org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCNVHybridADVIArgumentCollection Maven / Gradle / Ivy
package org.broadinstitute.hellbender.tools.copynumber.arguments;
import java.util.EnumMap;
/**
* @author Mehrtash Babadi <[email protected]>
*/
public final class GermlineCNVHybridADVIArgumentCollection extends HybridADVIArgumentCollection {
private static final long serialVersionUID = 1L;
private static final EnumMap defaultValue = new EnumMap<>(HybridADVIArgument.class);
static {
defaultValue.put(HybridADVIArgument.LEARNING_RATE, 0.01);
defaultValue.put(HybridADVIArgument.ADAMAX_BETA_1, 0.9);
defaultValue.put(HybridADVIArgument.ADAMAX_BETA_2, 0.99);
defaultValue.put(HybridADVIArgument.LOG_EMISSION_SAMPLES_PER_ROUND, 50);
defaultValue.put(HybridADVIArgument.LOG_EMISSION_SAMPLING_MEDIAN_REL_ERROR, 0.005);
defaultValue.put(HybridADVIArgument.LOG_EMISSION_SAMPLING_ROUNDS, 10);
defaultValue.put(HybridADVIArgument.MAX_ADVI_ITER_FIRST_EPOCH, 5000);
defaultValue.put(HybridADVIArgument.MAX_ADVI_ITER_SUBSEQUENT_EPOCHS, 200);
defaultValue.put(HybridADVIArgument.MIN_TRAINING_EPOCHS, 10);
defaultValue.put(HybridADVIArgument.MAX_TRAINING_EPOCHS, 50);
defaultValue.put(HybridADVIArgument.INITIAL_TEMPERATURE, 1.5);
defaultValue.put(HybridADVIArgument.NUM_THERMAL_ADVI_ITERS, 2500);
defaultValue.put(HybridADVIArgument.CONVERGENCE_SNR_AVERAGING_WINDOW, 500);
defaultValue.put(HybridADVIArgument.CONVERGENCE_SNR_TRIGGER_THRESHOLD, 0.1);
defaultValue.put(HybridADVIArgument.CONVERGENCE_SNR_COUNTDOWN_WINDOW, 10);
defaultValue.put(HybridADVIArgument.MAX_CALLING_ITERS, 10);
defaultValue.put(HybridADVIArgument.CALLER_UPDATE_CONVERGENCE_THRESHOLD, 0.001);
defaultValue.put(HybridADVIArgument.CALLER_INTERNAL_ADMIXING_RATE, 0.75);
defaultValue.put(HybridADVIArgument.CALLER_EXTERNAL_ADMIXING_RATE, 1.0);
defaultValue.put(HybridADVIArgument.DISABLE_ANNEALING, false);
defaultValue.put(HybridADVIArgument.DISABLE_CALLER, false);
defaultValue.put(HybridADVIArgument.DISABLE_SAMPLER, false);
}
@Override
public Object getDefaultValue(HybridADVIArgument arg) {
return defaultValue.get(arg);
}
}