public RecalibrationTables(StandardCovariateList covariates, final int numReadGroups) {
this.covariates = covariates;
this.additionalTables = new ArrayList<>();
this.allTables = new ArrayList<>();
this.covariateToTable = new LinkedHashMap<>();
this.tableToCovariate = new LinkedHashMap<>();
this.qualDimension = covariates.getQualityScoreCovariate().maximumKeyValue() + 1;
this.numReadGroups = numReadGroups;
// two special tables
this.readGroupTable = new NestedIntegerArray<>(numReadGroups, eventDimension);
allTables.add(readGroupTable);
covariateToTable.put(covariates.getReadGroupCovariate(), readGroupTable);
tableToCovariate.put(readGroupTable, covariates.getReadGroupCovariate());
this.qualityScoreTable = makeQualityScoreTable();
allTables.add(qualityScoreTable);
covariateToTable.put(covariates.getQualityScoreCovariate(), qualityScoreTable);
tableToCovariate.put(qualityScoreTable, covariates.getQualityScoreCovariate());
// Non-special tables
for (Covariate cov : covariates.getAdditionalCovariates()) {
final NestedIntegerArray<RecalDatum> table =
new NestedIntegerArray<>(
numReadGroups, qualDimension, cov.maximumKeyValue() + 1, eventDimension);
additionalTables.add(table);
allTables.add(table);
covariateToTable.put(cov, table);
tableToCovariate.put(table, cov);
}
}
public RecalibrationTables(final StandardCovariateList covariates) {
this(covariates, covariates.getReadGroupCovariate().maximumKeyValue() + 1);
}