Read filter for unmapped reads and their mates

[meganshand]

This read filter removes unnmapped reads and reads with unmapped mates. When used in combination with MateOnSameContigOrNoMappedMateReadFilter this subsets down to reads only on chrM whose mate is also on chrM. If we only used the MateOnSameContigOrNoMappedMateReadFilter we end up with reads whose mate is unmapped still in the BAM, but not the unmapped read, which causes problems downstream in the mitochondria pipeline. This read filter will make the subsetting step faster when we no longer need the NuMTs.

I would really appreciate this getting in before the next release (on Tuesday). (fyi @droazen) @ldgauthier @jsotobroad

[codecov-io]

Codecov Report

Merging #5826 into master will increase coverage by <.01%.
The diff coverage is 90.9%.

@@             Coverage Diff              @@
##             master    #5826      +/-   ##
============================================
+ Coverage     87.04%   87.04%   +<.01%     
- Complexity    32153    32155       +2     
============================================
  Files          1975     1975              
  Lines        147415   147426      +11     
  Branches      16225    16226       +1     
============================================
+ Hits         128315   128329      +14     
+ Misses        13185    13181       -4     
- Partials       5915     5916       +1

Impacted Files	Coverage Δ	Complexity Δ
...nder/engine/filters/ReadFilterLibraryUnitTest.java	100% <100%> (ø)	59 <1> (+1)	⬆️
...e/hellbender/engine/filters/ReadFilterLibrary.java	94.56% <66.66%> (-0.95%)	1 <0> (ø)
...utils/smithwaterman/SmithWatermanIntelAligner.java	90% <0%> (+10%)	3% <0%> (ø)	⬇️
...ithwaterman/SmithWatermanIntelAlignerUnitTest.java	90% <0%> (+30%)	2% <0%> (ø)	⬇️

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[ldgauthier]

👍