Hayden Metsky

Sure, let's talk about this -- it's not so trivial. I haven't yet run the update from #356 so I'm not certain, but this is something I had in mind...

I think that's one reasonable option. I'm not sure how vphaser works and easy it would be to make that change. One other option to consider is for the `map_reads_to_self`...

Why is it in the wrong coordinate space? I thought the opposite, that it's the coordinate space we want the coverage in. Here's how I understood it, but let me...