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im3sanger / dndscv

dN/dS methods to quantify selection in cancer and somatic evolution
GNU General Public License v3.0
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Changed error to warning #8

Closed AJBerle closed 6 years ago

AJBerle commented 6 years ago

Old code on line 238, new warning on line 239

im3sanger commented 6 years ago

Thanks. Some users may prefer to have a warning in this line. I opted for an error to force the user to be very familiar with the mutation table used. The problem with a warning is that users could successfully run dndscv and get an output by using mutations from a different assembly or even a different species, without thinking about it.

However, I will consider other solutions, such as outputting a table of mutations with a wrong reference base.

Best wishes, Inigo

AJBerle commented 6 years ago

Thank you very much for the response. Sorry, I am new to GitHub so I accidentally submitted the pull request when trying to just send the changes to a group I am working with, but I really appreciate you getting back with me.

Thanks, AJ