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parser does not track whether FILTER was explicitly set #114

AndrewUzilov opened this Issue · 1 comment

2 participants


Very nice tool, but one nitpick.

If the FILTER column is . (meaning no filters applied) or PASS, the _Record.FILTER attribute is an empty list. So, it impossible to tell whether the original VCF contained a . or PASS, since the convention for storing both is the same.

Yes, I know that it only makes sense to EITHER have the entire VCF file contain . in that col, OR have that col always explicitly specify PASS or the rejection criteria string. But in some use cases, PASS and . might be mixed in the same file, and that should be stored --- perhaps I am actually writing a parser designed to catch and fix malformed VCFs with this fixing, which are other syntactically valid.

A backwards-compatible solution is to just add a new attribute to _Record that tracks whether the FILTER value was ever set or not.

I cloned this repo and hacked in the change ( [] ), so pull from there or I can do a pull request if OK.


Thanks for the report, I propose another implementation in #115.

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