lib: take into account the variant type: COPY_NUMBER, #TASK-284
@@ -1262,8 +1262,8 @@ public class VariantAnnotationCalculator {
case MNV:
return new ConsequenceTypeMNVCalculator(genomeManager);
case CNV:
-// case COPY_NUMBER_GAIN:
-// case COPY_NUMBER:
+ case COPY_NUMBER_GAIN:
+ case COPY_NUMBER:
if (variant.getSv().getCopyNumber() == null) {
return new ConsequenceTypeGenericRegionCalculator();
} else if (variant.getSv().getCopyNumber() > 2) {
@@ -1471,8 +1471,8 @@ public class VariantAnnotationCalculator {
regionList.add(new Region(variant.getChromosome(), variant.getStart(), variant.getStart()));
break;
case CNV:
-// case COPY_NUMBER_GAIN:
-// case COPY_NUMBER:
+ case COPY_NUMBER_GAIN:
+ case COPY_NUMBER:
if (imprecise) {
regionList.add(new Region(variant.getChromosome(), variant.getStart() - cnvExtraPadding,
variant.getStart() + cnvExtraPadding));
