Ensure that multimappers are being removed

[petercombs]

I thought I was doing this, but I'm hitting Lysine tRNA genes on a few different chromosomes, which suggests that I am probably not.

[petercombs]

So this shouldn't be the issue, because CountSNPASE uses the monomap reads, but bcf_call_variants doesn't use monomap-only reads. I should definitely fix that, but gotta figure out how much mapping I'm getting at tRNA genes to begin with. Maybe the reads are long enough to truly only get monomappers, but I'm skeptical.