QUAL gets changed from unknown (.) to zero.

[al-dunstan]

If I read a VCF record with an unknown QUAL (a period) and write it back out, it gets changed from '.' to '0'. My (limited) understanding of the VCF format is that unknown and zero mean different things.

I think it could be fixed by setting Variant::quality to infinity() if the value read from the file is ".". Then, on output, check for isinf(var.quality) - if true, write a ".". Otherwise, write the value.

If QUAL is unknown and calculations are made with it, the value of infinity() will taint all subsequent values. But I'd expect something like that, since I don't actually have a value to start with.

[pjotrp]

Hi @al-dunstan, feel free to submit a fix.