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Add VCF header for any expressions that are requested

This commit is contained in:
Eric Banks 2011-10-28 10:22:19 -04:00
parent 8b1a62da27
commit 649dfe98f0
2 changed files with 3 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -232,6 +232,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
if ( isUniqueHeaderLine(line, hInfo) )
hInfo.add(line);
}
for ( String expression : expressionsToUse )
hInfo.add(new VCFInfoHeaderLine(expression, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Value transferred from another external VCF resource"));
engine.invokeAnnotationInitializationMethods(hInfo);

2
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -120,7 +120,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testUsingExpression() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
Arrays.asList("e9c0d832dc6b4ed06c955060f830c140"));
Arrays.asList("ae30a1ac7bfbc3d22a327f8b689cad31"));
executeTest("using expression", spec);
}