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At the moment, the first "Toy Example" reads from a .vcz file but then when setting ancestral states assumes that these variants have 0-based positions. However, I thought that VCF files were basically not allowed to be 0-based, so this is might be confusing to most users, who will pretty much always be using 1-based indexing, I imagine.
Should we simply assume that example_data.vcz is 1-based, and hence append a padding character to the FASTA string? The example code is there, just commented out, so it's a trivial change.
I'm tidying this bit of the manual, so can implement this if that seems like a good idea.