v1.0-rc1

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

v0.5 - Hypotheticals: rule them all(most)

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

v0.4 - Let there be tests...

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

v0.3.2

Fix breaking bug in annotation statistics.

Patching the first bugs

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

Initial Release

The first public release for broad testing & debugging.