def LoadCondition(vcffile, condition, sample_order): reader2 = VCF(vcffile) #reader2 = vcf.Reader(open(vcffile, "rb")) chrom, start = condition.split(":") region = "%s:%s-%s" % (chrom, start, int(start) + 1) reader2.fetch(region) reader2 = reader2(region) for record in reader2: print(record.start, int(start), record.ID) if record.POS == int(start): is_str = True if len(record.REF) == 1 and len(record.ALT) == 1 and len( record.ALT[0]) == 1: is_str = False return LoadGT(record, sample_order, is_str=is_str, vcf_samples=reader2.samples) common.ERROR("Could not find SNP to condition on")