Duplicate ALT allele in VCF causes exception

[bartcharbon]

Description of the issue:

When reading a VCF with HTSJDK it causes an exception when there is a duplicate ALT allele.
I believe duplicate ALT alleles are allowed in VCF, and are used in cases when there are multiple symbolic alleles at a certain position.
e.g. CNV:TR,CNV:TR

the exception that occurs:
The provided VCF file is malformed at approximately line number 530: Duplicate allele added to VariantContext: <CNV:TR>, for input source:input.vcf.gz

Both BcfTools and EBIvariation/vcf-validator/ read/validate the lines with the duplicate ALT without problems.

Your environment:

• version of htsjdk: 4.1.0
• version of java: 17
• which OS: CentOS

Expected behaviour

The file should not cause an exception

Actual behaviour

The file should does cause an exception

[lindenb]

I believe duplicate ALT alleles are allowed in VCF,

hum , I don't think so. How would you know which ALT allele is associated to a genotype ?

[bartcharbon]

the INFO fields that are related to the ALT are required to be comma separated in the same order as the ALT's
Genotypes are associated just like any other multiallic, by index.

I cannot find any mention that ALT should be unique in VCF spec 4.2
For the 4.5 VCF draft there are even examples of this case CNV:TR,CNV:TR in the spec itself

[lbergelson]

@bartcharbon Interesting. I believe the restriction makes sense with non symbolic alleles, even if it's not in the spec specifically. It looks like we should relax it for structural variants though.