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added the 'reference' header line too. We are now header-compliant for vcf4.1.

This commit is contained in:
Eric Banks 2011-08-09 11:45:54 -04:00
parent ec76bf6d4a
commit 78aa6db076
1 changed files with 2 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
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@ -192,6 +192,8 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
String assembly = getReferenceAssembly(engine.getArguments().referenceFile.getName());
for ( SAMSequenceRecord contig : engine.getReferenceDataSource().getReference().getSequenceDictionary().getSequences() )
vcfHeader.addMetaDataLine(getContigHeaderLine(contig, assembly));
vcfHeader.addMetaDataLine(new VCFHeaderLine("reference", "file://" + engine.getArguments().referenceFile.getAbsolutePath()));
}
outputTracker.getStorage(this).writeHeader(vcfHeader);