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")
