/** Add some lines to header before showing it */
@Override
public boolean addHeaders(VcfFileIterator vcfFile) {
super.addHeaders(vcfFile);
for (String key : fieldsToAdd.keySet()) {
// Get type
String type = fieldsType.get(key);
if (type == null) {
System.err.println("WARNING: Cannot find type for field '" + key + "', using 'String'.");
type = VcfInfoType.String.toString();
}
String infoKey = VcfEntry.vcfInfoKeySafe(DBNSFP_VCF_INFO_PREFIX + key);
vcfFile
.getVcfHeader()
.addLine(
"##INFO=<ID="
+ infoKey
+ ",Number=A,Type="
+ type
+ ",Description=\""
+ fieldsToAdd.get(key)
+ "\">");
}
return false;
}
@Override
public boolean annotate(VcfEntry vcfEntry) {
boolean annotated = false;
Map<String, String> info = new HashMap<>();
// Find annotations for each variant in this VcfEntry
for (Variant var : vcfEntry.variants()) annotated |= annotate(var, info);
// Add annotations to VcfEntry
if (annotated) {
// Sort keys and add them to VcfEntry
ArrayList<String> keys = new ArrayList<>();
keys.addAll(info.keySet());
Collections.sort(keys);
// Add INFO fields
for (String key : keys) {
String infoKey = VcfEntry.vcfInfoKeySafe(DBNSFP_VCF_INFO_PREFIX + key);
vcfEntry.addInfo(infoKey, info.get(key));
}
}
return annotated;
}