Add a --min-fragment-length argument to FragmentLengthReadFilter

[droazen]

Also improved the existing tests for FragmentLengthReadFilter

Resolves #5884

[droazen]

@samuelklee or @mwalker174 please review, as this feature originated as a request for the CNV pipeline (#5884)

[mwalker174]

👍 Thanks @droazen - this looks good to me.

[codecov-io]

Codecov Report

Merging #5886 into master will increase coverage by 0.009%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #5886       +/-   ##
===============================================
+ Coverage     86.823%   86.833%   +0.009%     
- Complexity     32291     32297        +6     
===============================================
  Files           1991      1991               
  Lines         149120    149202       +82     
  Branches       16477     16480        +3     
===============================================
+ Hits          129471    129556       +85     
+ Misses         13636     13633        -3     
  Partials        6013      6013

Impacted Files	Coverage Δ	Complexity Δ
...lbender/cmdline/ReadFilterArgumentDefinitions.java	0% <ø> (ø)	0 <0> (ø)	⬇️
...ender/engine/filters/FragmentLengthReadFilter.java	100% <100%> (ø)	5 <0> (+1)	⬆️
...nder/engine/filters/ReadFilterLibraryUnitTest.java	100% <100%> (ø)	62 <3> (+3)	⬆️
...ithwaterman/SmithWatermanIntelAlignerUnitTest.java	60% <0%> (ø)	2% <0%> (ø)	⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java	80% <0%> (+30%)	3% <0%> (+2%)	⬆️

[samuelklee]

Thanks for adding this!