fix: escaped equal sign in INFO fields #172
Open
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
The change made escapes equal sign (
=
) in INFO fields.However, the column characters
:
are also escaped on output, as recommended by the vcf 4.3 format.It is unclear if the column character
:
should be escaped in INFO fields of vcf files in 4.2 format. The 4.2 format documentation seems to suggest that only whitespace, semicolons, and equals-sign are forbidden (and therefore should be escaped).In its current incarnation,
vcfpy
escapes of column characters regardless of the vcf version. It is unclear to me what is the best practical approach forvcfpy
, as I am unsure how strictly commonly used software is following the format.