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Added iterator for tribble, fixing GS bug report. Removed unnecessary tabix double wrapping. Intergation tests to ensure the BTI works with both vcfs and vcf.gz 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4287 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-09-15 16:38:04 +00:00
parent d7b5baf8e5
commit 41fa323e63
1 changed files with 11 additions and 0 deletions
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11
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -106,4 +106,15 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
Arrays.asList("ff6b3468f21b262de671e823349cbb3c"));
executeTest("getting DB tag with HM3", spec);
}
@Test
public void testTabixAnnotations() {
final String MD5 = "6c7a6a1c0027bf82656542a9b2671a35";
for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -A HomopolymerRun -B:variant,VCF " + validationDataLocation + "/" + file + " -BTI variant -NO_HEADER", 1,
Arrays.asList(MD5));
executeTest("Testing lookup vcf tabix vs. vcf tribble", spec);
}
}
}