childsish / sofia Goto Github PK

The entities would greatly benefit from is_a relationships and a overall hierachical structure.

Reimplement the execution engine to enable actions on the whole set. This will allow the integration of command line tools that require the whole set.

This will allow greater generalisation of the steps.

Create a formal definition for entities and directly integrate them into the templates. This requires a few steps:

1. Create a Entity class that actually carries entity information (rename the current to EntityType?).
2. Extend/Update the entities.json file in the template definition to follow new entity definition rules.
3. Implement the template entities in a new "entities" folder.

Useful for fairly universal things such as the genetic codes and molecular weights

Reduce or remove dependency on pysam and htslib for indexing files.