From 379584f1bfdfbe205ae3f349f2e991370f548c74 Mon Sep 17 00:00:00 2001 From: ebanks Date: Sun, 18 Jul 2010 03:24:28 +0000 Subject: [PATCH] Re-enable (most of) these tests. Guillermo will re-enable the other one when the VCF->VC conversion is done for indels git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3821 348d0f76-0448-11de-a6fe-93d51630548a --- .../indels/RealignerTargetCreatorIntegrationTest.java | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java index f2d069845..230a25736 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java @@ -8,11 +8,6 @@ import java.util.Arrays; public class RealignerTargetCreatorIntegrationTest extends WalkerTest { @Test - public void emptyTest() { - // TODO: matt remove this test when the below test is fixed - System.err.println("FIX ME MATT :-)"); - } - //@Test public void testIntervals() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( @@ -28,9 +23,10 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest { executeTest("test dbsnp", spec2); WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( - "-T RealignerTargetCreator -R " + oneKGLocation + "reference/human_b36_both.fasta -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf -BTI indels -o %s", + "-T RealignerTargetCreator -R " + oneKGLocation + "reference/human_b36_both.fasta -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s", 1, Arrays.asList("1a11cfc9cc713617c82bdec503ebe02a")); - executeTest("test rods only", spec3); + //TODO -- Guillermo, re-enable this when the VCF->VC conversion works with indels + //executeTest("test rods only", spec3); } }