*/
private BQSRArgumentSet bqsrArgumentSet = null;
public BQSRArgumentSet getBQSRArgumentSet() { return bqsrArgumentSet; }
public boolean hasBQSRArgumentSet() { return bqsrArgumentSet != null; }
public void setBaseRecalibration(final GATKArgumentCollection args) {
bqsrArgumentSet = new BQSRArgumentSet(args);
}