/** Annotate a VCF entry */
public boolean annotate(Variant variant, Map<String, String> info) {
if (verbose) Gpr.showMark(++countVariants, SHOW_EVERY);
// Find in database
Collection<DbNsfpEntry> dbEntries = dbNsfp.query(variant);
if (dbEntries == null || dbEntries.isEmpty()) return false;
// Add all INFO fields that refer to this allele
boolean annotated = false;
for (String fieldKey : fieldsToAdd.keySet()) {
// Are there any values to annotate?
String infoValue = getVcfInfo(dbEntries, fieldKey);
// Missing or empty?
if (annotateEmpty) {
if (infoValue.isEmpty()) infoValue = ".";
} else if (isDbNsfpValueEmpty(infoValue)) {
infoValue = null;
}
// Add annotations
if (infoValue != null) {
String oldInfo = info.get(fieldKey);
if (oldInfo == null) oldInfo = "";
info.put(fieldKey, oldInfo + (oldInfo.isEmpty() ? "" : ",") + infoValue);
annotated = true;
}
}
// Show progress
if (annotated) {
countAnnotated++;
if (debug) Gpr.debug("Annotated: " + variant.toStr());
}
return annotated;
}
