Providing counts for supporting alt reads in the validation normal.

[LeeTL1220]

• ValidateBasicSomaticShortMutations will now provide a count of supporting alt alleles in the validation normals. This value does not affect the validation status. Closes ValidateBasicSomaticShortMutations will validate variants with reads in the validation normal #5059
• Note that there are indels that will not be caught by this functionality. See GATKProtectedVariantContextUtils.chooseAlleleForRead(...) will not recognize equivalent alleles #5061

[LeeTL1220]

@davidbenjamin Testing failure is transient. Please review...

[codecov-io]

Codecov Report

Merging #5062 into master will decrease coverage by <.001%.
The diff coverage is 100%.

@@              Coverage Diff               @@
##             master     #5062       +/-   ##
==============================================
- Coverage     86.35%   86.349%   -<.001%     
- Complexity    28824     28826        +2     
==============================================
  Files          1791      1791               
  Lines        133601    133619       +18     
  Branches      14920     14920               
==============================================
+ Hits         115364    115379       +15     
- Misses        12834     12837        +3     
  Partials       5403      5403

Impacted Files	Coverage Δ	Complexity Δ
...bender/utils/GATKProtectedVariantContextUtils.java	65.746% <ø> (ø)	61 <0> (ø)	⬇️
...ion/basicshortmutpileup/PowerCalculationUtils.java	96.667% <100%> (+1.429%)	18 <7> (+3)	⬆️
...tmutpileup/BasicSomaticShortMutationValidator.java	62.5% <100%> (+1.974%)	5 <0> (ø)	⬇️
...ion/basicshortmutpileup/BasicValidationResult.java	96.774% <100%> (+0.222%)	16 <2> (+1)	⬆️
...tmutpileup/ValidateBasicSomaticShortMutations.java	83.636% <100%> (+0.15%)	19 <0> (ø)	⬇️
...dateBasicSomaticShortMutationsIntegrationTest.java	100% <100%> (ø)	5 <0> (ø)	⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java	50% <0%> (-30%)	1% <0%> (-2%)
...ithwaterman/SmithWatermanIntelAlignerUnitTest.java	60% <0%> (ø)	2% <0%> (ø)	⬇️

[davidbenjamin]

Looks fine. Are you punting the decision as to how the normal alt count affects the validation status downstream?