Sofia

Domain templates release
- SoFIA can now support multiple templates. Each template is stored in a separate folder in the templates directory.
- Custom indexing relieves the pysam dependency. pysam is still supported, but fasta files and most column based formats are now supported. As it is difficult to get pysam working on Windows, this should make SoFIA relatively platform independent.
- Extensive testing is required to ensure everything works.

- Enabled python string formatting in entity request
- Fixed many small bugs in the actions
- Fixed amino_acid_variant formatting

Entity Update

Major points:
- The user now requests entities on the command line, not the actions that produce them
- The lhc-python library has been embedded in the project.

- Implemented a heuristic at each step that yields only solutions that have the minimum extra number of resources
- More renaming

Fixed some rather urgent bugs
- Finished renaming framework
- Added None check to feature: GetDownstream1000

SoFIA (Software for the Flexible Integration of Annotation)

The first release of SoFIA.
https://github.com/childsish/sofia/releases/latest

Features
- Automatic workflow resolution
- Extensible features
- Automatic identifier resolution (entity attribute conversion)