Better default AF for M2 tumor-normal mode; improved M2 STR filter

[davidbenjamin]

@takutosato The first commit gives tumor-normal the old default AF. The second commit is a more intelligent STR contraction filter that improves both sensitivity and precision.

[davidbenjamin]

@takutosato The one test failure occurs because when there is low normal coverage germline risk might get triggered too often. I might need to adjust the default value but it won't affect the code otherwise.

[takutosato]

Look good to me!

[codecov-io]

Codecov Report

Merging #4690 into master will increase coverage by 0.082%.
The diff coverage is 73.333%.

@@               Coverage Diff               @@
##              master     #4690       +/-   ##
===============================================
+ Coverage     79.852%   79.934%   +0.082%     
- Complexity     17336     17432       +96     
===============================================
  Files           1074      1074               
  Lines          62938     63305      +367     
  Branches       10186     10319      +133     
===============================================
+ Hits           50257     50602      +345     
- Misses          8701      8709        +8     
- Partials        3980      3994       +14

Impacted Files	Coverage Δ	Complexity Δ
...der/tools/walkers/mutect/M2ArgumentCollection.java	94.118% <0%> (-5.882%)	3 <2> (+2)
...ls/walkers/mutect/M2FiltersArgumentCollection.java	100% <100%> (ø)	1 <0> (ø)	⬇️
.../tools/walkers/mutect/SomaticGenotypingEngine.java	89.82% <100%> (ø)	65 <0> (ø)	⬇️
...r/tools/walkers/mutect/Mutect2FilteringEngine.java	82.237% <70%> (-0.64%)	41 <0> (+1)
...utils/smithwaterman/SmithWatermanIntelAligner.java	50% <0%> (-30%)	1% <0%> (-2%)
...lkers/ReferenceConfidenceVariantContextMerger.java	95.5% <0%> (+0.243%)	101% <0%> (+30%)	⬆️
...stitute/hellbender/tools/walkers/CombineGVCFs.java	94.631% <0%> (+0.881%)	61% <0%> (+1%)	⬆️
.../discovery/alignment/ContigAlignmentsModifier.java	88.353% <0%> (+1.158%)	50% <0%> (+5%)	⬆️
...park/sv/discovery/alignment/AlignmentInterval.java	94.402% <0%> (+1.362%)	143% <0%> (+59%)	⬆️