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fix consequence types for CNVs with 2 copies #629

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fix consequence types for CNVs with 2 copies #629

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2 changes: 1 addition & 1 deletion ...src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1279,7 +1279,7 @@ private ConsequenceTypeCalculator getConsequenceTypeCalculator(Variant variant)
case CNV:
case COPY_NUMBER_GAIN:
case COPY_NUMBER:
if (variant.getSv().getCopyNumber() == null) {
if (variant.getSv().getCopyNumber() == null || variant.getSv().getCopyNumber() == 2) {
return new ConsequenceTypeGenericRegionCalculator();
} else if (variant.getSv().getCopyNumber() > 2) {
return new ConsequenceTypeCNVGainCalculator();
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