Bakta

This is a `v1.0` release candidate introducing expert annotation systems incorporating AMRFinderPlus, BlastRules and VFDB.

Further improvements:
- db download logic
- parallelized sORF overlap filter
- support for EMBL flat file output
- replicon files can also be provided as csv
- more integration tests added
- several code reviews & optimizations

Bug fixes:
- fix max sORF length to 29

Improvements:

- analysis & output of hypothetical proteins added (pfam detection & calculation of sequence statistics)
- improved CI
- improved DB compilation process
- added annotation summary to GenBank output files
- added CWL file

Bug fixes:
- fix error msgs

**Improvements**:
- automated integration tests added
- genome & plasmid test sequences added
- massively improved fasta output performance
- several genbank flat file output improvements
- code reviews
- adhere to translation table in sORF detection

**Bug fixes**:
- fix annotations of truncated CDS
- fix truncated CDS positions in GenBank

Fix breaking bug in annotation statistics.

This is a patch release comprising the following fixes:
- fix Prodigal training file logic (creation & usage)
- fix coding density calculation on edge features

as well as some minor improvements:
- introduce `omit_readlock` PRAGMA for SQLite queries
- add genome completeness info to `JSON` output

The first public release for broad testing & debugging.