/** Check that all fields to add are available */
public void checkFieldsToAdd() throws IOException {
// Check that all fields have a descriptor (used in VCF header)
if (verbose) {
for (String filedName : dbNsfp.getFieldNames())
if (fieldsDescription.get(filedName) == null)
System.err.println(
"WARNING: Field (column) '"
+ filedName
+ "' does not have an approriate field descriptor.");
}
// Check that all "field to add" are in the database
for (String fieldKey : fieldsToAdd.keySet())
if (!dbNsfp.hasField(fieldKey))
fatalError("dbNsfp does not have field '" + fieldKey + "' (file '" + dbFileName + "')");
}
/** Initialize annotation process */
@Override
public boolean annotateInit(VcfFileIterator vcfFile) {
this.vcfFile = vcfFile;
// Get database name from config file?
// Note this can happen when invoked a VcfAnnotator (e.g. form ClinEff)
if (dbFileName == null && config != null) {
String configKey = CONFIG_DBNSFP_DB_FILE;
String coordinates = config.getString(Config.KEY_COORDINATES);
if (coordinates != null) configKey += "." + coordinates;
dbFileName = config.getString(configKey);
}
// Check and open dbNsfp
dbNsfp = new DbNsfp(dbFileName);
dbNsfp.setDebug(debug);
dbNsfp.setVerbose(verbose);
dbNsfp.open();
// Initialize fields to annotate
annotateInitFields();
return true;
}
/** 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;
}
/** Initialize fields to annotate */
void annotateInitFields() {
// ---
// Fields to use
// ---
VcfInfoType types[] = dbNsfp.getTypes();
String fieldNames[] = dbNsfp.getFieldNamesSorted();
if (verbose) Timer.showStdErr("Database fields:");
for (int i = 0; i < fieldNames.length; i++) {
String type = (types[i] != null ? types[i].toString() : "String");
fieldsType.put(fieldNames[i], type);
fieldsDescription.put(fieldNames[i], "Field '" + fieldNames[i] + "' from dbNSFP");
if (verbose) System.err.println("\t'" + fieldNames[i] + "'");
}
currentDbEntry = null;
if (inverseFieldSelection) {
// Inverted selection: Start with ALL fields and then remove the ones selected
// Add all fields
Set<String> fields = new HashSet<String>();
fields.addAll(fieldsDescription.keySet());
// Remove selected fields
if (fieldsNamesToAdd != null) {
for (String fn : fieldsNamesToAdd.split(",")) fields.remove(fn);
}
// Sort
ArrayList<String> fieldsSort = new ArrayList<String>();
fieldsSort.addAll(fields);
Collections.sort(fieldsSort);
// Fields to be added
for (String fn : fieldsSort) fieldsToAdd.put(fn, fieldsDescription.get(fn));
} else {
// No fields specified? Use default list of fields to add
if (fieldsNamesToAdd == null) fieldsNamesToAdd = DEFAULT_FIELDS_NAMES_TO_ADD;
// Add them to the list
for (String fn : fieldsNamesToAdd.split(",")) {
if (fieldsDescription.get(fn) == null) {
// Field not found
if (fieldsNamesToAdd == DEFAULT_FIELDS_NAMES_TO_ADD) {
// Was it one of the default fields? => Ignore
if (verbose)
Timer.showStdErr("Warning: Default field name '" + fn + "' not found, ignoring");
} else usage("Error: Field name '" + fn + "' not found");
} else fieldsToAdd.put(fn, fieldsDescription.get(fn)); // Add field
}
}
// Show selected fields
if (verbose) {
ArrayList<String> fieldsSort = new ArrayList<String>();
fieldsSort.addAll(fieldsToAdd.keySet());
Collections.sort(fieldsSort);
Timer.showStdErr("Fields to add:");
for (String fn : fieldsSort) System.err.println("\t\t\t" + fn);
}
}
@Override
public boolean annotateFinish() {
if (dbNsfp != null) dbNsfp.close();
return true;
}
