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compomics / compomics-utilities

Open source Java library for computational proteomics
http://compomics.github.io/projects/compomics-utilities.html
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Min isotope correction #14

Closed chambm closed 7 years ago

chambm commented 7 years ago

I'm not sure how this is supposed to work, but it seems messed up. The default is zero, yet in IdentificationParametersInputBean.java it is tested to be a positive integer.

if (aLine.hasOption(IdentificationParametersCLIParams.MIN_ISOTOPE.id)) {
            String arg = aLine.getOptionValue(IdentificationParametersCLIParams.MIN_ISOTOPE.id);
            if (!CommandParameter.isPositiveInteger(IdentificationParametersCLIParams.MIN_ISOTOPE.id, arg, true)) {
                return false;
            }
        }

Shouldn't this parameter be allowed to be negative?

hbarsnes commented 7 years ago

Hi Matt,

Yes, this is clearly an error in our checking of the command line input parameter. Thanks for pointing this out. We'll correct it and release a new version next week.

Best regards, Harald

hbarsnes commented 7 years ago

Hi Matt,

A new version of utilities (v4.8.8) has now been deployed fixing the issue with the isotope range setting via the command line. New versions of all the tools using this feature have also been released.

Best regards, Harald