Dependencies and not existing file checks

[julianu]

No description provided.

[codecov-commenter]

Codecov Report

Attention: 114 lines in your changes are missing coverage. Please review.

Comparison is base (2221c5c) 61.73% compared to head (4ec1ce5) 62.01%.
Report is 54 commits behind head on main.

Files	Patch %	Lines
src/main/java/de/mpc/pia/PIACli.java	18.39%	63 Missing and 8 partials ⚠️
src/main/java/de/mpc/pia/tools/MzIdentMLTools.java	0.00%	16 Missing ⚠️
src/main/java/de/mpc/pia/JsonAnalysis.java	36.36%	7 Missing ⚠️
src/main/java/de/mpc/pia/modeller/PSMModeller.java	33.33%	5 Missing and 1 partial ⚠️
...ediate/compiler/parser/InputFileParserFactory.java	37.50%	4 Missing and 1 partial ⚠️
.../pia/modeller/report/filter/RegisteredFilters.java	50.00%	3 Missing and 1 partial ⚠️
...ermediate/compiler/parser/MzIdentMLFileParser.java	75.00%	1 Missing and 2 partials ⚠️
...main/java/de/mpc/pia/modeller/PeptideModeller.java	50.00%	0 Missing and 1 partial ⚠️
...main/java/de/mpc/pia/modeller/ProteinModeller.java	0.00%	0 Missing and 1 partial ⚠️

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Additional details and impacted files

@@             Coverage Diff              @@
##               main     #200      +/-   ##
============================================
+ Coverage     61.73%   62.01%   +0.28%     
- Complexity     2490     2492       +2     
============================================
  Files           140      139       -1     
  Lines         14958    14902      -56     
  Branches       2641     2635       -6     
============================================
+ Hits           9234     9242       +8     
+ Misses         4668     4601      -67     
- Partials       1056     1059       +3     

Flag	Coverage Δ
unittests	62.01% <28.30%> (+0.28%)	⬆️

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