/**
* For each site of interest, annotate based on the requested annotation types
*
* @param tracker the meta-data tracker
* @param ref the reference base
* @param context the context for the given locus
* @return 1 if the locus was successfully processed, 0 if otherwise
*/
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (tracker == null) return 0;
// get the variant contexts for all the variants at the location
Collection<VariantContext> VCs =
tracker.getValues(variantCollection.variants, context.getLocation());
if (VCs.isEmpty()) return 0;
Collection<VariantContext> annotatedVCs = VCs;
// if the reference base is not ambiguous, we can annotate
Map<String, AlignmentContext> stratifiedContexts;
if (BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1) {
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getBasePileup());
annotatedVCs = new ArrayList<>(VCs.size());
for (VariantContext vc : VCs)
annotatedVCs.add(engine.annotateContext(tracker, ref, stratifiedContexts, vc));
}
for (VariantContext annotatedVC : annotatedVCs) vcfWriter.add(annotatedVC);
return 1;
}
/** 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);
}