fix join aligner not setting scans
@@ -218,6 +218,9 @@ public class JoinAlignerTask extends AbstractTask {
.max(Comparator.comparingLong(e -> e.getValue())).get().getKey();
leftoverFlists.remove(nextBaseList);
+ nextBaseList.getRawDataFiles().forEach(
+ file -> alignedFeatureList.setSelectedScans(file, nextBaseList.getSeletedScans(file)));
+
// we add a new set of unaligned rows to the feature list that we can align on.
List<FeatureListRow> nextBaseRows = new ArrayList<>(
leftoverRows.stream().filter(row -> row.getFeatureList().equals(nextBaseList)).map(
