public boolean useValidation(VariantContext validation, ReferenceContext ref) {
if (goodSite(validation)) {
// if using record keeps us below expected proportion, use it
logger.debug(
String.format(
"boot: %d, test: %d, total: %d",
bootstrapSetSize, testSetSize, bootstrapSetSize + testSetSize + 1));
if ((bootstrapSetSize + 1.0) / (1.0 + bootstrapSetSize + testSetSize) <= bootstrap) {
if (bootstrapVCFOutput != null) {
bootstrapVCFOutput.add(
new VariantContextBuilder(validation).filters(BOOTSTRAP_FILTER).make());
}
bootstrapSetSize++;
return true;
} else {
if (bootstrapVCFOutput != null) {
bootstrapVCFOutput.add(validation);
}
testSetSize++;
return false;
}
} else {
if (validation != null && bootstrapVCFOutput != null) {
bootstrapVCFOutput.add(validation);
}
return false;
}
}
private void initializeVcfWriter() {
final List<String> inputNames = Arrays.asList(validation.getName());
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
hInfo.add(
new VCFFilterHeaderLine(
"bootstrap",
"This site used for genotype bootstrapping with ProduceBeagleInputWalker"));
bootstrapVCFOutput.writeHeader(
new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
}