6464fd212b")); executeTest("test mask all", spec1); WalkerTestSpec spec2 = new WalkerTestSpec( - baseTestString() + " -mask foo --mask:VCF " + validationDataLocation + "vcfMask.vcf --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -maskName foo --mask:VCF " + validationDataLocation + "vcfMask.vcf --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("bfa86a674aefca1b13d341cb14ab3c4f")); executeTest("test mask some", spec2); WalkerTestSpec spec3 = new WalkerTestSpec( - baseTestString() + " -mask foo -maskExtend 10 --mask:VCF " + validationDataLocation + "vcfMask.vcf --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + validationDataLocation + "vcfMask.vcf --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("5939f80d14b32d88587373532d7b90e5")); executeTest("test mask extend", spec3); }