public boolean goodSite(VariantContext v) {
if (canBeOutputToBeagle(v)) {
if (VQSRCalibrator != null && VQSRCalibrator.certainFalsePositive(VQSLOD_KEY, v)) {
certainFPs++;
return false;
} else {
return true;
}
} else {
return false;
}
}
public void initialize() {
samples =
SampleUtils.getSampleListWithVCFHeader(
getToolkit(), Arrays.asList(variantCollection.variants.getName()));
beagleWriter.print("marker alleleA alleleB");
for (String sample : samples)
beagleWriter.print(String.format(" %s %s %s", sample, sample, sample));
beagleWriter.println();
if (bootstrapVCFOutput != null) {
initializeVcfWriter();
}
if (VQSRCalibrationFile != null) {
VQSRCalibrator = VQSRCalibrationCurve.readFromFile(VQSRCalibrationFile);
logger.info("Read calibration curve");
VQSRCalibrator.printInfo(logger);
}
}
private void writeSampleLikelihoods(
StringBuffer out, VariantContext vc, double[] log10Likelihoods) {
if (VQSRCalibrator != null) {
log10Likelihoods =
VQSRCalibrator.includeErrorRateInLikelihoods(VQSLOD_KEY, vc, log10Likelihoods);
}
double[] normalizedLikelihoods = MathUtils.normalizeFromLog10(log10Likelihoods);
// see if we need to randomly mask out genotype in this position.
for (double likeVal : normalizedLikelihoods) {
out.append(formatter.format(likeVal));
// out.append(String.format("%5.4f ",likeVal));
}
}