public void onTraversalDone(Integer includedSites) {
logger.info("Sites included in beagle likelihoods file : " + includedSites);
logger.info(
String.format(
"Certain false positive found from recalibration curve : %d (%.2f%%)",
certainFPs, (100.0 * certainFPs) / (Math.max(certainFPs + includedSites, 1))));
}
/**
* Compares the covariate report lists.
*
* @param diffs map where to annotate the difference.
* @param other the argument collection to compare against.
* @param thisRole the name for this argument collection that makes sense to the user.
* @param otherRole the name for the other argument collection that makes sense to the end user.
* @return <code>true</code> if a difference was found.
*/
@Requires("diffs != null && other != null && thisRole != null && otherRole != null")
private boolean compareRequestedCovariates(
final Map<String, String> diffs,
final RecalibrationArgumentCollection other,
final String thisRole,
final String otherRole) {
final Set<String> beforeNames = new HashSet<>(this.COVARIATES.length);
final Set<String> afterNames = new HashSet<>(other.COVARIATES.length);
Utils.addAll(beforeNames, this.COVARIATES);
Utils.addAll(afterNames, other.COVARIATES);
final Set<String> intersect = new HashSet<>(Math.min(beforeNames.size(), afterNames.size()));
intersect.addAll(beforeNames);
intersect.retainAll(afterNames);
String diffMessage = null;
if (intersect.size()
== 0) { // In practice this is not possible due to required covariates but...
diffMessage =
String.format(
"There are no common covariates between '%s' and '%s'"
+ " recalibrator reports. Covariates in '%s': {%s}. Covariates in '%s': {%s}.",
thisRole,
otherRole,
thisRole,
Utils.join(", ", this.COVARIATES),
otherRole,
Utils.join(",", other.COVARIATES));
} else if (intersect.size() != beforeNames.size() || intersect.size() != afterNames.size()) {
beforeNames.removeAll(intersect);
afterNames.removeAll(intersect);
diffMessage =
String.format(
"There are differences in the set of covariates requested in the"
+ " '%s' and '%s' recalibrator reports. "
+ " Exclusive to '%s': {%s}. Exclusive to '%s': {%s}.",
thisRole,
otherRole,
thisRole,
Utils.join(", ", beforeNames),
otherRole,
Utils.join(", ", afterNames));
}
if (diffMessage != null) {
diffs.put("covariate", diffMessage);
return true;
} else {
return false;
}
}
/**
* Creates a new LRU cache.
*
* @param cacheSize the maximum number of entries that will be kept in this cache.
*/
public LRUCache(int cacheSize) {
this.cacheSize = cacheSize;
int hashTableCapacity = (int) Math.ceil(cacheSize / hashTableLoadFactor) + 1;
map =
new LinkedHashMap<K, V>(hashTableCapacity, hashTableLoadFactor, true) {
// (an anonymous inner class)
private static final long serialVersionUID = 1;
@Override
protected boolean removeEldestEntry(Map.Entry<K, V> eldest) {
return size() > LRUCache.this.cacheSize;
}
};
}