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EVA-3544 - Fix SPLIT candidate accession #446

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May 10, 2024
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EVA-3544 - Fix SPLIT candidate accession #446

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6 changes: 2 additions & 4 deletions ...n-clustering/src/main/java/uk/ac/ebi/eva/accession/clustering/batch/io/RSMergeWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -423,13 +423,11 @@ private void updateSplitCandidates(ClusteredVariantMergingPolicy.Priority priori
.collect(Collectors.toSet());
// Condition for generating split operation: ensure that there is more than one locus sharing the target RS
if (targetRSDistinctLoci.size() > 1) {
// Use a convention of lowest SS for testability
Long lowestSS = ssClusteredUnderTargetRS.stream().map(InactiveSubDocument::getAccession)
.min(Comparator.naturalOrder()).get();
// The new SPLIT candidate is for rs prioritised.accessionToKeep
SubmittedVariantOperationEntity newSplitCandidateRecord = new SubmittedVariantOperationEntity();
// TODO: Refactor to use common fill method for split candidates generation
// to avoid duplicating reason text and call semantics
newSplitCandidateRecord.fill(EventType.RS_SPLIT_CANDIDATES, lowestSS,
newSplitCandidateRecord.fill(EventType.RS_SPLIT_CANDIDATES, prioritised.accessionToKeep,
"Hash mismatch with " + prioritised.accessionToKeep,
ssClusteredUnderTargetRS);
newSplitCandidateRecord.setId(ClusteringWriter.getSplitCandidateId(newSplitCandidateRecord));
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