IIUC, in today's world the way you find mates is you look for reads that share a qname and contig, and match the specified position. Not very elegant from first principles, but changing it adds a bunch of burden to repository implementors that I'm very leery of doing in v0.5. (Since they'd have to build a whole new index.)

I'm inclined to leave it as proposed for now, and know we'll be changing it (e.g. by adding alternate options for specifying mate pairs) down the road. I'm open to other suggestions, but every time we tried it got hairy; this approach by @lh3 feels like a nice balance between the past and the future.