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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
This commit is contained in:
ebanks 2010-07-18 03:24:28 +00:00
parent 982947d328
commit 379584f1bf
1 changed files with 3 additions and 7 deletions
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10
java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
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@ -8,11 +8,6 @@ import java.util.Arrays;
public class RealignerTargetCreatorIntegrationTest extends WalkerTest { public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
@Test @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() { public void testIntervals() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
@ -28,9 +23,10 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
executeTest("test dbsnp", spec2); executeTest("test dbsnp", spec2);
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( 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, 1,
Arrays.asList("1a11cfc9cc713617c82bdec503ebe02a")); 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);
} }
} }