def _add_necessary_columns(self, custom_columns):
        """
        Convenience function to tack on columns that are necessary for
        the functionality of the tool but yet have not been specifically
        requested by the user.
        """
        # we need to add the variant's chrom, start and gene if
        # not already there.
        custom_columns = [x.strip() for x in custom_columns.split(",")]
        if "*" in custom_columns:
            return ",".join(custom_columns)
        self.added = []
        for col in ("gene", "chrom", "start", "ref", "alt", "variant_id"):
            if not col in custom_columns:
                custom_columns.append(col)
                if col != "variant_id":
                    self.added.append(col)
        return ",".join(custom_columns)
dataset/ETHPy150Open arq5x/gemini/gemini/gim.py/CompoundHet._add_necessary_columns/original