def _fix_genotypes_object(self, genotypes, variant_info):
        """Fixes a genotypes object (variant name, multi-allelic value."""
        # Checking the name (if there were duplications)
        if self.has_index and variant_info.name != genotypes.variant.name:
            if not variant_info.name.startswith(genotypes.variant.name):
                raise ValueError("Index file not synced with IMPUTE2 file")
            genotypes.variant.name = variant_info.name

        # Trying to set multi-allelic information
        if self.has_index and self._index_has_location:
            # Location was in the index, so we can automatically set the
            # multi-allelic state of the genotypes
            genotypes.multiallelic = variant_info.multiallelic

        else:
            # Location was not in the index, so we check one marker before and
            # after the one we found
            logging.warning("Multiallelic variants are not detected on "
                            "unindexed files.")
def _fix_genotypes_object ( self , genotypes , variant_info ) : if self . has_index and variant_info . name != genotypes . variant . name : if not variant_info . name . startswith ( genotypes . variant . name ) : raise ValueError ( "Index file not synced with IMPUTE2 file" ) genotypes . variant . name = variant_info . name if self . has_index and self . _index_has_location : genotypes . multiallelic = variant_info . multiallelic else : logging . warning ( "Multiallelic variants are not detected on " "unindexed files." )
Fixes a genotypes object (variant name, multi-allelic value.