Return a Variant object

        Format variant make a variant that includes enough information for
        the variant view.
        If add_all_info then all transcripts will be parsed

        Args:
            variant (cython2.Variant): A variant object
            index (int): The index of the variant
            case_obj (puzzle.models.Case): A case object

def _format_variants(self, variant, index, case_obj, add_all_info=False):
        """Return a Variant object

        Format variant make a variant that includes enough information for
        the variant view.
        If add_all_info then all transcripts will be parsed

        Args:
            variant (cython2.Variant): A variant object
            index (int): The index of the variant
            case_obj (puzzle.models.Case): A case object

        """
        header_line = self.head.header
        # Get the individual ids for individuals in vcf file
        vcf_individuals = set([ind_id for ind_id in self.head.individuals])

        #Create a info dict:
        info_dict = dict(variant.INFO)

        chrom = variant.CHROM
        if chrom.startswith('chr') or chrom.startswith('CHR'):
            chrom = chrom[3:]

        variant_obj = Variant(
                CHROM=chrom,
                POS=variant.POS,
                ID=variant.ID,
                REF=variant.REF,
                ALT=variant.ALT[0],
                QUAL=variant.QUAL,
                FILTER=variant.FILTER,
            )
        variant_obj._set_variant_id()

        logger.debug("Creating a variant object of variant {0}".format(
            variant_obj.variant_id))

        variant_obj.index = index
        logger.debug("Updating index to: {0}".format(
            index))

        ########### Get the coordinates for the variant ##############
        variant_obj.start = variant.start
        variant_obj.stop = variant.end

        #SV variants needs to be handeled a bit different since the can be huge
        #it would take to much power to parse all vep/snpeff entrys for these.
        if self.variant_type == 'sv':
            variant_obj.stop = int(info_dict.get('END', variant_obj.POS))
            self._add_sv_coordinates(variant_obj)
            variant_obj.sv_type = info_dict.get('SVTYPE')

            # Special for FindSV software:
            # SV specific tag for number of occurances
            occurances = info_dict.get('OCC')
            if occurances:
                logger.debug("Updating occurances to: {0}".format(
                    occurances))
                variant_obj['occurances'] = float(occurances)
                variant_obj.add_frequency('OCC', occurances)

        else:
            self._add_thousand_g(variant_obj, info_dict)
            self._add_cadd_score(variant_obj, info_dict)
            self._add_genetic_models(variant_obj, info_dict)
            self._add_transcripts(variant_obj, info_dict)
            self._add_exac(variant_obj, info_dict)
            
        self._add_hgnc_symbols(variant_obj)

        if add_all_info:
            self._add_genotype_calls(variant_obj, str(variant), case_obj)
            self._add_compounds(variant_obj, info_dict)
            self._add_gmaf(variant_obj, info_dict)
            self._add_genes(variant_obj)


        ##### Add consequences ####
        self._add_consequences(variant_obj, str(variant))
        self._add_most_severe_consequence(variant_obj)
        self._add_impact_severity(variant_obj)
        self._add_rank_score(variant_obj, info_dict)
        variant_obj.set_max_freq()
        return variant_obj