private static boolean isValidDeletionFraction(double d) {
return ( d >= 0.0 && d <= 1.0 );
}</BUG>
public void initialize() {
<BUG>UG_args = getUnifiedCalculationArguments(getToolkit(), UAC, writer);
if ( verboseWriter != null ) {</BUG>
StringBuilder header = new StringBuilder("AFINFO\tLOC\tMAF\tF\tNullAFpriors\t");
for ( char altAllele : BaseUtils.BASES ) {
char base = Character.toUpperCase(altAllele);
header.append("POfDGivenAFFor" + base + "\t");

long nBasesCalledConfidently = 0;
double percentCallableOfAll()    { return (100.0 * nBasesCallable) / nBasesVisited; }
double percentCalledOfAll()      { return (100.0 * nBasesCalledConfidently) / nBasesVisited; }
double percentCalledOfCallable() { return (100.0 * nBasesCalledConfidently) / nBasesCallable; }
}
public void initialize() {
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, writer, verboseWriter, beagleWriter);
if ( verboseWriter != null ) {
StringBuilder header = new StringBuilder("AFINFO\tLOC\tMAF\tF\tNullAFpriors\t");
for ( char altAllele : BaseUtils.BASES ) {
char base = Character.toUpperCase(altAllele);
header.append("POfDGivenAFFor" + base + "\t");
