private void outputMissingInterval(final IntervalStratification stats) {
final GenomeLoc interval = stats.getInterval();
final boolean missing[] = new boolean[interval.size()];
Arrays.fill(missing, true);
for (AbstractStratification sample : stats.getElements()) {
if (hasMissingStatuses(sample)) {
int pos = 0;
for (AbstractStratification locus : sample.getElements()) {
if (locus.callableStatuses().isEmpty()) {
missing[pos] = false;
}
pos++;
}
}
}
int start = -1;
boolean insideMissing = false;
for (int i = 0; i < missing.length; i++) {
if (missing[i] && !insideMissing) {
start = interval.getStart() + i;
insideMissing = true;
} else if (!missing[i] && insideMissing) {
final int stop = interval.getStart() + i - 1;
outputMissingInterval(interval.getContig(), start, stop);
insideMissing = false;
}
}
if (insideMissing) {
outputMissingInterval(interval.getContig(), start, interval.getStop());
}
}
/** Prepare the output file and the list of available features. */
public void initialize() {
if (LIST) {
AnnotationHelpUtils.listAnnotations();
System.exit(0);
}
// get the list of all sample names from the variant VCF input rod, if applicable
final List<String> rodName = Arrays.asList(variantCollection.variants.getName());
final Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName);
if (USE_ALL_ANNOTATIONS)
engine = new VariantAnnotatorEngine(annotationsToExclude, this, getToolkit());
else
engine =
new VariantAnnotatorEngine(
annotationGroupsToUse, annotationsToUse, annotationsToExclude, this, getToolkit());
engine.initializeExpressions(expressionsToUse);
engine.setExpressionAlleleConcordance(expressionAlleleConcordance);
// setup the header fields
// note that if any of the definitions conflict with our new ones, then we want to overwrite the
// old ones
final Set<VCFHeaderLine> hInfo = new HashSet<>();
hInfo.addAll(engine.getVCFAnnotationDescriptions());
for (final VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), rodName)) {
if (isUniqueHeaderLine(line, hInfo)) hInfo.add(line);
}
// for the expressions, pull the info header line from the header of the resource rod
for (final VariantAnnotatorEngine.VAExpression expression : engine.getRequestedExpressions()) {
// special case the ID field
if (expression.fieldName.equals("ID")) {
hInfo.add(
new VCFInfoHeaderLine(
expression.fullName,
1,
VCFHeaderLineType.String,
"ID field transferred from external VCF resource"));
continue;
}
VCFInfoHeaderLine targetHeaderLine = null;
for (final VCFHeaderLine line :
GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName()))) {
if (line instanceof VCFInfoHeaderLine) {
final VCFInfoHeaderLine infoline = (VCFInfoHeaderLine) line;
if (infoline.getID().equals(expression.fieldName)) {
targetHeaderLine = infoline;
break;
}
}
}
if (targetHeaderLine != null) {
if (targetHeaderLine.getCountType() == VCFHeaderLineCount.INTEGER)
hInfo.add(
new VCFInfoHeaderLine(
expression.fullName,
targetHeaderLine.getCount(),
targetHeaderLine.getType(),
targetHeaderLine.getDescription()));
else
hInfo.add(
new VCFInfoHeaderLine(
expression.fullName,
targetHeaderLine.getCountType(),
targetHeaderLine.getType(),
targetHeaderLine.getDescription()));
} else {
hInfo.add(
new VCFInfoHeaderLine(
expression.fullName,
VCFHeaderLineCount.UNBOUNDED,
VCFHeaderLineType.String,
"Value transferred from another external VCF resource"));
}
}
engine.makeHeaderInfoMap(hInfo);
engine.invokeAnnotationInitializationMethods(hInfo);
VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader);
}