/** Is 'fieldName' a per-allele annotation */
boolean isVcfInfoPerAllele(String fieldName) {
// Look up information and cache it
if (vcfInfoPerAllele.get(fieldName) == null) {
VcfHeaderInfo vcfInfo = dbVcf.getVcfHeader().getVcfInfo(fieldName);
boolean isPerAllele =
vcfInfo != null && (vcfInfo.isNumberOnePerAllele() || vcfInfo.isNumberAllAlleles());
vcfInfoPerAllele.put(fieldName, isPerAllele);
}
return vcfInfoPerAllele.get(fieldName);
}
/** Is this a "per-allele + REF" INFO field? */
boolean isVcfInfoPerAlleleRef(String fieldName) {
// Look up information and cache it
if (vcfInfoPerAlleleRef.get(fieldName) == null) {
VcfHeaderInfo vcfInfo = dbVcf.getVcfHeader().getVcfInfo(fieldName);
boolean isPerAlleleRef = (vcfInfo != null && vcfInfo.isNumberAllAlleles());
vcfInfoPerAlleleRef.put(fieldName, isPerAlleleRef);
hasVcfInfoPerAlleleRef |=
isPerAlleleRef; // Do we have any INFO field requiring 'REF' annotation?
}
return vcfInfoPerAlleleRef.get(fieldName);
}
protected void discoverInfoFields() {
if (infoFields == null) infoFields = new HashSet<String>();
// Discover some INFO fields
if (!useAllInfoFields) return;
// Find INFO form VcfHeader
if (dbVcf != null && dbVcf.getVcfHeader() != null) {
for (VcfHeaderInfo vcfInfo : dbVcf.getVcfHeader().getVcfInfo()) {
// Don't add implicit fields at this stage
// Note: They are added if they are found in a VCF entry later
if (!vcfInfo.isImplicit()) {
String infoFieldName = vcfInfo.getId();
infoFields.add(infoFieldName);
// Cache values for future use
isVcfInfoPerAllele(infoFieldName);
isVcfInfoPerAlleleRef(infoFieldName);
}
}
}
}
/** Query database and find results matching 'variant' */
protected Collection<VariantVcfEntry> query(Variant variant) {
// Query database
Collection<VariantVcfEntry> results = dbVcf.query(variant);
// Filter results to match 'variant'
List<VariantVcfEntry> list = new LinkedList<>();
for (VariantVcfEntry dbEntry : results) {
if (match(variant, dbEntry)) {
if (debug)
Gpr.debug("dbEntry matches query\tvariant: " + variant + "\tdbEntry: " + dbEntry);
list.add(dbEntry);
} else {
if (debug)
Gpr.debug("dbEntry does NOT match query\tvariant: " + variant + "\tdbEntry: " + dbEntry);
}
}
if (debug) Gpr.debug("Match query results: " + list.size());
return list;
}
public void setVerbose(boolean verbose) {
this.verbose = verbose;
dbVcf.setVerbose(verbose);
}
public void setDebug(boolean debug) {
this.debug = debug;
dbVcf.setDebug(debug);
}
public void open() {
dbVcf.open();
discoverInfoFields();
}
public void close() {
dbVcf.close();
}