Clean up code and fix typos

[magicDGS]

IMPORTANT: for developers, there is a change in class names that could affect builds/branches

• Fix typos everywhere (documentation and java classes/comments)
• Simplify code after code inspection (e.g., remove unused imports)
• Small non-function changes to bash scripts

[codecov[bot]]

Codecov Report

Merging #521 into master will increase coverage by 0.123%. The diff coverage is 96.875%.

@@               Coverage Diff               @@
##              master      #521       +/-   ##
===============================================
+ Coverage     93.559%   93.682%   +0.123%     
+ Complexity      1078      1077        -1     
===============================================
  Files            103       103               
  Lines           2841      2833        -8     
  Branches         303       301        -2     
===============================================
- Hits            2658      2654        -4     
+ Misses           137       133        -4     
  Partials          46        46

Impacted Files	Coverage Δ	Complexity Δ
...org/magicdgs/readtools/engine/ReadToolsWalker.java	100% <ø> (ø)	17 <0> (ø)	:arrow_down:
...tools/engine/sourcehandler/FastqSourceHandler.java	83.333% <ø> (ø)	7 <0> (ø)	:arrow_down:
...ls/utils/mappability/gem/GemMappabilityReader.java	98.765% <ø> (ø)	28 <0> (ø)	:arrow_down:
...ools/barcodes/dictionary/decoder/BarcodeMatch.java	97.778% <ø> (ø)	29 <0> (ø)	:arrow_down:
...ls/read/transformer/trimming/TrailingNtrimmer.java	100% <ø> (ø)	2 <0> (ø)	:arrow_down:
...ls/tools/mapped/ComputeProperStatByWindowArgs.java	86.957% <ø> (ø)	5 <0> (ø)	:arrow_down:
...readtools/tools/distmap/DownloadDistmapResult.java	97.143% <ø> (ø)	14 <0> (ø)	:arrow_down:
.../read/stats/engine/ProperStatWindowCalculator.java	95.652% <ø> (ø)	43 <0> (ø)	:arrow_down:
.../magicdgs/readtools/utils/fastq/FastqGATKRead.java	100% <ø> (ø)	4 <0> (ø)	:arrow_down:
...gicdgs/readtools/utils/read/ReadReaderFactory.java	80% <ø> (ø)	6 <0> (ø)	:arrow_down:
... and 26 more