samtools / hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

http://samtools.github.io/hts-specs/

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vcf: Invalid unstructured header line in VCF 4.3 example `complexfile_passed_000.vcf` #772

Open zaeleus opened 1 month ago

zaeleus commented 1 month ago

test/vcf/4.3/passed/complexfile_passed_000.vcf has an invalid unstructured header line:

https://github.com/samtools/hts-specs/blob/401e2ec3e8ecf19fa89def74e9c27c1e40df341e/test/vcf/4.3/passed/complexfile_passed_000.vcf#L44

As per The Variant Call Format Specification: VCFv4.3 and BCFv2.2 § 1.4 "Meta-information lines" (2022-11-27):

An unstructured meta-information line consists of [...] a value (which may not be empty and must not start with a ‘<’ character)...

jmarshall commented 1 month ago

Previously reported in #608 and #620, but perhaps this time the VCF maintainers will be moved to address this. 😃

620 lists some options for resolving this.

jmarshall commented 2 weeks ago

For ease of reference, here is the relevant comment from #620:

The _test/vcf/4.[123]/passed/complexfile_passed000.vcf test files still contain another unstructured meta-information line with angle bracket delimiters: [##AnalysisTitleBrackets=<…> as above]

The maintainers should also update the ##AnalysisTitleBrackets lines, either just removing them or perhaps rewriting them as ##AnalysisTitleStructured=<ID="FINRISK: … (DILGOM)">.