filter_alignment.py is "lying" to us:

• filter_by_score and filter_by_qlength only select the best alignment for each marker. This is done to remove multi-alignment case but not for real filtering.

• Order of filters could be improved but we need for that to regroup all the filtering operation in the same place in the code.

We also want to make new and more clearer filters and not remove immediatly in the files, markers that are filtered.