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Error when reading a VCF 4.3 file with spaces in INFO field values #1667

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jkmatila opened this issue May 26, 2023 · 1 comment
Open

Error when reading a VCF 4.3 file with spaces in INFO field values #1667

jkmatila opened this issue May 26, 2023 · 1 comment

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@jkmatila
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According to the VCF 4.3 specification, spaces are allowed in INFO field values (unlike in VCF 4.2). However, trying to parse such a file fails with an error message "The VCF specification does not allow for whitespace in the INFO field", which seems to come from AbstractVCFCodec.java:515.

See VCF 4.3 spec, Section 1.6.1:

  1. INFO — [...] Space characters are allowed in values.
@cmnbroad
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cmnbroad commented Jun 1, 2023

Yes, thanks for reporting this. This is fixed in #1581 (and the commit with the fix is also in #1596).
@cmnbroad cmnbroad mentioned this issue Jun 1, 2023
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