Proposing a few changes

[fluhus]

Hi,

First thanks a lot for making this tool. It's super useful in my research on gut metagenomics.

While using it I came up with a few modifications that helped me and I thought could be beneficial to others as well. I'd like to humbly propose them, hoping it can help more users.

Happy to know what you think. I can send you pull requests with the changes that interest you.

1. Speed up overlap lookup - significantly improves performance on large genomes.
2. Add flag for skipping GeneBank output - tbl2asn is slow and may be skippable for some users.
3. Add flag for skipping CRISPR search - the lost sibling of --norrna and --notrna.
4. Add date to log prints - small but helpful, especially for long runs that span days.
5. Make prodigal parallel if in meta mode - meta mode is significantly slower so it can benefit from running in parallel.
6. Add an option for keeping raw prodigal output - prodigal outputs useful information that prokka ignores. This may need a more systematic solution. My hack is a quick way to still get that information.

Note: this is my first time writing perl, so there may be better ways to achieve what I did. Feel free to correct me.

Cheers, Amit