Removing WellformedReadFilter from CountReadsSpark

[jamesemery]

I have been burned one too many times by the fact that this count silently filters reads for you. Since there is no logging output printing the number of filtered reads in spark it makes more sense to remove filtering from the tool altogether.

[lbergelson]

This make sense to me.

[codecov-io]

Codecov Report

Merging #5329 into master will decrease coverage by 1.16%.
The diff coverage is 100%.

@@             Coverage Diff              @@
##             master    #5329      +/-   ##
============================================
- Coverage     86.79%   85.62%   -1.17%     
+ Complexity    30124    29844     -280     
============================================
  Files          1843     1843              
  Lines        139480   139481       +1     
  Branches      15376    15376              
============================================
- Hits         121060   119433    -1627     
- Misses        12827    14515    +1688     
+ Partials       5593     5533      -60

Impacted Files	Coverage Δ	Complexity Δ
...lbender/tools/spark/pipelines/CountReadsSpark.java	90.9% <100%> (+0.9%)	5 <1> (+1)	⬆️
...s/GermlineContigPloidyModelArgumentCollection.java	0% <0%> (-100%)	0% <0%> (-4%)
...mlineContigPloidyHybridADVIArgumentCollection.java	0% <0%> (-100%)	0% <0%> (-3%)
...er/utils/python/PythonScriptExecutorException.java	0% <0%> (-100%)	0% <0%> (-1%)
...ments/GermlineCNVHybridADVIArgumentCollection.java	0% <0%> (-100%)	0% <0%> (-3%)
...r/arguments/GermlineCallingArgumentCollection.java	0% <0%> (-100%)	0% <0%> (-4%)
...tools/examples/ExampleStreamingPythonExecutor.java	0% <0%> (-96.67%)	0% <0%> (-8%)
.../walkers/vqsr/CNNScoreVariantsIntegrationTest.java	4.16% <0%> (-95.84%)	2% <0%> (-8%)
...der/utils/python/PythonScriptExecutorUnitTest.java	3.84% <0%> (-94.24%)	1% <0%> (-11%)
...number/arguments/HybridADVIArgumentCollection.java	0% <0%> (-94.12%)	0% <0%> (-3%)
... and 36 more

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