Use a single variable to mark pLS not to be included in TCs #331
Description
It is confusing that in the second pass of the checkHitspLS kernel, as well as in the crossCleanpLS kernel, the triplet and duplicate pLSs are skipped from the checks (for no obvious reason at this stage). This happens because they are in any case not considered for addition to the TCs and, therefore, we don't want to waste time checking something that we are going to drop later in any case.
This coding choice may make sense performance-wise but causes extra difficulties when changing the characteristics of the pLSs to be added in the TCs. For example, to include properly cleaned triplet pLSs in the TCs, one needs to change the same line in 3 (if not more) places.
To facilitate such changes, as well as making the code clearer, it was proposed to add a new variable (or overloading the isDup variable) that is set in one place and marks the pLSs to be skipped from addition to the TCs.