Final figure generation updates prior to publication

Two minor updates to ensure manuscript can be reproduced on a fresh clone of the repository.

• fixed pandas syntax when reading in genotype file for QTL mapping
• remove epoch covariate from linear model predicting C>A fractions as function of generation time

Minor updates prior to publication

Very minor changes to code prior to final acceptance at journal.

• fixed import statements in two scripts
• minor formatting changes
• updated method for converting between BXD line identifiers to be more pythonic

initial release of manuscript code for archive

Initial release of manuscript code -- purpose is to generate a DOI using Zenodo.