Thanks for the suggestions - I've incorporated those.

Presumably by references you mean something like:

$positions{$file} = \@nreg;
[download]

Then calling subroutines with:

&msatminer::addregion($positions{$file},$start,$stop);
[download]

If so, that would be a quick solution that might allow me to do one thing the code doesn't currently do (and should) — identify points that are found between two close features (there are various biologically interesting cases).