Dynamic error rate fix

[standage]

In the process of evaluating whether kevlar was correctly calculating the probability of a k-mer abundance when conditioned on a 0/0 genotype, we reformulated the calculation. We now have the following.

Here, mu is the mean coverage, epsilon is the sequencing error rate, k_a is the observed k-mer abundance (alternate allele), and r is the copy number of the corresponding reference allele in the reference genome. In log space the calculation is:

This formulation changed many of the probabilities in the test suite, but for the most part these were slight changes. There was only 1 substantial change, but it didn't end up affecting the overall likelihood score. Tests on simulated data are pending.

[codecov-io]

Codecov Report

Merging #363 into master will increase coverage by 0.04%. The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #363      +/-   ##
==========================================
+ Coverage   96.79%   96.83%   +0.04%     
==========================================
  Files          48       48              
  Lines        2899     2902       +3     
  Branches      537      537              
==========================================
+ Hits         2806     2810       +4     
  Misses         58       58              
+ Partials       35       34       -1

Impacted Files	Coverage Δ
kevlar/cli/simlike.py	100% <ø> (ø)	:arrow_up:
kevlar/simlike.py	99.12% <100%> (+0.46%)	:arrow_up:

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