public static Covariate[] makeInitializedStandardCovariates() {
final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
final Covariate[] covariates = new Covariate[4];
covariates[0] = new ReadGroupCovariate();
covariates[1] = new QualityScoreCovariate();
covariates[2] = new ContextCovariate();
covariates[3] = new CycleCovariate();
for (Covariate cov : covariates) cov.initialize(RAC);
return covariates;
}
public RecalibrationReport(final File recalFile, final SortedSet<String> allReadGroups) {
final GATKReport report = new GATKReport(recalFile);
argumentTable = report.getTable(RecalUtils.ARGUMENT_REPORT_TABLE_TITLE);
RAC = initializeArgumentCollectionTable(argumentTable);
GATKReportTable quantizedTable = report.getTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE);
quantizationInfo = initializeQuantizationTable(quantizedTable);
Pair<ArrayList<Covariate>, ArrayList<Covariate>> covariates =
RecalUtils.initializeCovariates(RAC); // initialize the required and optional covariates
ArrayList<Covariate> requiredCovariates = covariates.getFirst();
ArrayList<Covariate> optionalCovariates = covariates.getSecond();
requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()];
optionalCovariateIndexes = new HashMap<String, Integer>(optionalCovariates.size());
int covariateIndex = 0;
for (final Covariate covariate : requiredCovariates)
requestedCovariates[covariateIndex++] = covariate;
for (final Covariate covariate : optionalCovariates) {
requestedCovariates[covariateIndex] = covariate;
final String covariateName =
covariate
.getClass()
.getSimpleName()
.split("Covariate")[
0]; // get the name of the covariate (without the "covariate" part of it) so we can
// match with the GATKReport
optionalCovariateIndexes.put(covariateName, covariateIndex - 2);
covariateIndex++;
}
for (Covariate cov : requestedCovariates)
cov.initialize(
RAC); // initialize any covariate member variables using the shared argument collection
recalibrationTables = new RecalibrationTables(requestedCovariates, allReadGroups.size());
initializeReadGroupCovariates(allReadGroups);
parseReadGroupTable(
report.getTable(RecalUtils.READGROUP_REPORT_TABLE_TITLE),
recalibrationTables.getReadGroupTable());
parseQualityScoreTable(
report.getTable(RecalUtils.QUALITY_SCORE_REPORT_TABLE_TITLE),
recalibrationTables.getQualityScoreTable());
parseAllCovariatesTable(
report.getTable(RecalUtils.ALL_COVARIATES_REPORT_TABLE_TITLE), recalibrationTables);
}