trioeval stuff

[nhartwic]

continuing from #17, I have tried to use trio eval. It too has a bunch of undocumented output fields but lets ignore that.

When you say "father and mother specific counts", you mean count of kmers right? If so, something seems wrong. Meryl results suggest that about 8% of the kmers in my HiC reads are haplotype specific. Yak trioeval is only reporting <0.01% as being haplotype specific. Any idea what is happening here?

To be clear, I have two assemblies, hap1 and hap2. I want to use those for getting haplotype specific kmers, then score each hic read that I have with counts of: hap1 specific, hap2 specific, both, neither.