update to use manager
@@ -337,7 +337,7 @@ public class HgvsDeletionCalculator extends HgvsCalculator {
Query query = new Query(GenomeDBAdaptor.QueryParams.REGION.key(), chromosome
+ ":" + genomicCoordinate
+ "-" + (genomicCoordinate + 1));
- substitutingNt = genomeDBAdaptor
+ substitutingNt = genomeManager
.getGenomicSequence(query, new QueryOptions()).getResults().get(0).getSequence().charAt(0);
if (POSITIVE.equals(transcript.getStrand())) {
