private boolean isConcordant(VariantContext vc, Collection<VariantContext> compVCs) {
if (vc == null || compVCs == null || compVCs.isEmpty()) return false;
// if we're not looking for specific samples then the fact that we have both VCs is enough to
// call it concordant.
if (NO_SAMPLES_SPECIFIED) return true;
// make a list of all samples contained in this variant VC that are being tracked by the user
// command line arguments.
Set<String> variantSamples = vc.getSampleNames();
variantSamples.retainAll(samples);
// check if we can find all samples from the variant rod in the comp rod.
for (String sample : variantSamples) {
boolean foundSample = false;
for (VariantContext compVC : compVCs) {
Genotype varG = vc.getGenotype(sample);
Genotype compG = compVC.getGenotype(sample);
if (haveSameGenotypes(varG, compG)) {
foundSample = true;
break;
}
}
// if at least one sample doesn't have the same genotype, we don't have concordance
if (!foundSample) {
return false;
}
}
return true;
}
/**
* 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;
}
}