multiple allele separated by semicolon in ALT field

[marbeno]

Multiple alleles are separated by a ";" insted of "," when VCF.Record is used

The vcf looks like this:

$ tail -2 test_single.vcf
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
20	259054	.	CTG	CTC,C	2862	.	.	GT	0/1

If I do not use VCF.Record, the result is correct:

reader=VCF.Reader(open("test_single.vcf","r"));
fl=read(reader);
writer = open(VCF.Writer, "out1.vcf",VCF.header(reader));
write(writer,fl)
close(writer)

Gives:

tail -2 out1.vcf
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
20	259054	.	CTG	CTC,C	2862	.	.	GT	0/1

If I use VCF.Record:

writer = open(VCF.Writer, "out2.vcf",VCF.header(reader));
write(writer,VCF.Record(fl))
close(writer)

Results in:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	SAMPLE
20	259054	.	CTG	CTC;C	2862	.	.	GT	0/1

Notice that CTC and C in ALT are separated by a ";".

I think the problem might be this:

GeneticVariation.jl/src/vcf/record.jl

Lines 188 to 191 in f61b9db

	for (i, x) in enumerate(alt)
	if i != 1
	print(buf, ';')
	end