/**
* Merge all of the thread local recalibration tables into a single one.
*
* <p>Reuses one of the recalibration tables to hold the merged table, so this function can only
* be called once in the engine.
*
* @return the merged recalibration table
*/
@Requires("! finalized")
private RecalibrationTables mergeThreadLocalRecalibrationTables() {
if (recalibrationTablesList.isEmpty()) {
recalibrationTablesList.add(
new RecalibrationTables(covariates, numReadGroups, maybeLogStream));
}
RecalibrationTables merged = null;
for (final RecalibrationTables table : recalibrationTablesList) {
if (merged == null)
// fast path -- if there's only only one table, so just make it the merged one
merged = table;
else {
merged.combine(table);
}
}
return merged;
}
