final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalDataManager.EVENT_TYPE_COLUMN_NAME));
tempCOVarray[3] = event.index;
recalibrationTables.getTable(RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + covIndex).put(getRecalDatum(reportTable, i, false), tempCOVarray);
}
}
<BUG>private void parseQualityScoreTable(final GATKReportTable reportTable, final IntegerIndexedNestedHashMap<RecalDatum> qualTable) {
</BUG>
for ( int i = 0; i < reportTable.getNumRows(); i++ ) {
final Object rg = reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME);
tempQUALarray[0] = requestedCovariates[0].keyFromValue(rg);

final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalDataManager.EVENT_TYPE_COLUMN_NAME));
tempCOVarray[3] = event.index;
recalibrationTables.getTable(RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + covIndex).put(getRecalDatum(reportTable, i, false), tempCOVarray);
}
}
private void parseQualityScoreTable(final GATKReportTable reportTable, final NestedIntegerArray<RecalDatum> qualTable) {
for ( int i = 0; i < reportTable.getNumRows(); i++ ) {
final Object rg = reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME);
tempQUALarray[0] = requestedCovariates[0].keyFromValue(rg);
