Fix overfiltering in M2 in GGA alleles with no reads

[davidbenjamin]

Closes #5695.

[LeeTL1220]

If you are sure that there is no downstream issues with doing this. then merge away.

[LeeTL1220]

Are you sure you want to do this for all runs of M2, not just the GGA runs?

[LeeTL1220]

Just seems like there could be a downstream effect.

[davidbenjamin]

Yes, because any allele with no reads should have no say either way. But also, an allele with no reads can't occur outside of GGA mode.

[codecov-io]

Codecov Report

Merging #5743 into master will decrease coverage by 6.821%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #5743       +/-   ##
===============================================
- Coverage     87.079%   80.259%   -6.821%     
+ Complexity     31918     30263     -1655     
===============================================
  Files           1942      1942               
  Lines         146909    146909               
  Branches       16242     16242               
===============================================
- Hits          127927    117907    -10020     
- Misses         13062     23290    +10228     
+ Partials        5920      5712      -208

Impacted Files	Coverage Δ	Complexity Δ
...bender/tools/walkers/annotator/MappingQuality.java	100% <100%> (ø)	7 <2> (ø)	⬇️
...llbender/tools/walkers/annotator/ReadPosition.java	87.5% <100%> (ø)	8 <2> (ø)	⬇️
...kers/filters/VariantFiltrationIntegrationTest.java	0.826% <0%> (-99.174%)	1% <0%> (-25%)
...dorientation/CollectF1R2CountsIntegrationTest.java	0.917% <0%> (-99.083%)	1% <0%> (-12%)
.../walkers/bqsr/BaseRecalibratorIntegrationTest.java	1.031% <0%> (-98.969%)	1% <0%> (-7%)
...ers/vqsr/FilterVariantTranchesIntegrationTest.java	1.053% <0%> (-98.947%)	1% <0%> (-5%)
...s/variantutils/VariantsToTableIntegrationTest.java	1.205% <0%> (-98.795%)	1% <0%> (-20%)
...ientation/ReadOrientationModelIntegrationTest.java	1.667% <0%> (-98.333%)	1% <0%> (-5%)
...on/FindBreakpointEvidenceSparkIntegrationTest.java	1.754% <0%> (-98.246%)	1% <0%> (-6%)
...bender/tools/spark/PileupSparkIntegrationTest.java	2.041% <0%> (-97.959%)	2% <0%> (-13%)
... and 154 more