/**
* Gets the appropriately formatted header for a VCF file describing this GATK run
*
* @param engine the GATK engine that holds the walker name, GATK version, and other information
* @param argumentSources contains information on the argument values provided to the GATK for
* converting to a command line string. Should be provided from the data in the parsing
* engine. Can be empty in which case the command line will be the empty string.
* @return VCF header line describing this run of the GATK.
*/
public static VCFHeaderLine getCommandLineArgumentHeaderLine(
final GenomeAnalysisEngine engine, final Collection<Object> argumentSources) {
if (engine == null) throw new IllegalArgumentException("engine cannot be null");
if (argumentSources == null)
throw new IllegalArgumentException("argumentSources cannot be null");
final Map<String, String> attributes = new LinkedHashMap<>();
attributes.put("ID", engine.getWalkerName());
attributes.put("Version", CommandLineGATK.getVersionNumber());
final Date date = new Date();
attributes.put("Date", date.toString());
attributes.put("Epoch", Long.toString(date.getTime()));
attributes.put(
"CommandLineOptions",
engine.createApproximateCommandLineArgumentString(argumentSources.toArray()));
return new VCFSimpleHeaderLine(GATK_COMMAND_LINE_KEY, attributes);
}
