Mark prophage regions at the end of contigs

[linsalrob]

Very often contig breaks in draft genomes occur within prophages. This is because the prophage contains repeat regions (like IS elements), the prophage has unusual coverage (e.g. because it is induced during growth/library prep), or they are just downright tricky!

We should mark prophage regions at the end of contigs using different criteria (fewer genes, more hypotheticals, etc) than we use for the rest of the genome. This could potentially assist in recircularizing the genome.