/**
* 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());
}
