Parsing problems with MutSig2CV

[Diogo Pellegrina]

Hi,

I'm running MutSig2CV on a linux server, and I have a problem with the parameter file.

I tried to change one of the settings adding the line:

remove_duplicate_patients false

But it didn't appear to change anything, no errors where shown and the log still reported duplicate patients being removed.

In order to figure out what was going on I used the following parameter_file:

remove_duplicate_patients false

remove_duplicate_patients 0

remove_duplicate_patients False

remove_duplicate_patients FALSE

are_you_reading_me true

what_happens_if_I_only_use_1_column

No error appeared, and again it ran as if the parameters file wasn't being read.

But when I tried to add the following line:

remove_duplicate_patients=false

And it printed this error:

Error setting field "remove_duplicate_patients=false"

  MException with properties:

    identifier: 'MATLAB:AddField:InvalidFieldName'

       message: 'Invalid field name: 'remove_duplicate_patients=false'.'

         cause: {}

         stack: [5x1 struct]

Invalid field name: 'remove_duplicate_patients=false'.

This means that the parameter file is indeed being read, but I still couldn't manage to actually change remove_duplicate_patients to false. I also tried each of the above lines separately, but nothing changed.

Thanks again,

Diogo