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ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
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Feature: Simplify Genotype Likelihoods #225

Closed reedacartwright closed 7 years ago

reedacartwright commented 7 years ago

Using a mixture of 2 DM for genotype likelihoods ended up being too complicated from the standpoint of the end user. The gamma parameter was too complicated. The solution is to change the model to a single dirichlet multinomial, which allows the command line parameters to be simplified.

The benefit is that calculating genotype likelihoods becomes faster.

While creating unit tests, bugs in the calculation of haploid genotype likelihoods were discovered and fixed. Other tests were adjusted to reflect the new genotype likelihood model and default parameters.

This pull request also includes improvements to some additional unit tests that began on another branch, but needed to be merged into this one.

codecov[bot] commented 7 years ago

Codecov Report

Merging #225 into develop will decrease coverage by 0.42%. The diff coverage is 83%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #225      +/-   ##
===========================================
- Coverage    67.99%   67.57%   -0.43%     
===========================================
  Files           68       68              
  Lines         6384     6440      +56     
  Branches      1123     1126       +3     
===========================================
+ Hits          4341     4352      +11     
- Misses        1576     1630      +54     
+ Partials       467      458       -9
Impacted Files Coverage Δ
src/include/dng/probability.h 100% <ø> (ø) :arrow_up:
src/include/dng/depths.h 94.07% <ø> (ø) :arrow_up:
src/lib/ad.cc 67.66% <ø> (ø) :arrow_up:
src/lib/task/loglike.cc 0% <0%> (ø) :arrow_up:
src/lib/probability.cc 46.57% <100%> (ø) :arrow_up:
src/include/dng/task/call.xmh 100% <100%> (ø) :arrow_up:
src/include/dng/utility.h 88% <100%> (+4.32%) :arrow_up:
src/include/dng/genotyper.h 100% <100%> (+13.33%) :arrow_up:
src/include/dng/task/loglike.xmh 100% <100%> (ø) :arrow_up:
src/lib/task/call.cc 81.3% <100%> (+0.32%) :arrow_up:
... and 5 more

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