Revised manuscript submission

This release contains code used to generate figures in the revised manuscript submission.

Major changes since the previous release:

1. Restructured codebase so that figures are created with specific scripts, rather than subcommands from python -m vacv-plot.

2. Cleaned up potentially confusing variable names throughout the codebase; namely, changing "genomes" to "arrays," to better reflect the fact that the code only considers reads aligned to the K3L locus, and doesn't analyze any other loci in the genome.

3. Updated README to include instructions for reproducing new supplementary figures in the manuscript, and provided accession/DOI information for aligned BAM files that are now uploaded to the SRA/Zenodo.

Manuscript submission

This release contains code used to generate figures for manuscript submission.