Description

Implemented a very basic fitness metric. The fitness of a virus is given by its average risk of infection for a random sample of hosts. Also includes a new parameter fitnessSampleSize that allows the user to specify how many random hosts to sample for fitness calculations.

Fitness values are stored in the .tips file and written as header metadata in the .fasta file of antigen-prime output.

Closes #25

Tests

No unit tests (yet at least) --- but this code use a lot of the base code in antigen.

Checklist:

• The code uses informative and accurate variable and function names
• The functionality is factored out into functions and methods with logical interfaces
• Comments are up to date, document intent, and there are no commented-out code blocks
• Commenting and/or documentation is sufficient for others to be able to understand intent and implementation
• TODOs have been eliminated from the code
• The corresponding issue number (e.g. #278) has been searched for in the code to find relevant notes
• Documentation has been redeployed