New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

parser does not track whether FILTER was explicitly set #114

AndrewUzilov opened this Issue Aug 6, 2013 · 1 comment


None yet
2 participants

AndrewUzilov commented Aug 6, 2013

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.


This comment has been minimized.


martijnvermaat commented Aug 7, 2013

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

gotgenes pushed a commit to gotgenes/PyVCF that referenced this issue May 13, 2014

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment