add MSGF+ allowDenseCentroidedPeaks parameter

[bernt-matthias]

Description

• [ ] add MSGF+ -allowDenseCentroidedPeaks parameter
• [ ] add test
• [ ] always output MSGF+ commandline, stdout and stderr in case of error?

Checklist

• [ ] Make sure that you are listed in the AUTHORS file
• [ ] Add relevant changes and new features to the CHANGELOG file
• [ ] I have commented my code, particularly in hard-to-understand areas
• [ ] New and existing unit tests pass locally with my changes
• [ ] Updated or added python bindings for changed or new classes (Tick if no updates were necessary.)

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[jpfeuffer]

You have to decide if you want the param with underscores or camelCase. But it needs to be consistent!

[jpfeuffer]

I think you made the right choice with underscores but it needs to be with underscores in the test as well.

[bernt-matthias]

@jpfeuffer user provided me a ~3MB test file that could not be parsed before. Would this be fine?

Is there a way to get the binaries that are generated by the CI for this PR? Could you remind me where I find the compilation instructions if not.

[jpfeuffer]

If possible, try to run a FileFilter and remove any MS1 spectra and filter for a few MS2 spectra that would fail without the flag. It is on the high end.

Just develop on https://gitpod.io#github.com/OpenMS/OpenMS/pull/6606 . It will be (mostly) precompiled. Change back the files to separate files (i.e. just copy MSGFPlus_1_out)! Otherwise, you will overwrite. Run ctest -R MSGFPlusAdapter_2 to check. And ./tools/overwriteTOPPtests.sh MSGFPlusAdapter_2 to overwrite the "groundtruth test files" with the output from the current test run.