/**
* 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);
}
}
}
}
}
private void initTargetCall(
int aTargetCallNo, Class<?> aCallClass, Class<?> aOutClass, Class<?> aEventClass) {
EventType eventKey = EventTypesFactory.get().toType(aEventClass);
int eventIndex = eventKey.ordinal();
List<CallType> callTargets = mEvents.get(eventIndex);
//
CallType callTarget = CallTypesFactory.get().toType(aCallClass);
callTargets.add(callTarget);
}
public List<CallType> getTargets(EventType aEventType) {
int eventIndex = aEventType.ordinal();
return mEvents.get(eventIndex);
}