/**
* Finalize, if appropriate, all derived data in recalibrationTables.
*
* <p>Called once after all calls to updateDataForRead have been issued.
*
* <p>Assumes that all of the principal tables (by quality score) have been completely updated,
* and walks over this data to create summary data tables like by read group table.
*/
public void finalizeData() {
if (finalized) throw new IllegalStateException("FinalizeData() has already been called");
// merge all of the thread-local tables
finalRecalibrationTables = mergeThreadLocalRecalibrationTables();
final NestedIntegerArray<RecalDatum> byReadGroupTable =
finalRecalibrationTables.getReadGroupTable();
final NestedIntegerArray<RecalDatum> byQualTable =
finalRecalibrationTables.getQualityScoreTable();
// iterate over all values in the qual table
for (final NestedIntegerArray.Leaf<RecalDatum> leaf : byQualTable.getAllLeaves()) {
final int rgKey = leaf.keys[0];
final int eventIndex = leaf.keys[2];
final RecalDatum rgDatum = byReadGroupTable.get(rgKey, eventIndex);
final RecalDatum qualDatum = leaf.value;
if (rgDatum == null) {
// create a copy of qualDatum, and initialize byReadGroup table with it
byReadGroupTable.put(new RecalDatum(qualDatum), rgKey, eventIndex);
} else {
// combine the qual datum with the existing datum in the byReadGroup table
rgDatum.combine(qualDatum);
}
}
finalized = true;
}
