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EBIvariation / vcf-validator

Validation suite for Variant Call Format (VCF) files, implemented using C++11
Apache License 2.0
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validator: Allow AF Info field to contain missing value. #130

Open blankenberg opened 6 years ago

blankenberg commented 6 years ago

Also, Fix for text report AF error.

jmmut commented 6 years ago

Good spot! thanks for the contribution.

The code you added to allow missing values not only allows simple missing values, e.g. AF=. but also to mixed (missing and non-missing) values such as AF=.,0.3, which we need to check with the spec to see if it's valid before merging.

Also, this made us realise we need to allow missing in other fields as well.

blankenberg commented 6 years ago

Great, let me know what you are able to decipher as far as the spec is concerned.

I'll also just briefly mention that the original error was quite cryptic (in contrast to other 'real' validation errors) as it was just an uncaught stold conversion. It may be worthwhile to check for additional places in the code and where this sort of unchecked error could occur and provide one of the much more meaningful errors that vcf_validator generally provides.

./vcf_validator -i ../../test.vcf 
[info] Reading from input file...
[error] stold