Modify optimize_lfn_variant_replicate_specific.tsv and optimize_lfn_variant_specific.tsv

[meglecz]

At the moment optimize_lfn_variant_replicate_specific.tsv and optimize_lfn_variant_specific.tsv contains all variants that have 'delete' occurrence in the know_occurrences.tsv

• Do not print out lines, if lfn_variant_replicate_cutoff > max_lfn_variant_replicate_cutoff (new variable; 0.05 by default)
• Do not print out lines, if N_i (or N_ik) < min_variant_read_count (new variable; 1000 by default)
• If possible, flag lines if they are eliminated using the best combination of lfn_read_count_cutoff and lfn_variant_cutoff (lfn_variant_replicate_cutoff) suggested by optimize_lfn_read_count_and_lfn_variant.tsv (or optimize_lfn_read_count_and_lfn_variant_replicate.tsv)