/** * Add / replace the contig header lines in the VCFHeader with the information in the GATK engine * * @param header the header to update * @param engine the GATK engine containing command line arguments and the master sequence dictionary */ public static VCFHeader withUpdatedContigs(final VCFHeader header, final GenomeAnalysisEngine engine) { return VCFUtils.withUpdatedContigs(header, engine.getArguments().referenceFile, engine.getMasterSequenceDictionary()); }