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vcf: Invalid FORMAT key in passed example #689
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Agreed. This touches on a two larger problems with percent encoding in VCF:
This results in a parsing ambiguity as an INFO field can have the form Missing from the specs are 1) an explicit list of where percent encoded can/cannot be used, 2) an explicit list of what does/does not require percent encoding, and 3) what to do other values that looks percent-encoded IIRC, the intent was for |
The other interpretation of the specs is that percent-encoding works on any of the 8 reserved characters anywhere in a VCF file. I'm less keen on this interpretation as it's really not needed elsewhere except if you want to use contig names with characters that are no reserved in SAM but are in VCF. |
Rereading the specs, s1.2 could do with a bit more clarification. Namely:
|
Previously @d-cameron wrote:
Which characters do you have in mind that are reserved in one but not the other? As far as I am aware, the rules are aligned between SAM and VCF. The only potential difference I am aware of is #711, on which your opinion would be appreciated. |
The last record in
test/vcf/4.3/passed/passed_body_format.vcf
has a FORMAT key namedG%3AS
(percent-decoded toG:S
), which is an invalid identifier. From The Variant Call Format Specification: VCFv4.3 and BCFv2.2 (2022-08-22) § 1.6.2 "Genotype fields":The text was updated successfully, but these errors were encountered: