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

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zaeleus opened this issue May 31, 2024 · 2 comments · May be fixed by #773
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vcf: Invalid unstructured header line in VCF 4.3 example complexfile_passed_000.vcf #772

zaeleus opened this issue May 31, 2024 · 2 comments · May be fixed by #773
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@d-cameron
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@zaeleus
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zaeleus commented May 31, 2024

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

hts-specs/test/vcf/4.3/passed/complexfile_passed_000.vcf

Line 44 in 401e2ec

##AnalysisTitleBrackets=<"FINRISK: Whole-exome sequencing of Dietary, life style, and genetic determinants of obesity and metabolic syndrome (DILGOM)">

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
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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 jmarshall added the vcf label May 31, 2024
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For ease of reference, here is the relevant comment from #620:

The test/vcf/4.[123]/passed/complexfile_passed_000.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)">.

@d-cameron d-cameron self-assigned this Jun 18, 2024
@jmarshall jmarshall moved this to New items in GA4GH File Formats Jun 18, 2024
@jmarshall jmarshall moved this from New items to Progressing in GA4GH File Formats Jun 18, 2024
jmarshall added a commit to jmarshall/hts-specs that referenced this issue Jun 18, 2024
@jmarshall
Add ID subfield to VCF v4.3 test file's structured header
5f49f9a 
In VCF v4.3 structured meta-information lines must have an ID subfield.
Split the value into identifier-like ID and text Description subfields
to demonstrate the structured benefit, though for a non-INFO/FORMAT/etc
line there's probably nothing requiring ID's value to be identifier-like.
Fixes samtools#772.

This leaves the similar 4.1 and 4.2 files as is, as it is less clear
whether ID-less structured headers are merely discouraged there.
@jmarshall jmarshall linked a pull request Jun 18, 2024 that will close this issue
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@daviesrob daviesrob mentioned this issue Jun 19, 2024
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@d-cameron d-cameron

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Add ID subfield to VCF v4.3 test file's structured header jmarshall/hts-specs
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@jmarshall @zaeleus @d-cameron