From 41fa323e63e5ce85a1ea4d44d2062968eee2f626 Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 15 Sep 2010 16:38:04 +0000 Subject: [PATCH] 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 --- .../annotator/VariantAnnotatorIntegrationTest.java | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 953e1bf3f..ab0b6c019 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -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); + } + } }