positive-containing DFE from Zhen et al 2021 (GammaPos_Z21, HomSap and DroMel)

[petrelharp]

This is as recommended by @klohmueller over in #1469. It's really just Huber et al's Gamma_H17 except a proportion p of the changes are beneficial with coefficient s; the paper shows that p and s are highly confounded (and ps can be estimated better); but these are the MLE values. These values are using divergence to chimp.

Kirk said:

For a DFE with positive selection in humans—we could use this one from Table S6 of Zhen et al. (2021). This DFE is for nonsynonymous mutations. We inferred 1.55% of nonsynonymous mutations were positively selected in humans with a s of 0.0001124605. The remaining nonsynonymous mutations came from a DFE for negative selection (parameters for this are in Table S3). The shape parameter is 0.19 and the scale (beta) in terms of s is 0.074.

What I've implemented is this, and I've verified all those parameters above - so, I figure this is actually mostly QC'ed (since Kirk pulled out those numbers and I verified them). So, I'm tempted to just put in the QC code also - but that wouldn't catch coding errors.

Edit: I've also added the estimated one for DroMelfrom Table S6 as above.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.84%. Comparing base (6218f3d) to head (8aba4cf).

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  Lines        4584     4616   +32     
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+ Hits         4577     4609   +32     
  Misses          3        3           
  Partials        4        4           

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