Qual = 0 sites don't count as polymorphic for GVCF mode

[davidbenjamin]

@ldgauthier This is for #4614.

[codecov-io]

Codecov Report

Merging #4967 into master will increase coverage by 0.005%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #4967       +/-   ##
===============================================
+ Coverage     80.789%   80.793%   +0.005%     
- Complexity     17945     17947        +2     
===============================================
  Files           1094      1094               
  Lines          64524     64524               
  Branches       10392     10392               
===============================================
+ Hits           52128     52131        +3     
+ Misses          8374      8371        -3     
  Partials        4022      4022

Impacted Files	Coverage Δ	Complexity Δ
.../walkers/genotyper/afcalc/AFCalculationResult.java	67.164% <100%> (ø)	20 <0> (ø)	⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java	80% <0%> (+30%)	3% <0%> (+2%)	⬆️

[ldgauthier]

Lovely. Thanks for the explanation in the comments. When do you want to change -stand-call-conf in GenotypeCalculationArgumentCollection? It will probably break a bunch of tests, but you could also change the test commands to set it back to 10.

[davidbenjamin]

I was assuming I would change the default in the same PR that makes new qual default.

[ldgauthier]

Fair point. I'll try to help remember.

[davidbenjamin]

Is this PR good to merge then?

[ldgauthier]

👍