Thanks for your input. Unfortunately, this won't work as there isn't a good selection of unique identifiers to use as Keys for the Hash. So, using the code you provide, I'd end up with 23 key-value combinations, when I need 330k :). A hash of arrays would work better, in that I could have the values appended to the arrays for each chromosome, but then getting the data out would be a bit of a nightmare. I will look to cleaning up the globals though, as I was being a bit lazy there :).
EDIT: Actually, 24 combinations, as there are both x and y to consider :).