This release contains code used to generate figures in the revised manuscript submission.
Major changes since the previous release:
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Restructured codebase so that figures are created with specific scripts, rather than subcommands from
python -m vacv-plot. -
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.
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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.