} else {
collapsedDatum.combine( fullDatum ); // using combine instead of increment in order to calculate overall aggregateQReported
}
}
for( int iii = 0; iii < dataCollapsedByCovariate.size(); iii++ ) {
<BUG>if( iii == 0 || !(qscore < IGNORE_QSCORES_LESS_THAN) ) { // use all data for the plot versus reported quality, but not for the other plots versus cycle and etc.
newKey = new ArrayList<Comparable>();
newKey.add( key.get(0) ); // Make a new key with the read group ...
Comparable theCovariateElement = key.get(iii + 1); //           and the given covariate
</BUG>
if( theCovariateElement != null ) {

} else {
collapsedDatum.combine( fullDatum ); // using combine instead of increment in order to calculate overall aggregateQReported
}
}
for( int iii = 0; iii < dataCollapsedByCovariate.size(); iii++ ) {
if( iii == 0 || !(qscore < IGNORE_QSCORES_LESS_THAN) ) { // use all data for the plot versus reported quality, but not for the other plots versus cycle and etc.
covariateCollapsedKey[0] = key[0]; // Make a new key with the read group ...
Object theCovariateElement = key[iii + 1]; //           and the given covariate
