@Override
public boolean evaluate(Alignment align) {
// if has splice junctions --> return false
if (!align.getSpliceConnections().isEmpty()) {
return false;
}
return true;
}
@Override
public boolean evaluate(Alignment align) {
return ((align.isPaired() && align.getMappingQuality() >= minPairedEndQuality)
|| (!align.isPaired() && align.getMappingQuality() >= minSingleEndQuality));
}