lib: support multiple splice score sources,
@@ -1886,15 +1886,18 @@ public class VariantAnnotationCalculator {
CellBaseDataResult<SpliceScore> spliceScoreResult = spliceCellBaseDataResults.get(i);
if (spliceScoreResult != null && CollectionUtils.isNotEmpty(spliceScoreResult.getResults())) {
for (SpliceScore spliceScore : spliceScoreResult.getResults()) {
+ for (ConsequenceType ct : variantAnnotationList.get(i).getConsequenceTypes()) {
+ List<SpliceScores> selectedScores = new ArrayList<>();
for (SpliceScoreAlternate spliceScoreAlt : spliceScore.getAlternates()) {
if (variantAnnotationList.get(i).getAlternate().equals(spliceScoreAlt.getAltAllele())) {
- for (ConsequenceType ct : variantAnnotationList.get(i).getConsequenceTypes()) {
if (spliceScore.getTranscriptId().equals(ct.getTranscriptId())) {
SpliceScores scores = new SpliceScores(spliceScore.getSource(), spliceScoreAlt.getScores());
- ct.setSpliceScores(Collections.singletonList(scores));
- break;
+ selectedScores.add(scores);
+ }
}
}
+ if (CollectionUtils.isNotEmpty(selectedScores)) {
+ ct.setSpliceScores(selectedScores);
}
}
}
