Add ComputeProperStatByWindow experimental tool

[magicDGS]

Implements a tool to count the number of reads over window with tags w.r.t. a threshold, with optional counts for reads with indels/softclips. This tool is experimental because it still requires integration with a barclay plugin to allow compute the statistics with user-specified StatFunctions (not mandatory int-tag-counter) and with more statistic implementations.

In addition, this commit introduces the following changes:

• ReadTools extension of GATK's ReadWalker (RTReadWalker)
• New program group for mapped reads
• Temporary argument collection for ComputeProperStatByWindow (instead of barclay plugin)

Closes #437 Closes #441

[codecov[bot]]

Codecov Report

Merging #464 into master will decrease coverage by 0.211%. The diff coverage is 79.71%.

@@               Coverage Diff               @@
##              master      #464       +/-   ##
===============================================
- Coverage     93.585%   93.374%   -0.211%     
- Complexity       966       990       +24     
===============================================
  Files             91        95        +4     
  Lines           2572      2641       +69     
  Branches         280       284        +4     
===============================================
+ Hits            2407      2466       +59     
- Misses           125       134        +9     
- Partials          40        41        +1

Impacted Files	Coverage Δ	Complexity Δ
...eadtools/cmd/programgroups/MappedProgramGroup.java	0% <0%> (ø)	0 <0> (?)
...n/java/org/magicdgs/readtools/RTHelpConstants.java	88.095% <100%> (+0.29%)	13 <0> (ø)	:arrow_down:
...va/org/magicdgs/readtools/engine/RTReadWalker.java	37.5% <37.5%> (ø)	3 <3> (?)
...ls/tools/mapped/ComputeProperStatByWindowArgs.java	86.957% <86.957%> (ø)	5 <5> (?)
...dtools/tools/mapped/ComputeProperStatByWindow.java	91.176% <91.176%> (ø)	13 <13> (?)
...tils/read/stats/engine/ProperStatWindowEngine.java	93.443% <0%> (+3.279%)	20% <0%> (+1%)	:arrow_up:
... and 1 more