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Don't output source and ref header lines anymore. Short-term motivation for this is that I'd like this tool when run on a VCF to emit the exact same VCF. Long-term motivation is that these tags should be output by the VCF writer itself for all tools.

This commit is contained in:
Eric Banks 2011-07-13 14:40:01 -04:00
parent 969227c657
commit 6a431da554
2 changed files with 30 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
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@ -199,8 +199,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
hInfo.add(new VCFHeaderLine("source", "VariantsToVCF"));
hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
//hInfo.add(new VCFHeaderLine("source", "VariantsToVCF"));
//hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY);
for ( VCFHeaderLine field : hInfo ) {

28
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java 100644
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@ -0,0 +1,28 @@
package org.broadinstitute.sting.utils.codecs.vcf;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import java.io.File;
import java.util.Arrays;
import java.util.List;
public class VCFIntegrationTest extends WalkerTest {
@Test
public void testReadingAndWritingWitHNoChanges() {
String md5ofInputVCF = "a990ba187a69ca44cb9bc2bb44d00447";
String testVCF = validationDataLocation + "vcf4.1.example.vcf";
String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
String test1 = baseCommand + "-T VariantAnnotator -BTI variant -B:variant,vcf " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF));
List<File> result = executeTest("Test Variant Annotator with no changes", spec1).getFirst();
String test2 = baseCommand + "-T VariantsToVCF -B:variant,vcf " + result.get(0).getAbsolutePath();
WalkerTestSpec spec2 = new WalkerTestSpec(test2, 1, Arrays.asList(md5ofInputVCF));
executeTest("Test Variants To VCF from new output", spec2);
}
}