Refactor

[kwkroll32]

The main mucor.py could use a good refactoring. There are a lot of little, specific functions that would be cleaner and more logical as part of the separate class files.

Goals:

1. move class-specific functions into the respective class files
2. reduce the number of arguments to (and returned by) these functions
3. reduce the length and complexity of mucor.py and sub-functions

Bonus:

1. it would be easier to unit test smaller, self-contained pieces
2. better suited to take advantage of object oriented programming

[jblachly]

Agree 100% should be refactored.
We need to set some milestones for 2.0.

I recently realized that mucor was responsible for establishing an entirely new category on OmicsTools:
https://omictools.com/variant-aggregation-summarization-category
...and we should carry on in that spirit of innovation.

Please create one enhancement issue per goal, and we can leave this issue open as meta discussion.