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