From 78aa6db076b69a1ad0ebec9bb11b2c2337322c53 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 9 Aug 2011 11:45:54 -0400 Subject: [PATCH] added the 'reference' header line too. We are now header-compliant for vcf4.1. --- .../org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java index 6ade8e78c..936243f9d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java @@ -192,6 +192,8 @@ public class VCFWriterStub implements Stub, 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);