/** Fill values for INFO fields requiring 'REF' value */
protected void findDbInfoRef(Map<String, String> info, Set<VcfEntry> uniqueVcfEntries) {
if (!useInfoFields || !hasVcfInfoPerAlleleRef) return; // Nothing to do
for (String infoFieldName : infoFields) {
// Does this field require 'REF' annotation?
if (!isVcfInfoPerAlleleRef(infoFieldName)) continue;
// Try to find 'REF' information in any entry
String val = null;
for (VcfEntry dbVcfEntry : uniqueVcfEntries) {
val = dbVcfEntry.getInfo(infoFieldName, dbVcfEntry.getRef());
if (VcfEntry.isEmpty(val)) val = null; // Only add non-empty
else break; // We need only one value
}
// Nothing found? Use 'MISSING' value
if (val == null) val = VcfFileIterator.MISSING;
// Store value
info.put(infoFieldName, val);
}
}
