projectglow / glow

An open-source toolkit for large-scale genomic analysis
https://projectglow.io
Apache License 2.0
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Fix Infinity/NaN parsing to allow full set of values from VCF specification #519

Closed dtzeng closed 1 year ago

dtzeng commented 1 year ago

What changes are proposed in this pull request?

Issue raised here: https://github.com/projectglow/glow/issues/517 In short, the VCF allows infinity/nan that follow this regex ^[-+]?(INF|INFINITY|NAN)$ case insensitively

The code that parses the INFO and genotype columns do not allow the full range of valid values.

How is this patch tested?

Verified that unit tests failed before applying changes. And unit tests passed after applying my changes.

williambrandler commented 1 year ago

@henrydavidge could you take a look at this please?

dtzeng commented 1 year ago

What's the process to get this merged?

williambrandler commented 1 year ago

looks like the relevant tests passed, I don't see why this cannot be merged in

williambrandler commented 1 year ago

thanks @dtzeng for your contribution