Using adaptive pruning in mitochondria pipeline

[meganshand]

This uses the new defaults with adaptive pruning in version 4.1.0.0 in Mutect and removes the old ad hoc pruning argument. @ldgauthier can you please take a look when you get a chance?

[codecov-io]

Codecov Report

Merging #5669 into master will decrease coverage by 0.003%.
The diff coverage is n/a.

@@              Coverage Diff               @@
##             master     #5669       +/-   ##
==============================================
- Coverage     87.05%   87.047%   -0.003%     
+ Complexity    31700     31696        -4     
==============================================
  Files          1938      1938               
  Lines        146097    146097               
  Branches      16128     16128               
==============================================
- Hits         127178    127173        -5     
- Misses        13033     13039        +6     
+ Partials       5886      5885        -1

Impacted Files	Coverage Δ	Complexity Δ
...utils/smithwaterman/SmithWatermanIntelAligner.java	50% <0%> (-30%)	1% <0%> (-2%)
...tools/walkers/haplotypecaller/graphs/SeqGraph.java	87.059% <0%> (-2.353%)	23% <0%> (-2%)
...ools/walkers/haplotypecaller/graphs/BaseGraph.java	82.49% <0%> (-0.389%)	94% <0%> (ø)
...ithwaterman/SmithWatermanIntelAlignerUnitTest.java	60% <0%> (ø)	2% <0%> (ø)	⬇️
...nder/utils/runtime/StreamingProcessController.java	67.773% <0%> (+0.474%)	33% <0%> (ø)	⬇️

[ldgauthier]

Looks good!