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Should writing Strings to INFO be escaped #300

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holtgrewe opened this issue Sep 6, 2024 · 2 comments
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Should writing Strings to INFO be escaped #300

holtgrewe opened this issue Sep 6, 2024 · 2 comments
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bug Something isn't working vcf

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@holtgrewe
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Hi, when writing a STRING value to an INFO field that contains a semicolon ; then this file cannot be imported any more.

Should I escape this in my code using noodles-vcf or should noodles do it?
@zaeleus zaeleus added vcf bug Something isn't working labels Sep 6, 2024
@zaeleus zaeleus self-assigned this Sep 6, 2024
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zaeleus commented Sep 6, 2024

Thanks for the report.

The output is correct. Semicolons (;) in info string values are being percent-encoded to %3B (e.g., "a;b" => "a%3Bb"). However, vcf::Record is not decoding them, which in turn makes the writer, essentially, double encode.

The buffered record reader (Reader::read_record_buf and Reader::record_bufs) can be used as a workaround for now.

zaeleus added a commit that referenced this issue Sep 6, 2024
@zaeleus
vcf/variant/record/info/field/value/array/values: Percent-decode stri…
410b94e 
…ng values

This changes the values iterator item from `&str` to `Cow<'_, str>`.

See #300.
@zaeleus zaeleus closed this as completed in 6a91b5a Sep 6, 2024
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zaeleus commented Sep 9, 2024

This is now fixed in noodles 0.81.0 / noodles-vcf 0.64.0.

This was referenced Oct 8, 2024
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