msconvert.exe: The ignoreUnknownInstrumentError true/false assignment is backwards when a config file is used

[austinkeller]

This is a really minor issue but I wanted to document it. Adding the --ignoreUnknownInstrumentError flag on the command line bypasses the error as expected. I would expect when using a config file that adding a line of ignoreUnknownInstrumentError=true would give the same behavior. However, I need to add ignoreUnknownInstrumentError=false instead.

Contents of my config file:

zlib=true
mz64=true
inten64=true
simAsSpectra=true
ignoreUnknownInstrumentError=false
filter="peakPicking vendor msLevel=1-2"

Using ProteoWizard 3.0.18250.994311be0

I noticed in the code there is a line that is used to flip the logic for use with the unknownInstrumentIsError variable when using the command line flag.

pwiz/pwiz_tools/commandline/msconvert.cpp

Lines 358 to 359 in 2f477cf

	// negate unknownInstrumentIsError value since command-line parameter (ignoreUnknownInstrumentError) and the Config parameters use inverse semantics
	config.unknownInstrumentIsError = !config.unknownInstrumentIsError;

I didn't see an obvious way to fix this without breaking the command line flag logic, so I'm leaving this here for later.