Added command-line option for distant cassette-side seqs in one mutant.

Added command-line option for the max readcount ratio that determines
whether only the variant position or the whole mutant will be removed -
-R/--max_cassette_side_ratio_to_ignore in mutant_count_aln_IB+RISCC.py,
propagated to add_RISCC_alignment_files_to_data and to
mutant.decide_and_check_position.

Also updated add_RISCC_alignment_files_to_data docstring.