private static void findIndividualPerSequenceCoverage(
Calibrator calibrator,
Map<String, Integer> sequenceLengths,
Map<String, String> readGroupToSampleId,
final Map<String, HashMap<String, CalibrationStats>> local,
RegionRestriction restriction) {
final Covariate rgCovariate =
calibrator.getCovariate(calibrator.getCovariateIndex(CovariateEnum.READGROUP));
final Covariate seqCovariate =
calibrator.getCovariate(calibrator.getCovariateIndex(CovariateEnum.SEQUENCE));
for (final Map.Entry<String, Integer> entry : sequenceLengths.entrySet()) {
final String sequenceName = entry.getKey();
if (restriction != null && !sequenceName.equals(restriction.getSequenceName())) {
continue;
}
for (final Map.Entry<String, String> e2 : readGroupToSampleId.entrySet()) {
final String readGroup = e2.getKey();
final String sampleName = e2.getValue();
final int rgValue = rgCovariate.valueOf(readGroup);
final int seqValue = seqCovariate.valueOf(sequenceName);
if (rgValue == -1 || seqValue == -1) {
add(local, sampleName, sequenceName, new CalibrationStats(null));
} else {
final Calibrator.QuerySpec spec = calibrator.initQuery();
spec.setValue(CovariateEnum.READGROUP, rgValue);
spec.setValue(CovariateEnum.SEQUENCE, seqValue);
calibrator.processStats(new LocalStatsProcessor(local, sampleName, sequenceName), spec);
}
}
}
}
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;
}
private static void findIndividualGlobalCoverage(
Calibrator calibrator,
Map<String, String> readGroupToSampleId,
final Map<String, HashMap<String, CalibrationStats>> local) {
final Covariate rgCovariate =
calibrator.getCovariate(calibrator.getCovariateIndex(CovariateEnum.READGROUP));
for (final Map.Entry<String, String> e2 : readGroupToSampleId.entrySet()) {
final String readGroup = e2.getKey();
final String sampleName = e2.getValue();
final int rgValue = rgCovariate.valueOf(readGroup);
if (rgValue == -1) {
add(local, sampleName, DUMMY_SEQ, new CalibrationStats(null));
} else {
final Calibrator.QuerySpec spec = calibrator.initQuery();
spec.setValue(CovariateEnum.READGROUP, rgValue);
calibrator.processStats(new LocalStatsProcessor(local, sampleName, DUMMY_SEQ), spec);
}
}
}