Closed standage closed 5 years ago
Merging #363 into master will increase coverage by
0.04%
. The diff coverage is100%
.
@@ 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: |
Continue to review full report at Codecov.
Legend - Click here to learn more
Δ = absolute <relative> (impact)
,ø = not affected
,? = missing data
Powered by Codecov. Last update 0efd11c...e6b5f9c. Read the comment docs.
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, ka 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.