diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index e7d7300ae..37dc7adba 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -172,6 +172,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { executeTest("getting DB tag with HM3", spec); } + @Test + public void testDBTagWithTwoComps() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1, + Arrays.asList("6afbf05090ae139f53467cf6e0e71cf4")); + executeTest("getting DB tag with 2 comps", spec); + } + @Test public void testNoQuals() { WalkerTestSpec spec = new WalkerTestSpec( diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java index 07af4bd74..6b89ab4f4 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java @@ -136,7 +136,7 @@ public final class VariantOverlapAnnotator { VariantContext annotated = vcToAnnotate; final GenomeLoc loc = getLoc(vcToAnnotate); for ( final Map.Entry, String> overlapBinding : overlapBindings.entrySet() ) { - annotated = annotateOverlap(tracker.getValues(overlapBinding.getKey(), loc), overlapBinding.getValue(), vcToAnnotate); + annotated = annotateOverlap(tracker.getValues(overlapBinding.getKey(), loc), overlapBinding.getValue(), annotated); } return annotated;