Bakta

This is the 3rd v1.0 release candidate introducing expert annotation systems incorporating AMRFinderPlus, BlastRules and VFDB.

Bug fixes over rc2:
- several INSDC qualifier issues (1d0f6dcc8a388935881bcdb001507fda05076c27 1d0f6dcc8a388935881bcdb001507fda05076c27)
- INSDC tRNA anticodon and pseudo qualifier issues (ff668d5ee3b8fbdda5f5eddb01b5c033da550c61 fb03559c160bcf921fea1931b6c3c8ede406f57d)
- lacking python `__init__` file (0560102fe7c1fc57fe2900bc75dde955e827d976)

Plus several minor bug fixes & improvements.

This is the 2nd v1.0 release candidate introducing expert annotation systems incorporating AMRFinderPlus, BlastRules and VFDB.

Improvements over rc1:
- added parameter argument checks
- added more tests
- updated usage and readme

Bug fixes:
- fixed name of main entry module

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.