hotfix-4.5.x: imprecise queries by variant now double-check that all Variant.sv.getCi* fields are != null before continuing
@@ -88,7 +88,11 @@ public interface VariantDBAdaptor<T> extends FeatureDBAdaptor<T> {
// if (VariantType.CNV.equals(variant.getType())) {
// Queries for CNVs,SVs are different from simple short variants queries
- if (variant.getSv() != null) {
+ if (variant.getSv() != null
+ && variant.getSv().getCiStartLeft() != null
+ && variant.getSv().getCiStartRight() != null
+ && variant.getSv().getCiEndLeft() != null
+ && variant.getSv().getCiEndRight() != null) {
query = new Query(QueryParams.CHROMOSOME.key(), variant.getChromosome());
// Imprecise queries can just be enabled for structural variants providing CIPOS positions. Imprecise queries
// can be disabled by using the imprecise=false query option
