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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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Remove write_outputs backward compatibility #396

Open isaacovercast opened 4 years ago

isaacovercast commented 4 years ago

Starting on line 662:

        self.fmaxsnps = self.data.params.max_SNPs_locus
        if isinstance(self.fmaxsnps, tuple):
            self.fmaxsnps = self.fmaxsnps[0]
        if isinstance(self.fmaxsnps, int):
            self.fmaxsnps = 0.10  # backwards compatibility make as a float

        self.fmaxhet = self.data.params.max_shared_Hs_locus
        if isinstance(self.fmaxhet, tuple):
            self.fmaxhet = self.fmaxhet[0]
        # TODO: This backwards compatibility is hard coded. Maybe better to 
        # just raise an error here, or really during parsing of the params
        # file is best.
        if isinstance(self.fmaxhet, int):
            self.fmaxhet = 0.5  # backwards compatibility make as a float

We should remove the backwards compatibility here or at least try to honor the settings in the backward params file, otherwise you get weird behavior where the results don't reflect the values in the params.