/** Find all non-empty INFO fields 'infoFieldName' in results */
protected String findDbInfo(String infoFieldName, QueryResult qr) {
if (debug) Gpr.debug("Finding DB data for INFO field: " + infoFieldName);
StringBuilder sb = new StringBuilder();
for (VariantVcfEntry varVe : qr.results) {
if (varVe != null) {
String val = varVe.getVcfEntry().getInfo(infoFieldName);
if (!VcfEntry.isEmpty(val)) {
if (debug) Gpr.debug("\tFound: " + val);
if (sb.length() > 0) sb.append(',');
sb.append(val);
}
}
}
return sb.length() <= 0 ? null : sb.toString();
}
/** Add INFO fields. */
protected boolean annotateInfo(VcfEntry vcfEntry, Map<String, String> info) {
if (info == null || info.isEmpty()) return false;
// Sort keys alphabetically
ArrayList<String> keys = new ArrayList<String>();
keys.addAll(info.keySet());
Collections.sort(keys);
// Add keys sorted alphabetically
for (String key : keys) {
String value = info.get(key);
// Skip empty fields?
if (!annotateEmpty && VcfEntry.isEmpty(value)) continue;
// Add INFO entry
if (prependInfoFieldName != null) key = prependInfoName(key);
vcfEntry.addInfo(key, value);
}
return true;
}
/** 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);
}
}
/** Find the first non-empty INFO field 'infoFieldName' in results Note: ALT must match */
protected String findDbInfoAlt(String infoFieldName, QueryResult qr) {
for (VariantVcfEntry varVe : qr.results) {
if (varVe != null) {
// IMPORTANT: When a variant is parse, the original 'ALT' entry is stored in
// the 'Variant.genotype' whereas 'variant.alt' contains
// a 'minimal ALT'. E.g. if we have
// vcfEntry.ref = 'AC'
// vcfEntry.alt = 'A'
// Then
// variant.ref = 'C'
// variant.alt = ''
// variant.genotype = 'A' <-- This is the 'original' ALT field from
// vcfEntry
// That's why we use 'var.getGenotype()' in the following 'getInfo()' method.
String vcfAlt = qr.variant.getGenotype();
String val = varVe.getVcfEntry().getInfo(infoFieldName, vcfAlt);
if (!VcfEntry.isEmpty(val)) return val;
}
}
return VcfFileIterator.MISSING;
}