public GenotypeWriter writer = null;
@Argument(fullName = "verbose_mode", shortName = "verbose", doc = "File to print all of the annotated and detailed debugging output", required = false)
public PrintStream verboseWriter = null;
@Argument(fullName = "beagle_file", shortName = "beagle", doc = "File to print BEAGLE-specific data for use with imputation", required = false)
public PrintStream beagleWriter = null;
<BUG>private UGCalculationArguments UG_args = null;
public boolean includeReadsWithDeletionAtLoci() { return true; }</BUG>
public class UGStatistics {
long nBasesVisited = 0;
long nBasesCallable = 0;

public GenotypeWriter writer = null;
@Argument(fullName = "verbose_mode", shortName = "verbose", doc = "File to print all of the annotated and detailed debugging output", required = false)
public PrintStream verboseWriter = null;
@Argument(fullName = "beagle_file", shortName = "beagle", doc = "File to print BEAGLE-specific data for use with imputation", required = false)
public PrintStream beagleWriter = null;
private UnifiedGenotyperEngine UG_engine = null;
public boolean includeReadsWithDeletionAtLoci() { return true; }
public class UGStatistics {
long nBasesVisited = 0;
long nBasesCallable = 0;
