virsorter.smk - new way to handle contig names that are changed by VirSorter.
reverse_engineer_id_virsorter.pl - perl script used by virsorter.smk to handle name changes
virsorter2.smk - change to use recommended "--high-confidence-only" and "--exclude-lt2gene" options. Also fix the columns to take the predicted prophage coordinates
compare_predictions_to_phages.py - no meaningful change, but some print that were later commented. Can be ignored.
The main changes are as follows: