def make_separate_indels_and_one_alt_with_all_snps_no_combinations(self, ref_seq):
final_start_position = min([x.POS for x in self.vcf_records])<EOL>final_end_position = max([x.ref_end_pos() for x in self.vcf_records])<EOL>snps = []<EOL>new_vcf_records = []<EOL>for record in self.vcf_records:<EOL><INDENT>if record.is_snp():<EOL><INDENT>snps.append(copy.copy(record))<EOL><DEDENT>else:<EOL><INDENT>new_record = copy.copy(record)<EOL>new_record.add_flanking_seqs(ref_seq, final_start_position, final_end_position)<EOL>new_vcf_records.append(new_record)<EOL><DEDENT><DEDENT>if len(snps):<EOL><INDENT>new_record = copy.copy(snps[<NUM_LIT:0>])<EOL>for snp in snps[<NUM_LIT:1>:]:<EOL><INDENT>merged = new_record.merge(snp, ref_seq)<EOL>if merged is not None:<EOL><INDENT>new_record = merged<EOL><DEDENT><DEDENT>new_record.add_flanking_seqs(ref_seq, final_start_position, final_end_position)<EOL>new_vcf_records.append(new_record)<EOL><DEDENT>alts = '<STR_LIT:U+002C>'.join(sorted(list(set([x.ALT[<NUM_LIT:0>] for x in new_vcf_records]))))<EOL>new_record = vcf_record.VcfRecord('<STR_LIT:\t>'.join([self.vcf_records[<NUM_LIT:0>].CHROM, str(final_start_position + <NUM_LIT:1>), '<STR_LIT:.>', new_vcf_records[<NUM_LIT:0>].REF, alts, '<STR_LIT:.>', '<STR_LIT>', '<STR_LIT:.>']))<EOL>return new_record<EOL>
Returns a VCF record, where each indel from this
        cluster is in a separate ALT. Then all the remaining SNPs are
        applied to make one ALT. If >1 SNP in same place, either one
        might be used