Fixed M2 bug for germline resources with AF=.

[davidbenjamin]

Closes #5391.

@takutosato this will make several users happy: https://gatkforums.broadinstitute.org/gatk/discussion/13467/mutect2-pipeline-fails-for-some-inputs#latest, https://gatkforums.broadinstitute.org/gatk/discussion/12618/run-mutect2-in-gatk-4-0-4-0-with-an-error-java-lang-numberformatexception-for-input-string

Looping in @bhanugandham

[codecov-io]

Codecov Report

Merging #5442 into master will increase coverage by <.01%.
The diff coverage is 83.33%.

@@             Coverage Diff              @@
##             master    #5442      +/-   ##
============================================
+ Coverage        87%      87%   +<.01%     
- Complexity    31171    31175       +4     
============================================
  Files          1908     1908              
  Lines        143988   144007      +19     
  Branches      15925    15927       +2     
============================================
+ Hits         125279   125297      +18     
- Misses        12951    12953       +2     
+ Partials       5758     5757       -1

Impacted Files	Coverage Δ	Complexity Δ
...itute/hellbender/tools/walkers/SplitIntervals.java	88.88% <ø> (ø)	6 <0> (ø)	⬇️
.../walkers/mutect/GermlineProbabilityCalculator.java	93.54% <100%> (+3.22%)	12 <2> (ø)	⬇️
...r/tools/walkers/mutect/Mutect2IntegrationTest.java	94.48% <100%> (+0.11%)	72 <1> (+1)	⬆️
...hellbender/tools/walkers/mutect/Mutect2Engine.java	89.88% <66.66%> (-1.26%)	63 <3> (+3)
...utils/smithwaterman/SmithWatermanIntelAligner.java	50% <0%> (-30%)	1% <0%> (-2%)
...ithwaterman/SmithWatermanIntelAlignerUnitTest.java	60% <0%> (ø)	2% <0%> (ø)	⬇️
...oadinstitute/hellbender/utils/gcs/BucketUtils.java	81.09% <0%> (+0.6%)	42% <0%> (ø)	⬇️
...walkers/haplotypecaller/AssemblyRegionTrimmer.java	62.72% <0%> (+2.72%)	20% <0%> (+2%)	⬆️

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