/**
* 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;
}
/**
* Update the recalibration statistics using the information in recalInfo
*
* @param recalInfo data structure holding information about the recalibration values for a single
* read
*/
@Requires("recalInfo != null")
public void updateDataForRead(final ReadRecalibrationInfo recalInfo) {
final GATKSAMRecord read = recalInfo.getRead();
final ReadCovariates readCovariates = recalInfo.getCovariatesValues();
final RecalibrationTables tables = getUpdatableRecalibrationTables();
final NestedIntegerArray<RecalDatum> qualityScoreTable = tables.getQualityScoreTable();
for (int offset = 0; offset < read.getReadBases().length; offset++) {
if (!recalInfo.skip(offset)) {
for (final EventType eventType : EventType.values()) {
final int[] keys = readCovariates.getKeySet(offset, eventType);
final int eventIndex = eventType.ordinal();
final byte qual = recalInfo.getQual(eventType, offset);
final double isError = recalInfo.getErrorFraction(eventType, offset);
RecalUtils.incrementDatumOrPutIfNecessary(
qualityScoreTable, qual, isError, keys[0], keys[1], eventIndex);
for (int i = 2; i < covariates.length; i++) {
if (keys[i] < 0) continue;
RecalUtils.incrementDatumOrPutIfNecessary(
tables.getTable(i), qual, isError, keys[0], keys[1], keys[i], eventIndex);
}
}
}
}
}
/**
* 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;
}
