Breaking Changes
- Uses snakemake instead of internal scheduler code
- Use JSON config instead of large number of command-line arguments
- Use nested translations to allow polycistronic transcripts in annotations file
- Do not use to start header line in mavis tab files
New Features
- Add conversion tool for upgrading v3 annotations files and converting gtf/gff3 files
Improvements
- Upgraded pysam (no longer being used to load vcfs)