Add trimming support for ReadsToDistmap

[magicDGS]

• Move TrimAndFilterPipeline to utils package to re-use in other tools
• Extract TrimmerArgumentCollection to allow hiding some arguments
• Add trimming support to ReadsToDistmap (closes #343) using refactored code

[codecov[bot]]

Codecov Report

Merging #347 into master will increase coverage by 0.181%. The diff coverage is 97.5%.

@@               Coverage Diff               @@
##              master      #347       +/-   ##
===============================================
+ Coverage     92.403%   92.585%   +0.181%     
- Complexity       791       816       +25     
===============================================
  Files             79        83        +4     
  Lines           2251      2306       +55     
  Branches         248       250        +2     
===============================================
+ Hits            2080      2135       +55     
  Misses           132       132               
  Partials          39        39

Impacted Files	Coverage Δ	Complexity Δ
...g/magicdgs/readtools/tools/trimming/TrimReads.java	97.015% <ø> (ø)	16 <0> (ø)	:arrow_down:
...eadtools/utils/trimming/TrimAndFilterPipeline.java	100% <ø> (ø)	17 <0> (?)
...distmap/DistmapFilterPluginArgumentCollection.java	100% <100%> (ø)	4 <4> (?)
...istmap/DistmapTrimmerPluginArgumentCollection.java	100% <100%> (ø)	4 <4> (?)
...gicdgs/readtools/tools/distmap/ReadsToDistmap.java	96.552% <100%> (+7.078%)	16 <13> (+12)	:arrow_up:
...ming/TrimReadsTrimmerPluginArgumentCollection.java	100% <100%> (ø)	4 <4> (?)
...ntcollections/TrimmerPluginArgumentCollection.java	100% <100%> (ø)	1 <1> (?)
.../readtools/cmd/plugin/TrimmerPluginDescriptor.java	92.857% <89.474%> (-0.22%)	52 <11> (ø)
... and 2 more